Publications of Bork Group

Publications of Bork Group

Authors in this color are/were of Bork Group. [Altmetric off].
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2024 5 publication(s).
857.
Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing.
Chen J, Sun C, Dong Y, Jin M, Lai S, Jia L, Zhao X, Wang H, Gao NL, Bork P, Liu Z, Chen WH, Zhao XM
2024 Jan 19; : e2305818. PubMed: 38240578.
Abstract + PDF
856.
Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.
Mücke MM, Hernández-Tejero M, Gu W, Kuhn M, Janz M, Keller MI, Fullam A, Altepeter L, Mücke VT, Finkelmeier F, Schwarzkopf KM, Cremonese C, Hunyady PM, Heilani MW, Uschner FE, Schierwagen R, Brol MJ, Fischer J, Klein S, Peiffer KH, Hogardt M, Shoaie S, Coenraad MJ, Bojunga J, Arroyo V, Zeuzem S, Kempf VAJ, Welsch C, Laleman W, Bork P, Fernandez J, Trebicka J, MICROB-PREDICT and PREDICT Study Group of the EASL-CLIF Consortium
2024 Apr 27; 59(7): 877-888. PubMed: 38414095.
Abstract
855.
High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities.
Müller P, de la Cuesta-Zuluaga J, Kuhn M, Baghai Arassi M, Treis T, Blasche S, Zimmermann M, Bork P, Patil KR, Typas A, Garcia-Santamarina S, Maier L
2024 Mar 13; 19(3): 668-699. PubMed: 38092943.
Abstract
854.
Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez Del Río Á, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernández-Plaza A, Munar-Palmer M, Santamaría-Hernando S, Rodríguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, López-Solanilla E, Coelho LP, Huerta-Cepas J
2024 Feb 18; 626(7998): 377-384. PubMed: 38109938.
Abstract
853.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P
2024 Jan 5; 52: D777-D783. PubMed: 37897342.
Abstract + PDF
2023 14 publication(s).
852.
Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide.
Andrikopoulos P, Aron-Wisnewsky J, Chakaroun R, Myridakis A, Forslund SK, Nielsen T, Adriouch S, Holmes B, Chilloux J, Vieira-Silva S, Falony G, Salem JE, Andreelli F, Belda E, Kieswich J, Chechi K, Puig-Castellvi F, Chevalier M, Le Chatelier E, Olanipekun MT, Hoyles L, Alves R, Helft G, Isnard R, Køber L, Coelho LP, Rouault C, Gauguier D, Gøtze JP, Prifti E, Froguel P, MetaCardis Consortium , Zucker JD, Bäckhed F, Vestergaard H, Hansen T, Oppert JM, Blüher M, Nielsen J, Raes J, Bork P, Yaqoob MM, Stumvoll M, Pedersen O, Ehrlich SD, Clément K, Dumas ME
2023 Sep 20; 14(1): 5843. PubMed: 37730687.
Abstract + PDF
851.
Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases.
Botts RT, Page DM, Bravo JA, Brown ML, Castilleja CC, Guzman VL, Hall S, Henderson JD, Kenney SM, Lensink ME, Paternoster MV, Pyle SL, Ustick LJ, Walters-Laird CJ, Top EM, Cummings DE
2023 May; 126: 102682. PubMed: 37023995.
Abstract
850.
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR
2023 Jan 6; 51: D760-D766. PubMed: 36408900.
Abstract + PDF
849.
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J
2023 Jan 6; 51: D389-D394. PubMed: 36399505.
Abstract + PDF
848.
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.
Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O\'Mahony L, O\'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J
2023 Jan; 613(7945): 639-649. PubMed: 36697862.
Abstract
847.
Enterotypes of the human gut mycobiome.
Lai S, Yan Y, Pu Y, Lin S, Qiu JG, Jiang BH, Keller MI, Wang M, Bork P, Chen WH, Zheng Y, Zhao XM
2023 Aug 11; 11(1): 179. PubMed: 37563687.
Abstract + PDF
846.
InterPro in 2022.
Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A
2023 Jan 6; 51: D418-D427. PubMed: 36350672.
Abstract + PDF
845.
Ocean-wide comparisons of mesopelagic planktonic community structures.
Rigonato J, Budinich M, Murillo AA, Brandão MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Frémont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E, Tara Oceans coordinators , Bork P, Bowler C, De Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O
2023 Aug 18; 3(1): 83. PubMed: 37596349.
Abstract + PDF
844.
Computational exploration of the global microbiome for antibiotic discovery.
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Michael K, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP
2023 Sep 11; [Epub ahead of print] PubMed: 37693522.
Abstract
843.
Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases.
Sun C, Chen J, Jin M, Zhao X, Li Y, Dong Y, Gao N, Liu Z, Bork P, Zhao XM, Chen WH
2023 Sep 29; 10(25): e2302159. PubMed: 37382405.
Abstract + PDF
842.
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C
2023 Jan 6; 51: D638-D646. PubMed: 36370105.
Abstract + PDF
841.
SPHINGOLIPIDS ARE DEPLETED IN ALCOHOL-RELATED LIVER FIBROSIS.
Thiele M, Suvitaival T, Trošt K, Kim M, de Zawadzki A, Kjaergaard M, Rasmussen DN, Lindvig KP, Israelsen M, Detlefsen S, Andersen P, Juel HB, Nielsen T, Georgiou S, Filippa V, Kuhn M, Nishijima S, Moitinho-Silva L, Rossing P, Trebicka J, Anastasiadou E, Bork P, Hansen T, Quigley CL, Krag A, MicrobLiver , GALAXY Consortia
2023 Jun 26; 164(7): 1248-1260. PubMed: 36849086.
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840.
Global scale phylogeography of functional traits and microdiversity in Prochlorococcus.
Ustick LJ, Larkin AA, Martiny AC
2023 Oct; 17(10): 1671-1679. PubMed: 37454234.
Abstract
839.
Consistency across multi-omics layers in a drug-perturbed gut microbial community.
Wuyts S, Alves R, Zimmermann-Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P
2023 Sep 12; 19(9): e11525. PubMed: 37485738.
Abstract + PDF
2022 22 publication(s).
838.
Structure and function of DNA transposition assemblies involved in antibiotic resistance spreading.
Barabas O, Smyshlyaev G, Isbilir B, Khedkar S, Rojas-Cordova C, Bateman AG, Bork P
2022 May; 36 Suppl 1: . PubMed: 35553456.
Abstract
837.
Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.
Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann KE, Prifiti E, Aron-Wisnewsky J, Debédat J, Le Roy T, Nielsen T, Amouyal C, André S, Andreelli F, Blüher M, Chakaroun R, Chilloux J, Coelho LP, Dao MC, Das P, Fellahi S, Forslund S, Galleron N, Hansen TH, Holmes B, Ji B, Krogh Pedersen H, Le P, Le Chatelier E, Lewinter C, Mannerås-Holm L, Marquet F, Myridakis A, Pelloux V, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Sokolovska N, Søndertoft NB, Touch S, Vieira-Silva S, MetaCardis Consortium , Galan P, Holst J, Gøtze JP, Køber L, Vestergaard H, Hansen T, Hercberg S, Oppert JM, Nielsen J, Letunic I, Dumas ME, Stumvoll M, Pedersen OB, Bork P, Ehrlich SD, Zucker JD, Bäckhed F, Raes J, Clément K
Gut.
2022 Dec 11; 71(12): 2463-2480. PubMed: 35017197.
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836.
Towards the biogeography of prokaryotic genes.
Coelho LP, Alves RJ, Del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TSB, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P
2022 Jan 15; 601(7892): 252-256. PubMed: 34912116.
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835.
Microbiome and metabolome features of the cardiometabolic disease spectrum.
Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves RJ, Adiouch S, Bar N, Talmor-Barkan Y, Belda E, Caesar R, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Le Chatelier E, Julienne H, Olsson L, Pedersen HK, Pons N, Quinquis B, Rouault C, Roume H, Salem JE, Schmidt TSB, Vieira-Silva S, Li P, Zimmermann-Kogadeeva M, Lewinter C, Søndertoft NB, Hansen TH, Gauguier D, Gøtze JP, Køber L, Kornowski R, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Letunic I, Bäckhed F, Oppert JM, Nielsen J, Raes J, Bork P, Stumvoll M, Segal E, Clément K, Dumas ME, Ehrlich SD, Pedersen O
2022 Feb 17; 28(2): 303-314. PubMed: 35177860.
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834.
A faecal microbiota signature with high specificity for pancreatic cancer.
Kartal E, Schmidt TSB, Molina-Montes E, Rodríguez-Perales S, Wirbel J, Maistrenko OM, Akanni WA, Alashkar Alhamwe B, Alves RJ, Carrato A, Erasmus HP, Estudillo L, Finkelmeier F, Fullam A, Glazek AM, Gómez-Rubio P, Hercog R, Jung F, Kandels S, Kersting S, Langheinrich M, Márquez M, Molero X, Orakov A, Van Rossum T, Torres-Ruiz R, Telzerow A, Zych K, MAGIC Study investigators , PanGenEU Study investigators , Benes V, Zeller G, Trebicka J, X Real F, Malats N, Bork P
Gut.
2022 Jul 8; 71(7): 1359-1372. PubMed: 35260444.
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833.
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
2022 Apr 8; 50(6): 3155-3168. PubMed: 35323968.
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832.
Meconium Microbiome of Very Preterm Infants across Germany.
Klopp J, Ferretti P, Meyer CU, Hilbert K, Haiß A, Marißen J, Henneke P, Hudalla H, Pirr S, Viemann D, Zemlin M, Forslund SK, Härtel C, Bork P, Gehring S, Van Rossum T, and the PRIMAL Consortium
2022 Feb 23; 7(1): e0080821. PubMed: 35019670.
Abstract + PDF
831.
Microorganisms associated with , an invasive dimethylsulfoniopropionate producing salt marsh plant, are an unrecognized sink for dimethylsulfide.
Kröber E, Mankowski A, Schäfer H
2022; 13: 950460. PubMed: 36246216.
Abstract
830.
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.
Kunath BJ, Hickl O, Queirós P, Martin-Gallausiaux C, Lebrun LA, Halder R, Laczny CC, Schmidt TSB, Hayward MR, Becher D, Heintz-Buschart A, de Beaufort C, Bork P, May P, Wilmes P
2022 Dec 28; 10(1): 243. PubMed: 36578059.
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829.
Metagenomic identification of microbial signatures predicting pancreatic cancer from a multinational study.
Nagata N, Nishijima S, Kojima Y, Hisada Y, Imbe K, Miyoshi-Akiyama T, Suda W, Kimura M, Aoki R, Sekine K, Ohsugi M, Miki K, Osawa T, Ueki K, Oka S, Mizokami M, Kartal E, Schmidt TSB, Molina-Montes E, Estudillo L, Malats N, Trebicka J, Kersting S, Langheinrich M, Bork P, Uemura N, Itoi T, Kawai T
2022 Jul 8; 163(1): 222-238. PubMed: 35398347.
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828.
Biosynthetic potential of the global ocean microbiome.
Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlström CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sánchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL, Piel J, Sunagawa S
2022 Jul 22; 607(7917): 111-118. PubMed: 35732736.
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827.
Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.
Pryszlak A, Wenzel T, Seitz KW, Hildebrand F, Kartal E, Cosenza MR, Benes V, Bork P, Merten CA
2022 Jan 24; 2(1): None. PubMed: 35118437.
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826.
Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems.
Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, Tara Oceans Coordinators , Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-­Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, De Vargas C, d'Alcalà MR, Iudicone D, Jaillon O
2022 Aug 3; 11: . PubMed: 35920817.
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825.
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.
Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S
2022 Dec 5; 10(1): 212. PubMed: 36464731.
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824.
Dissecting the intracellular pancreatic tumor microbiome at single-cell level.
2022 Oct 10; 40(10): 1083-1085. PubMed: 36179685.
Abstract
823.
Drivers and determinants of strain dynamics following fecal microbiota transplantation.
Schmidt TSB, Li SS, Maistrenko OM, Akanni W, Coelho LP, Dolai S, Fullam A, Glazek AM, Hercog R, Herrema H, Jung F, Kandels S, Orakov A, Thielemann R, von Stetten M, Van Rossum T, Benes V, Borody TJ, de Vos WM, Ponsioen CY, Nieuwdorp M, Bork P
2022 Sep 15; 28(9): 1902-1912. PubMed: 36109636.
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822.
Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial.
Sowah SA, Milanese A, Schübel R, Wirbel J, Kartal E, Johnson TS, Hirche F, Grafetstätter M, Nonnenmacher T, Kirsten R, López-Nogueroles M, Lahoz A, Schwarz KV, Okun JG, Ulrich CM, Nattenmüller J, von Eckardstein A, Müller D, Stangl GI, Kaaks R, Kühn T, Zeller G
2022 Mar 14; 14(1): 30. PubMed: 35287713.
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821.
Priorities for ocean microbiome research.
Tara Ocean Foundation , Tara Oceans Coordinators, European Molecular Biology Laboratory (EMBL)
2022 Jul; 7(7): 937-947. PubMed: 35773399.
Abstract + PDF
820.
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Van Rossum T, Costea PI, Paoli L, Alves RJ, Thielemann R, Sunagawa S, Bork P
2022 Jan 27; 38(4): 1162-1164. PubMed: 34791031.
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819.
Visualizing translation dynamics at atomic detail inside a bacterial cell.
Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J
2022 Oct 28; 610(7930): 205-211. PubMed: 36171285.
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818.
Publisher Correction: Visualizing translation dynamics at atomic detail inside a bacterial cell.
Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J
2022 Nov 10; 611(7937): E13. PubMed: 36357800.
PDF
817.
Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome.
Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, Da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Tara Oceans coordinators , Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB, Acinas S, Babin M, Bork P, Boss E, Bowler C, Cochrane G, De Vargas C, Gorsky G, Guidi L, Grimsley N, Hingamp P, Iudicone PD, Jaillon O, Kandels S, Karp-Boss L, Karsenti E, Not F, Ogata H, Poulton N, Pesant S, Sardet C, Speich S, Stemmann L, Sullivan MB, Sungawa S, Wincker P
2022 Apr 8; 376(6589): 156-162. PubMed: 35389782.
Abstract
2021 35 publication(s).
816.
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.
Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM
2021 May 21; 4(1): 604. PubMed: 34021239.
Abstract + PDF
815.
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner AC, Mouktaroudi M, Krämer B, Oestreich M, Antonakos N, Nuesch-Germano M, Gkizeli K, Bonaguro L, Reusch N, Baßler K, Saridaki M, Knoll R, Pecht T, Kapellos TS, Doulou S, Kröger C, Herbert M, Holsten L, Horne A, Gemünd ID, Rovina N, Agrawal S, Dahm K, van Uelft M, Drews A, Lenkeit L, Bruse N, Gerretsen J, Gierlich J, Becker M, Händler K, Kraut M, Theis H, Mengiste S, De Domenico E, Schulte-Schrepping J, Seep L, Raabe J, Hoffmeister C, ToVinh M, Keitel V, Rieke G, Talevi V, Skowasch D, Aziz NA, Pickkers P, van de Veerdonk FL, Netea MG, Schultze JL, Kox M, Breteler MMB, Nattermann J, Koutsoukou A, Giamarellos-Bourboulis EJ, Ulas T, German COVID-19 Omics Initiative (DeCOI) , Altmüller J, Angelov A, Bals R, Bartholomäus A, Becker A, Bitzer M, Bonifacio E, Bork P, Casadei N, Clavel T, Colome-Tatche M, Diefenbach A, Dilthey A, Fischer N, Förstner K, Franzenburg S, Frick JS, Gabernet G, Gagneur J, Ganzenmüller T, Göpel S, Goesmann A, Hain T, Heimbach A, Hummel M, Iftner A, Iftner T, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Kim-Hellmuth S, Klein C, Kohlbacher O, Köhrer K, Korbel J, Kühnert D, Kurth I, Landthaler M, Li Y, Ludwig K, Makarewicz O, Marz M, McHardy A, Mertes C, Nöthen M, Nürnberg P, Ohler U, Ossowski S, Overmann J, Pfeffer K, Poetsch AR, Pühler A, Rajewsky N, Ralser M, Rieß O, Ripke S, Nunes da Rocha U, Rosenstiel P, Saliba AE, Sander LE, Sawitzki B, Schiffer P, Schneider W, Schulte EC, Schultze JL, Sczyrba A, Singh Y, Sonnabend M, Stegle O, Stoye J, Theis F, Vehreschild J, Vogel J, von Kleist M, Walker A, Walter J, Wieczorek D, Winkler S, Ziebuhr J
2021 01 13; 13(1): 7. PubMed: 33441124.
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814.
Metagenomic assessment of the global diversity and distribution of bacteria and fungi.
Bahram M, Netherway T, Frioux C, Ferretti P, Coelho LP, Geisen S, Bork P, Hildebrand F
2021 Jan; 23(1): 316-326. PubMed: 33185929.
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813.
Protein Intake, Metabolic Status and the Gut Microbiota in Different Ethnicities: Results from Two Independent Cohorts.
Bel Lassen P, Attaye I, Adriouch S, Nicolaou M, Aron-Wisnewsky J, Nielsen T, Chakaroun R, Le Chatelier E, Forslund S, Belda E, Bork P, Bäckhed F, Stumvoll M, Pedersen O, Herrema H, Groen AK, Pinto-Sietsma SJ, Zwinderman AH, Nieuwdorp M, Clement K, On Behalf Of Metacardis Consortium
2021 Sep 10; 13(9): . PubMed: 34579043.
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812.
The InterPro protein families and domains database: 20 years on.
Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD
2021 Jan 8; 49(D1): D344-D354. PubMed: 33156333.
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811.
Macroscale patterns of oceanic zooplankton composition and size structure.
Brandão MC, Benedetti F, Martini S, Soviadan YD, Irisson JO, Romagnan JB, Elineau A, Desnos C, Jalabert L, Freire AS, Picheral M, Guidi L, Gorsky G, Bowler C, Karp-Boss L, Henry N, De Vargas C, Sullivan MB, Tara Oceans Consortium Coordinators , Stemmann L, Lombard F, Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, De Vargas C, Gorsky G, Guidi L, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels S, Karp-Boss L, Karsenti E, Not F, Ogata H, Poulton N, Pesant S, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P
2021 08 3; 11(1): 15714. PubMed: 34344925.
Abstract + PDF
810.
Author Correction: Macroscale patterns of oceanic zooplankton composition and size structure.
Brandão MC, Benedetti F, Martini S, Soviadan YD, Irisson JO, Romagnan JB, Elineau A, Desnos C, Jalabert L, Freire AS, Picheral M, Guidi L, Gorsky G, Bowler C, Karp-Boss L, Henry N, De Vargas C, Sullivan MB, Tara Oceans Consortium Coordinators , Stemmann L, Lombard F, Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, De Vargas C, Gorsky G, Guidi L, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels S, Karp-Boss L, Karsenti E, Not F, Ogata H, Poulton N, Pesant S, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P
2021 Oct 6; 11(1): 20226. PubMed: 34615992.
PDF
809.
Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.
Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Olanipekun M, Hoyles L, Djouadi F, Neves AL, Rodriguez-Martinez A, Mouawad GI, Pons N, Forslund S, Le-Chatelier E, Le Lay A, Nicholson J, Hansen T, Hyötyläinen T, Clément K, Oresic M, Bork P, Ehrlich SD, Raes J, Pedersen OB, Gauguier D, Dumas ME
Gut.
2021 Nov 11; 70(11): 2105-2114. PubMed: 33975870.
Abstract + PDF
808.
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J
2021 Dec 9; 38(12): 5825-5829. PubMed: 34597405.
Abstract + PDF
807.
Combinatorial, additive and dose-dependent drug-microbiome associations.
Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, Markó L, Aron-Wisnewsky J, Nielsen T, Moitinho-Silva L, Schmidt TSB, Falony G, Vieira-Silva S, Adriouch S, Alves RJ, Assmann K, Bastard JP, Birkner T, Caesar R, Chilloux J, Coelho LP, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Le Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem JE, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Søndertoft NB, Pedersen HK, Hansen TH, MetaCardis Consortium , Gøtze JP, Køber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert JM, Letunic I, Nielsen J, Bäckhed F, Ehrlich SD, Dumas ME, Raes J, Pedersen O, Clément K, Stumvoll M, Bork P
2021 Dec 8; 600(7889): 500-505. PubMed: 34880489.
Abstract + PDF
806.
Recurrent Frameshift Neoantigen Vaccine Elicits Protective Immunity With Reduced Tumor Burden and Improved Overall Survival in a Lynch Syndrome Mouse Model.
Gebert J, Gelincik O, Oezcan-Wahlbrink M, Marshall JD, Hernandez-Sanchez A, Urban K, Long M, Cortes E, Tosti E, Katzenmaier EM, Song Y, Elsaadi A, Deng N, Vilar E, Fuchs V, Nelius N, Yuan YP, Ahadova A, Sei S, Shoemaker RH, Umar A, Wei L, Liu S, Bork P, Edelmann W, von Knebel Doeberitz M, Lipkin SM, Kloor M
2021 Oct 2; 161(4): 1288-1302.e13. PubMed: 34224739.
Abstract + PDF
805.
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH
2021 Jan 8; 49(D1): D998-D1003. PubMed: 33084874.
Abstract + PDF
804.
Dispersal strategies shape persistence and evolution of human gut bacteria.
Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P
2021 Jul 14; 29(7): 1167-1176.e9. PubMed: 34111423.
Abstract + PDF
803.
Bioaccumulation of therapeutic drugs by human gut bacteria.
Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR
2021 Sep 8; 597(7877): 533-538. PubMed: 34497420.
Abstract + PDF
802.
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Krämer B, Knoll R, Bonaguro L, ToVinh M, Raabe J, Astaburuaga-García R, Schulte-Schrepping J, Kaiser KM, Rieke GJ, Bischoff J, Monin MB, Hoffmeister C, Schlabe S, De Domenico E, Reusch N, Händler K, Reynolds G, Blüthgen N, Hack G, Finnemann C, Nischalke HD, Strassburg CP, Stephenson E, Su Y, Gardner L, Yuan D, Chen D, Goldman J, Rosenstiel P, Schmidt SV, Latz E, Hrusovsky K, Ball AJ, Johnson JM, Koenig PA, Schmidt FI, Haniffa M, Heath JR, Kümmerer BM, Keitel V, Jensen B, Stubbemann P, Kurth F, Sander LE, Sawitzki B, Deutsche COVID-19 OMICS Initiative (DeCOI) , Altmüller J, Angelov A, Bals R, Bartholomäus A, Becker A, Bitzer M, Bonifacio E, Bork P, Casadei N, Clavel T, Colome-Tatche M, Diefenbach A, Dilthey A, Fischer N, Förstner K, Franzenburg S, Frick JS, Gabernet G, Gagneur J, Ganzenmüller T, Göpel S, Goesmann A, Hain T, Heimbach A, Hummel M, Iftner A, Iftner T, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Kim-Hellmuth S, Klein C, Kohlbacher O, Köhrer K, Korbel J, Kühnert D, Kurth I, Landthaler M, Li Y, Ludwig K, Makarewicz O, Marz M, McHardy A, Mertes C, Nöthen M, Nürnberg P, Ohler U, Ossowski S, Overmann J, Pfeffer K, Poetsch AR, Pühler A, Rajewsky N, Ralser M, Rieß O, Ripke S, Nunes da Rocha U, Rosenstiel P, Saliba AE, Sander LE, Sawitzki B, Schiffer P, Schneider W, Schulte EC, Schultze JL, Sczyrba A, Singh Y, Sonnabend M, Stegle O, Stoye J, Theis F, Vehreschild J, Vogel J, von Kleist M, Walker A, Walter J, Wieczorek D, Winkler S, Ziebuhr J, Aschenbrenner AC, Schultze JL, Nattermann J
2021 11 9; 54(11): 2650-2669.e14. PubMed: 34592166.
Abstract + PDF
801.
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.
2021 Jul 2; 49(W1): W293-W296. PubMed: 33885785.
Abstract + PDF
800.
SMART: recent updates, new developments and status in 2020.
2021 Jan 8; 49(D1): D458-D460. PubMed: 33104802.
Abstract + PDF
799.
Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum.
Li YY, Kuhn M, Zukowska-Kasprzyk J, Hennrich ML, Kastritis PL, O'Reilly FJ, Phapale P, Beck M, Gavin AC, Bork P
2021; 16(7): e0254429. PubMed: 34242379.
Abstract + PDF
798.
Polarization of microbial communities between competitive and cooperative metabolism.
Machado D, Maistrenko OM, Andrejev S, Kim Y, Bork P, Patil KR, Patil KR
2021 Feb; 5(2): 195-203. PubMed: 33398106.
Abstract + PDF
797.
Unravelling the collateral damage of antibiotics on gut bacteria.
Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A
2021 Nov 13; 599(7883): 120-124. PubMed: 34646011.
Abstract + PDF
796.
Highly variable fidelity drives symbiont community composition in an obligate symbiosis
Mankowski A, Kleiner M, Erséus C, Leisch N, Sato Y, Volland J-M , Hüttel B, Wentrup C, Woyke T, Wippler J, Dubilier N, Gruber-Vodicka H
2021 4 28; [Epub ahead of print] PID: 868.
Abstract
795.
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution.
Musser JM, Schippers KJ, Nickel M, Mizzon G, Kohn AB, Pape C, Ronchi P, Papadopoulos N, Tarashansky AJ, Hammel JU, Wolf F, Liang C, Hernández-Plaza A, Cantalapiedra CP, Achim K, Schieber NL, Pan L, Ruperti F, Francis WR, Vargas S, Kling S, Renkert M, Polikarpov M, Bourenkov G, Feuda R, Gaspar I, Burkhardt P, Wang B, Bork P, Beck M, Schneider TR, Kreshuk A, Wörheide G, Huerta-Cepas J, Schwab Y, Moroz LL, Arendt D
2021 Nov 5; 374(6568): 717-723. PubMed: 34735222.
Abstract + PDF
794.
GUNC: detection of chimerism and contamination in prokaryotic genomes.
2021 Jun 13; 22(1): 178. PubMed: 34120611.
Abstract + PDF
793.
Prognostic performance of 7 biomarkers compared to liver biopsy in early alcohol-related liver disease.
Rasmussen DN, Thiele M, Johansen S, Kjærrgaard M, Lindvig KP, Israelsen M, Antonsen S, Detlefsen S, Krag A, GALAXY , MicrobLiver consortia , Anastasiadou E, Arumugam M, Bork P, Hansen T, Hartoft C, Israelsen H, Karsdal M, Legido-Quigley C, Melberg HO, Thiele M, Trebicka J, Krag A, Bork P, Mann M, Matthijnssens J, Krag A, Hansen T
2021 11; 75(5): 1017-1025. PubMed: 34118335.
Abstract + PDF
792.
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean.
Royo-Llonch M, Sánchez P, Ruiz-González C, Salazar G, Pedrós-Alió C, Sebastián M, Labadie K, Paoli L, M Ibarbalz F, Zinger L, Churcheward B, Tara Oceans coordinators , Chaffron S, Eveillard D, Karsenti E, Sunagawa S, Wincker P, Karp-Boss L, Bowler C, Acinas SG, Babin M, Bork P, Boss E, Cochrane G, De Vargas C, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Kandels S, Not F, Ogata H, Pesant S, Poulton N, Raes J, Sardet C, Speich S, Setmmann L, Sullivan MB
2021 12; 6(12): 1561-1574. PubMed: 34782724.
Abstract + PDF
791.
A 12-genus bacterial signature identifies a group of severe autistic children with differential sensory behavior and brain structures.
Shi K, Zhang L, Yu J, Chen Z, Lai S, Zhao X, Li WG, Luo Q, Lin W, Feng J, Bork P, Zhao XM, Li F
2021 Feb; 11(2): e314. PubMed: 33634969.
PDF
790.
SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells.
Singh Y, Trautwein C, Fendel R, Krickeberg N, Berezhnoy G, Bissinger R, Ossowski S, Salker MS, Casadei N, Riess O, Deutsche COVID-19 OMICS Initiate (DeCOI) , Altmüller J, Angelov A, Aschenbrenner AC, Bals R, Bartholomäus A, Becker A, Becker M, Bezdan D, Bitzer M, Blumert C, Bonifacio E, Bork P, Boyke B, Blum H, Casadei N, Clavel T, Colome-Tatche M, Cornberg M, Velázquez IADLR, Diefenbach A, Dilthey A, Fischer N, Förstner K, Franzenburg S, Frick JS, Gabernet G, Gagneur J, Ganzenmueller T, Gauder M, Geißert J, Goesmann A, Göpel S, Grundhoff A, Grundmann H, Hain T, Hanses F, Hehr U, Heimbach A, Hoeper M, Horn F, Hübschmann D, Hummel M, Iftner T, Iftner A, Illig T, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Keppler OT, Kim-Hellmuth S, Klein C, Knop M, Kohlbacher O, Köhrer K, Korbel JO, Kremsner PG, Kühnert D, Kurth I, Landthaler M, Li Y, Ludwig KU, Makarewicz O, Marz M, McHardy AC, Mertes C, Münchhoff M, Nahnsen S, Nöthen M, Ntoumi F, Nürnberg P, Ossowski S, Overmann J, Peter S, Pfeffer K, Pink I, Poetsch AR, Protzer U, Pühler A, Rajewsky N, Ralser M, Reiche K, Rieß O, Ripke S, da Rocha UN, Rosenstiel P, Saliba AE, Sander LE, Sawitzki B, Scheithauer S, Schiffer P, Schmid-Burgk J, Schneider W, Schulte EC, Schultze JL, Sczyrba A, Sharaf ML, Singh Y, Sonnabend M, Stegle O, Stoye J, Theis F, Ulas T, Vehreschild J, Velavan TP, Vogel J, Volland S, von Kleist M, Walker A, Walter J, Wieczorek D, Winkler S, Ziebuhr J.
2021 Jun; 7(6): e07147. PubMed: 34075347.
Abstract + PDF
789.
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C
2021 Jan 8; 49(D1): D605-D612. PubMed: 33237311.
Abstract + PDF
788.
Correction to 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets'.
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C
2021 Oct 11; 49(18): 10800. PubMed: 34530444.
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787.
Progressive alcohol-related liver fibrosis is characterised by imbalanced collagen formation and degradation.
Thiele M, Johansen S, Gudmann NS, Madsen B, Kjaergaard M, Nielsen MJ, Leeming DJ, Jacobsen S, Bendtsen F, Møller S, Detlefsen S, Karsdal M, Krag A, GALAXY consortium , Arumugam M, Bork P, Hansen T, Anastasiadou E, Hartoft C, Israelsen H, Legido-Quigley C, Melberg HO, Trebicka J
2021 10; 54(8): 1070-1080. PubMed: 34428307.
Abstract + PDF
786.
Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure.
Trebicka J, Bork P, Krag A, Arumugam M
2021 Mar; 18(3): 167-180. PubMed: 33257833.
Abstract + PDF
785.
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog.
Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J
2021 Oct 26; 6(5): e0038221. PubMed: 34665009.
Abstract + PDF
784.
Characterization of SARS-CoV-2 infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker A, Houwaart T, Finzer P, Ehlkes L, Tyshaieva A, Damagnez M, Strelow D, Duplessis A, Nicolai J, Wienemann T, Tamayo T, Kohns Vasconcelos M, Hülse L, Hoffmann K, Lübke N, Hauka S, Andree M, Däumer MP, Thielen A, Kolbe-Busch S, Göbels K, Zotz R, Pfeffer K, Timm J, Dilthey AT, German COVID-19 Omics Initiative (DeCOI) , Altmüller J, Angelov A, Aschenbrenner AC, Bals R, Bartholomäus A, Becker A, Bezdan D, Bitzer M, Blum H, Bonifacio E, Bork P, Casadei N, Clavel T, Colome-Tatche M, Velázquez IADLR, Diefenbach A, Dilthey A, Fischer N, Förstner K, Franzenburg S, Frick JS, Gabernet G, Gagneur J, Ganzenmüller T, Gauder M, Goesmann A, Göpel S, Grundhoff A, Grundmann H, Hain T, Heimbach A, Hummel M, Iftner T, Iftner A, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Keppler O, Kim-Hellmuth S, Klein C, Knop M, Kohlbacher O, Köhrer K, Korbel JO, Kremsner PG, Kühnert D, Kurth I, Landthaler M, Li Y, Ludwig K, Makarewicz O, Marz M, McHardy A, Mertes C, Münchhoff M, Nahnsen S, Nöthen M, Ntoumi F, Nürnberg P, Ohler U, Ossowski S, Overmann J, Peter S, Pfeffer K, Poetsch AR, Protzer U, Pühler A, Rajewsky N, Ralser M, Rieß O, Ripke S, Rocha U, Rosenstiel P, Saliba E, Sander LE, Sawitzki B, Scheithauer S, Schiffer P, Schmid-Burgk J, Schneider W, Schulte EC, Schultze J, Sczyrba A, Sharaf ML, Singh Y, Sonnabend M, Stegle O, Stoye J, Theis F, Vehreschild J, Velavan TP, Vogel J, von Kleist M, Walker A, Walter J, Wieczorek D, Winkler S, Ziebuhr J.
2021 Jun 28; [Epub ahead of print] PubMed: 34181711.
Abstract + PDF
783.
Swarm Learning for decentralized and confidential clinical machine learning.
Warnat-Herresthal S, Schultze H, Shastry KL, Manamohan S, Mukherjee S, Garg V, Sarveswara R, Händler K, Pickkers P, Aziz NA, Ktena S, Tran F, Bitzer M, Ossowski S, Casadei N, Herr C, Petersheim D, Behrends U, Kern F, Fehlmann T, Schommers P, Lehmann C, Augustin M, Rybniker J, Altmüller J, Mishra N, Bernardes JP, Krämer B, Bonaguro L, Schulte-Schrepping J, De Domenico E, Siever C, Kraut M, Desai M, Monnet B, Saridaki M, Siegel CM, Drews A, Nuesch-Germano M, Theis H, Heyckendorf J, Schreiber S, Kim-Hellmuth S, COVID-19 Aachen Study (COVAS) , Nattermann J, Skowasch D, Kurth I, Keller A, Bals R, Nürnberg P, Rieß O, Rosenstiel P, Netea MG, Theis F, Mukherjee S, Backes M, Aschenbrenner AC, Ulas T, Deutsche COVID-19 OMICS Initiative (DeCOI) , Breteler MMB, Giamarellos-Bourboulis EJ, Kox M, Becker M, Cheran S, Woodacre MS, Goh EL, Schultze JL, Balfanz P, Eggermann T, Boor P, Hausmann R, Kuhn H, Isfort S, Stingl JC, Schmalzing G, Kuhl CK, Röhrig R, Marx G, Uhlig S, Dahl E, Müller-Wieland D, Dreher M, Marx N, Angelov A, Bartholomäus A, Becker A, Bezdan D, Blumert C, Bonifacio E, Bork P, Boyke B, Blum H, Clavel T, Colome-Tatche M, Cornberg M, Velázquez IADL, Diefenbach A, Dilthey A, Fischer N, Förstner K, Franzenburg S, Frick JS, Gabernet G, Gagneur J, Ganzenmueller T, Gauder M, Geißert J, Goesmann A, Göpel S, Grundhoff A, Grundmann H, Hain T, Hanses F, Hehr U, Heimbach A, Hoeper M, Horn F, Hübschmann D, Hummel M, Iftner T, Iftner A, Illig T, Janssen S, Kalinowski J, Kallies R, Kehr B, Keppler OT, Klein C, Knop M, Kohlbacher O, Köhrer K, Korbel J, Kremsner PG, Kühnert D, Landthaler M, Li Y, Ludwig KU, Makarewicz O, Marz M, McHardy AC, Mertes C, Münchhoff M, Nahnsen S, Nöthen M, Ntoumi F, Overmann J, Peter S, Pfeffer K, Pink I, Poetsch AR, Protzer U, Pühler A, Rajewsky N, Ralser M, Reiche K, Ripke S, da Rocha UN, Saliba AE, Sander LE, Sawitzki B, Scheithauer S, Schiffer P, Schmid-Burgk J, Schneider W, Schulte EC, Sczyrba A, Sharaf ML, Singh Y, Sonnabend M, Stegle O, Stoye J, Vehreschild J, Velavan TP, Vogel J, Volland S, von Kleist M, Walker A, Walter J, Wieczorek D, Winkler S, Ziebuhr J
2021 06; 594(7862): 265-270. PubMed: 34040261.
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782.
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel J, Zych K, Essex M, Karcher N, Kartal E, Salazar G, Bork P, Sunagawa S, Zeller G
2021 Mar 30; 22(1): 93. PubMed: 33785070.
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2020 15 publication(s).
781.
Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.
Bahram M, Netherway T, Hildebrand F, Pritsch K, Drenkhan R, Loit K, Anslan S, Bork P, Tedersoo L
2020 Aug 12; 227(4): 1189-1199. PubMed: 32279325.
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780.
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.
Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, Köhler P, Künstner A, Rosati E, Aschenbrenner AC, Bacher P, Baran N, Boysen T, Brandt B, Bruse N, Dörr J, Dräger A, Elke G, Ellinghaus D, Fischer J, Forster M, Franke A, Franzenburg S, Frey N, Friedrichs A, Fuß J, Glück A, Hamm J, Hinrichsen F, Hoeppner MP, Imm S, Junker R, Kaiser S, Kan YH, Knoll R, Lange C, Laue G, Lier C, Lindner M, Marinos G, Markewitz R, Nattermann J, Noth R, Pickkers P, Rabe KF, Renz A, Röcken C, Rupp J, Schaffarzyk A, Scheffold A, Schulte-Schrepping J, Schunk D, Skowasch D, Ulas T, Wandinger KP, Wittig M, Zimmermann J, Busch H, Hoyer BF, Kaleta C, Heyckendorf J, Kox M, Rybniker J, Schreiber S, Schultze JL, Rosenstiel P, HCA Lung Biological Network , Deutsche COVID-19 OMICS Initiative (DeCOI) , Banovich NE, Desai T, Eickelberg O, Haniffa M, Horvath P, Kropski JA, Lafyatis R, Lundeberg J, Meyer K, Nawijn MC, Nikolic M, Montanes JO, Pe’er D, Tata PR, Rawlins E, Regev A, Reyfman P, Samakovlis C, Schultze J, Shalek A, Shepherd D, Spence J, Teichmann S, Theis F, Tsankov A, van den Berge M, von Papen M, Whitsett J, Zaragosi LE, Angelov A, Bals R, Bartholomäus A, Becker A, Bezdan D, Bonifacio E, Bork P, Clavel T, Colme-Tatche M, Diefenbach A, Dilthey A, Fischer N, Förstner K, Frick JS, Gagneur J, Goesmann A, Hain T, Hummel M, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Kim-Hellmuth S, Klein C, Kohlbacher O, Korbel JO, Kurth I, Landthaler M, Li Y, Ludwig K, Makarewicz O, Marz M, McHardy A, Mertes C, Nöthen M, Nürnberg P, Ohler U, Ossowski S, Overmann J, Peter S, Pfeffer K, Poetsch AR, Pühler A, Rajewsky N, Ralser M, Rieß O, Ripke S, da Rocha UN, Saliba AE, Sander LE
2020 12 15; 53(6): 1296-1314.e9. PubMed: 33296687.
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779.
Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology.
Hildebrand F, Pallen MJ, Bork P
Gut.
2020 Jul 15; 69(7): 1358-1359. PubMed: 31203204.
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778.
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li YY, Kuhn M, Gavin AC, Bork P
2020 Feb 15; 36(4): 1213-1218. PubMed: 31605112.
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777.
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
2020 May 11; 14(5): 1247-1259. PubMed: 32047279.
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776.
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
2020 Jan 8; 48: D621-D625. PubMed: 31647096.
Abstract + PDF
775.
(Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A.
Michalak M, Katzenmaier EM, Roeckel N, Woerner SM, Fuchs V, Warnken U, Yuan YP, Bork P, Neu-Yilik G, Kulozik A, von Knebel Doeberitz M, Kloor M, Kopitz J, Gebert J
2020 Jul 23; 21(15): . PubMed: 32718059.
Abstract + PDF
774.
Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.
Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium , Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F
2020 Dec 21; 11(1): 6448. PubMed: 33349634.
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773.
Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology.
Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, Bastard JP, Forslund S, Le Chatelier E, Falony G, Pons N, Prifti E, Quinquis B, Roume H, Vieira-Silva S, Hansen TH, Pedersen HK, Lewinter C, Sønderskov NB, MetaCardis Consortium , Køber L, Vestergaard H, Hansen T, Zucker JD, Galan P, Dumas ME, Raes J, Oppert JM, Letunic I, Nielsen J, Bork P, Ehrlich SD, Stumvoll M, Pedersen O, Aron-Wisnewsky J, Clément K, Bäckhed F
2020 Nov 18; 11(1): 5881. PubMed: 33208748.
Abstract + PDF
772.
Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells.
Poisa-Beiro L, Thoma J, Landry J, Sauer S, Yamamoto A, Eckstein V, Romanov N, Raffel S, Hoffmann GF, Bork P, Benes V, Gavin AC, Tanaka M, Ho AD
2020 Jul 14; 10(1): 11597. PubMed: 32665666.
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771.
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE, Deutsche COVID-19 OMICS Initiative (DeCOI) , Angelov A, Bals R, Bartholomäus A, Becker A, Bezdan D, Bonifacio E, Bork P, Clavel T, Colome-Tatche M, Diefenbach A, Dilthey A, Fischer N, Förstner K, Frick JS, Gagneur J, Goesmann A, Hain T, Hummel M, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Kim-Hellmuth S, Klein C, Kohlbacher O, Korbel J, Kurth I, Landthaler M, Li Y, Ludwig K, Makarewicz O, Marz M, McHardy A, Mertes C, Nöthen M, Nürnberg P, Ohler U, Ossowski S, Overmann J, Peter S, Pfeffer K, Poetsch AR, Pühler A, Rajewsky N, Ralser M, Rieß O, Ripke S, Nunes da Rocha U, Rosenstiel P, Saliba AE, Sander LE, Sawitzki B, Schiffer P, Schulte EC, Schultze JL, Sczyrba A, Stegle O, Stoye J, Theis F, Vehreschild J, Vogel J, von Kleist M, Walker A, Walter J, Wieczorek D, Ziebuhr J
2020 09 17; 182(6): 1419-1440.e23. PubMed: 32810438.
Abstract + PDF
770.
Tara Oceans: towards global ocean ecosystems biology.
Sunagawa S, Acinas SG, Bork P, Bowler C
2020 Aug 12; 18(8): 428-445. PubMed: 32398798.
Abstract + PDF
769.
Die Erforschung des menschlichen Mikrobioms
Trojahn U, Wirbel J, Bork P, Zeller G
In: Von der Datenanalyse zum Verstehen komplexer biologischer Systems01 pp.64-69. BID: 23.
Publisher: Bruns Druckwelt GmbH & Co. KG, Minden
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768.
Diversity within species: interpreting strains in microbiomes.
2020 Sep 4; 18(9): 491-506. PubMed: 32499497.
Abstract + PDF
767.
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis.
Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, Andreelli F, Bastard JP, Coelho LP, Galleron N, Hansen TH, Hulot JS, Lewinter C, Pedersen HK, Quinquis B, Rouault C, Roume H, Salem JE, Søndertoft NB, Touch S, MetaCardis Consortium: , Dumas E-M , Ehrlich SD, Galan P, Gøtze JP, Hansen T, Holst JJ, Køber L, Letunic I, Nielsen J, Oppert J-M , Stumvoll M, Vestergaard H, Zucker J-D , Bork P, Pedersen O, Bäckhed F, Clément K, Raes J
2020 May; 581(7808): 310-315. PubMed: 32433607.
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2019 27 publication(s).
766.
Consent insufficient for data release-Response.
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I
2019 May 3; 364(6439): 446. PubMed: 31048484.
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765.
Toward unrestricted use of public genomic data.
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I
2019 Jan 25; 363(6425): 350-352. PubMed: 30679363.
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764.
Cost-effectiveness of non-invasive screening for alcohol-related liver fibrosis.
Asphaug L, Thiele M, Krag A, Melberg HO, GALAXY consortium , Anastasiadou E, Arumugam M, Bork P, Hansen T, Israelsen H, Juul L, Karsdal M, Legido-Quickley C, Trebicka J
2019 Oct 8; [Epub ahead of print] PubMed: 31595545.
Abstract + PDF
763.
Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.
Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L
2019 Aug 30; 11(4): 487-494. PubMed: 30058291.
Abstract + PDF
762.
[The gut microbiome in Parkinson disease].
Bedarf JR, Hildebrand F, Goeser F, Bork P, Wüllner U
2019 Feb 31; 90(2): 160-166. PubMed: 30171304.
Abstract + PDF
761.
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho LP, Alves RJ, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P
2019 Jun 3; 7(1): 84. PubMed: 31159881.
Abstract + PDF
760.
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.
Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ, Timmermann B, Ralser M
2019 May 20; 29(10): 1712-1720.e7. PubMed: 31080084.
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759.
Marine DNA Viral Macro- and Microdiversity from Pole to Pole.
Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ , Vik D, Tara Oceans coordinators , Babin M, Bowler C, Culley AI, De Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB, Collaborators , Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, De Vargas C, Follows M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Not F, Ogata H, Pesant S, Poulton N, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P.
2019 May 16; 177(5): 1109-1123.e14. PubMed: 31031001.
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758.
Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.
Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R
2019 Nov 22; 21: 664-680. PubMed: 31733513.
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757.
Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome.
Hickl O, Heintz-Buschart A, Trautwein-Schult A, Hercog R, Bork P, Wilmes P, Becher D
2019 Sep 19; 7(9): . PubMed: 31546776.
Abstract + PDF
756.
Antibiotics-induced monodominance of a novel gut bacterial order.
Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Huerta-Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Aalvink S, Belzer C, Forslund SK, Sunagawa S, Hentschel U, Merten C, Patil KR, Benes V, Bork P
Gut.
2019 Oct 18; 68(10): 1781-1790. PubMed: 30658995.
Abstract + PDF
755.
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P
2019 Jan 8; 47: D309-D314. PubMed: 30418610.
Abstract + PDF
754.
Global Trends in Marine Plankton Diversity across Kingdoms of Life.
Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Tara Oceans coordinators , Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, De Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L, Collaborators , Acinas SG, Babin M, Bork P, Boss E, Bowler C, Cochrane G, De Vargas C, Follows M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Iudicone D, Jaillon O, Kandels S, Karp-Boss L, Karsenti E, Not F, Ogata H, Pesant S, Poulton N, Raes J, Sardet C, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P.
2019 Nov 14; 179(5): 1084-1097.e21. PubMed: 31730851.
Abstract + PDF
753.
Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
2019 Jul 2; 47: W256-W259. PubMed: 30931475.
Abstract + PDF
752.
Efficacy of probiotics to prevent gut dysbiosis in preterm infants of 28+0-32+6 weeks of gestation: a randomised, placebo-controlled, double-blind, multicentre trial: the PRIMAL Clinical Study protocol.
Marißen J, Haiß A, Meyer C, Van Rossum T, Bünte LM, Frommhold D, Gille C, Goedicke-Fritz S, Göpel W, Hudalla H, Pagel J, Pirr S, Siller B, Viemann D, Vens M, König I, Herting E, Zemlin M, Gehring S, Bork P, Henneke P, Härtel C, PRIMAL consortium
2019 Nov 21; 9(11): e032617. PubMed: 31753895.
Abstract + PDF
751.
Microbial abundance, activity and population genomic profiling with mOTUs2.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves RJ, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S
2019 Mar 4; 10(1): 1014. PubMed: 30833550.
Abstract + PDF
750.
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD
2019 Jan 8; 47: D351-D360. PubMed: 30398656.
Abstract + PDF
749.
Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals.
Romanov N, Kuhn M, Aebersold R, Ori A, Beck M, Bork P
2019 May 16; 177(5): 1308-1318.e10. PubMed: 31031010.
Abstract + PDF
748.
Minimum Information about an Uncultivated Virus Genome (MIUViG).
Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA
2019 Jan 17; 37(1): 29-37. PubMed: 30556814.
Abstract + PDF
747.
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Tara Oceans Consortium Coordinators , Acinas SG, Babin M, Bork P, Bowler C, De Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S
2019 Nov 14; 179(5): 1068-1083.e21. PubMed: 31730850.
Abstract + PDF
746.
Extensive transmission of microbes along the gastrointestinal tract.
Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, Wirbel J, Maistrenko OM, Alves RJ, Bergsten E, de Beaufort C, Sobhani I, Heintz-Buschart A, Sunagawa S, Zeller G, Wilmes P, Bork P
2019 Feb 12; 8: . PubMed: 30747106.
Abstract + PDF
745.
Effects of Weight-Loss Interventions on Short-Chain Fatty Acid Concentrations in Blood and Feces of Adults: A Systematic Review.
Sowah SA, Riedl L, Damms-Machado A, Johnson TS, Schübel R, Graf M, Kartal E, Zeller G, Schwingshackl L, Stangl GI, Kaaks R, Kühn T
2019 Jul 1; 10(4): 673-684. PubMed: 31075175.
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744.
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C
2019 Jan 8; 47: D607-D613. PubMed: 30476243.
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743.
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N
2019 Apr 1; 25(4): 667-678. PubMed: 30936548.
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742.
Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N
2019 Dec 29; 25(12): 1948. PubMed: 31664237.
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741.
Population-level analysis of subtype prevalence and variation in the human gut microbiota.
Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J
Gut.
2019 Jul 31; 68(7): 1180-1189. PubMed: 30171064.
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740.
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G
2019 Apr 1; 25(4): 679-689. PubMed: 30936547.
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2018 28 publication(s).
739.
Structure and function of the global topsoil microbiome.
Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P
2018 Aug 1; 560(7717): 233-237. PubMed: 30069051.
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738.
Pervasive Protein Thermal Stability Variation during the Cell Cycle.
Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM
2018 May 31; 173(6): 1495-1507.e18. PubMed: 29706546.
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737.
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C
2018 Feb 6; 36(2): 196. PubMed: 29406516.
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736.
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C
2018 Jul 6; 36(7): 660. PubMed: 29979671.
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735.
Species-specific activity of antibacterial drug combinations.
Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Savitski MM, Bork P, Göttig S, Typas A
2018 Jul 4; 559(7713): 259-263. PubMed: 29973719.
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734.
A global ocean atlas of eukaryotic genes.
Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Tara-Oceans-Coordinators : , Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, De Vargas C, Iudicone D, Bowler C, Wincker P
2018 Jan 25; 9(1): 373. PubMed: 29371626.
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733.
Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P
2018 Apr 19; 6(1): 72. PubMed: 29669589.
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732.
Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
2018 Jan; 3(1): 8-16. PubMed: 29255284.
Abstract + PDF
731.
Publisher Correction: Enterotypes in the landscape of gut microbial community composition.
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P
2018 Mar 13; 3(3): 388. PubMed: 29440750.
Abstract + PDF
730.
iPath3.0: interactive pathways explorer v3.
2018 Jul 2; 46: W510-W513. PubMed: 29718427.
Abstract + PDF
729.
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.
Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N
2018 Jul 11; 24(1): 133-145.e5. PubMed: 30001516.
Abstract + PDF
728.
MVP: a microbe-phage interaction database.
Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH
2018 Jan 4; 46: D700-D707. PubMed: 29177508.
Abstract + PDF
727.
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.
Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Bork P, Aloy P, Gavin AC, Ho AD
2018 Oct 1; 9(1): 4004. PubMed: 30275468.
Abstract + PDF
726.
Gut microbiota composition is associated with environmental landscape in honey bees.
Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO
2018 Jan; 8(1): 441-451. PubMed: 29321884.
Abstract + PDF
725.
The gut microbiome is associated with behavioural task in honey bees.
Jones JC, Fruciano C, Marchant J, Hildebrand F, Forslund SK, Bork P, Engel P, Hughes WOH
2018; 65(3): 419-429. PubMed: 30100619.
Abstract + PDF
724.
Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes.
Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, Bork P, Moebus S, Herms S, Fischer S, Hoffmann P, Aretz S, Steinke-Lange V
2018 Dec 1; 143(11): 2800-2813. PubMed: 29987844.
Abstract + PDF
723.
Selective maternal seeding and environment shape the human gut microbiome.
Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P
2018 Apr 1; 28(4): 561-568. PubMed: 29496731.
Abstract + PDF
722.
Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P
2018 Jul 28; 8(7): e021682. PubMed: 30056386.
Abstract + PDF
721.
20 years of the SMART protein domain annotation resource.
2018 Jan 4; 46: D493-D496. PubMed: 29040681.
Abstract + PDF
720.
Extensive impact of non-antibiotic drugs on human gut bacteria.
Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A
2018 Mar 29; 555(7698): 623-628. PubMed: 29555994.
Abstract + PDF
719.
Recovery of gut microbiota of healthy adults following antibiotic exposure.
Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O
2018 Nov 22; 3(11): 1255-1265. PubMed: 30349083.
Abstract + PDF
718.
Quantifying compartment-associated variations of protein abundance in proteomics data.
Parca L, Beck M, Bork P, Ori A
2018 Jul 2; 14(7): e8131. PubMed: 29967062.
Abstract + PDF
717.
A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.
Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB
2018 Dec 31; 13(12): 2781-2800. PubMed: 30382244.
Abstract + PDF
716.
Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.
Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O
2018 Mar 22; 173(1): 208-220.e20. PubMed: 29551265.
Abstract + PDF
715.
The Human Gut Microbiome: From Association to Modulation.
2018 Mar 8; 172(6): 1198-1215. PubMed: 29522742.
Abstract + PDF
714.
Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.
Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Tara-Oceans-Coordinators , Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, De Vargas C, Wincker P
2018 Jan 22; 9(1): 310. PubMed: 29358710.
Abstract + PDF
713.
Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites.
Tackmann J, Arora N, Schmidt TSB, Rodrigues JFM, von Mering C
2018 10 24; 6(1): 192. PubMed: 30355348.
Abstract + PDF
712.
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.
Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR
2018 Apr 19; 3(4): 514-522. PubMed: 29556107.
Abstract + PDF
2017 30 publication(s).
711.
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Genoscope Technical Team , Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Tara Oceans Consortium Coordinators , Pesant S, Karsenti E, Wincker P, Collaborators , Bazire P, Beluche O, Bertrand L, Besnard-Gonnet M, Bordelais I, Boutard M, Dubois M, Dumont C, Ettedgui E, Fernandez P, Garcia E, Aiach NG, Guerin T, Hamon C, Brun E, Lebled S, Lenoble P, Louesse C, Mahieu E, Mairey B, Martins N, Megret C, Milani C, Muanga J, Orvain C, Payen E, Perroud P, Petit E, Robert D, Ronsin M, Vacherie B, Acinas SG, Bork P, Boss E, Bowler C, De Vargas C, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Not F, Ogata H, Pesant S, Raes J, Sardet C, Sieracki ME, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Wincker P.
2017 08 1; 4: 170093. PubMed: 28763055.
Abstract + PDF
710.
Effects of oral antibiotics and isotretinoin on the murine gut microbiota.
Becker E, Schmidt TSB, Bengs S, Poveda L, Opitz L, Atrott K, Stanzel C, Biedermann L, Rehman A, Jonas D, von Mering C, Rogler G, Frey-Wagner I
2017 Sep; 50(3): 342-351. PubMed: 28689869.
Abstract
709.
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.
Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U
2017 Apr 28; 9(1): 39. PubMed: 28449715.
Abstract + PDF
708.
Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.
Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U
2017 Jun 29; 9(1): 61. PubMed: 28662719.
PDF
707.
Systematic identification of phosphorylation-mediated protein interaction switches.
Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB
2017 Mar 27; 13(3): e1005462. PubMed: 28346509.
Abstract + PDF
706.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C
2017 Aug 8; 35(8): 725-731. PubMed: 28787424.
Abstract + PDF
705.
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.
Chen WH, Lu G, Chen X, Zhao XM, Bork P
2017 Jan 4; 45(D1): D940-D944. PubMed: 27799467.
Abstract + PDF
704.
Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.
Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, De Vargas C
2017 Oct 31; 6: . PubMed: 29087936.
Abstract + PDF
703.
Subspecies in the global human gut microbiome.
2017 Dec 14; 13(12): 960. PubMed: 29242367.
Abstract + PDF
702.
metaSNV: A tool for metagenomic strain level analysis.
Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P
2017; 12(7): e0182392. PubMed: 28753663.
Abstract + PDF
701.
Towards standards for human fecal sample processing in metagenomic studies.
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P
2017 Nov 2; 35(11): 1069-1076. PubMed: 28967887.
Abstract + PDF
700.
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.
Czech L, Huerta-Cepas J, Stamatakis A
2017 Jun 1; 34(6): 1535-1542. PubMed: 28369572.
Abstract + PDF
699.
InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL
2017 Jan 4; 45(D1): D190-D199. PubMed: 27899635.
Abstract + PDF
698.
Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHit-Consortium , Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
2017 May 3; 545(7652): 116. PubMed: 28470190.
PDF
697.
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
2017 Aug 1; 34(8): 2115-2122. PubMed: 28460117.
Abstract + PDF
696.
Metabolic anchor reactions for robust biorefining.
Jouhten P, Huerta-Cepas J, Bork P, Patil KR
2017 Mar 21; 40: 1-4. PubMed: 28232136.
Abstract + PDF
695.
The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.
Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC
2017 Nov 24; 7(1): 16324. PubMed: 29176730.
Abstract + PDF
694.
Capturing protein communities by structural proteomics in a thermophilic eukaryote.
Kastritis PL, O'Reilly FJ, Bock T, Li YY, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC
2017 Jul 25; 13(7): 936. PubMed: 28743795.
Abstract + PDF
693.
Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change
Kleinteich J, Hildebrand F, Bahram M, Voigt AY, Wood SA, Jungblut AD, Küpper FC, Quesada A, Camacho A, Pearce DA, Convey P, Vincent WF, Zarfl C, Bork P, Dietrich DR
2017 Nov 10; 5: 1-11. PID: 725.
Abstract + PDF
692.
Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis.
Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S
2017 Apr 1; 312(4): G327-G339. PubMed: 28039159.
Abstract + PDF
691.
Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression.
Leonardi I, Gerstgrasser A, Schmidt TSB, Nicholls F, Tewes B, Greinwald R, von Mering C, Rogler G, Frey-Wagner I
2017 Nov 28; 7(1): 16500. PubMed: 29184071.
Abstract + PDF
690.
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis.
Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C
2017 Dec 1; 33(23): 3808-3810. PubMed: 28961926.
Abstract + PDF
689.
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
2017 Jan 4; 45(D1): D529-D534. PubMed: 28053165.
Abstract + PDF
688.
Bioinformatics Analysis of Functional Associations of PTMs.
2017; 1558: 303-320. PubMed: 28150244.
Abstract + PDF
687.
RTK: efficient rarefaction analysis of large datasets.
2017 Aug 15; 33(16): 2594-2595. PubMed: 28398468.
Abstract + PDF
686.
A family of interaction-adjusted indices of community similarity.
Schmidt TSB, Matias Rodrigues JF, von Mering C
2017 03; 11(3): 791-807. PubMed: 27935587.
Abstract + PDF
685.
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C
2017 Jan 4; 45(D1): D362-D368. PubMed: 27924014.
Abstract + PDF
684.
[Microbial Biomarkers for Early Cancer Detection].
2017 Feb; 142(4): 267-274. PubMed: 28235227.
Abstract + PDF
683.
GEAR: A database of Genomic Elements Associated with drug Resistance.
Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM
2017 Mar 15; 7: 44085. PubMed: 28294141.
Abstract + PDF
682.
Salt-responsive gut commensal modulates TH17 axis and disease.
Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN
2017 Nov 30; 551(7682): 585-589. PubMed: 29143823.
Abstract + PDF
2016 28 publication(s).
681.
Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M
2016 May 4; 13(5): 425-30. Epub 2016 Apr 4; PubMed: 27043882.
Abstract + PDF
680.
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.
Baa-Puyoulet P, Parisot N, Febvay G, Huerta-Cepas J, Vellozo AF, Gabaldón T, Calevro F, Charles H, Colella S
2016; 2016: . PubMed: 27242037.
Abstract + PDF
679.
Energy efficiency trade-offs drive nucleotide usage in transcribed regions.
Chen WH, Lu G, Bork P, Hu S, Lercher MJ
2016 Apr 21; 7: 11334. PubMed: 27098217.
Abstract + PDF
678.
Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.
Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P
2016 Feb 18; 44(3): 1192-202. Epub 2016 Jan 14; PubMed: 26773059.
Abstract + PDF
677.
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.
Cornejo-Castillo FM, Cabello AM, Salazar G, Sánchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, De Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG
2016 Mar 22; 7: 11071. PubMed: 27002549.
Abstract + PDF
676.
CART - a chemical annotation retrieval toolkit.
2016 Sep 15; 32(18): 2869-71. Epub 2016 Jun 2; PubMed: 27256313.
Abstract + PDF
675.
Plankton networks driving carbon export in the oligotrophic ocean.
Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, De Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G.
2016 Apr 28; 532(7600): 465-470. Epub 2016 Feb 10; PubMed: 26863193.
Abstract + PDF
674.
ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
2016 Jun 26; 33(6): 1635-8. Epub 2016 Feb 26; PubMed: 26921390.
Abstract + PDF
673.
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
2016 Jan 4; 44: D286-93. Epub 2015 Nov 17; PubMed: 26582926.
Abstract + PDF
672.
Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.
Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM
2016 Jan 26; 7: 10410. PubMed: 26811868.
Abstract + PDF
671.
The SIDER database of drugs and side effects.
2016 Jan 4; 44: D1075-9. Epub 2015 Oct 19; PubMed: 26481350.
Abstract + PDF
670.
MOCAT2: a metagenomic assembly, annotation and profiling framework.
2016 Aug 15; 32(16): 2520-3. Epub 2016 Apr 8; PubMed: 27153620.
Abstract + PDF
669.
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
2016 Jul 8; 44: W242-5. Epub 2016 Apr 19; PubMed: 27095192.
Abstract + PDF
668.
Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P
2016 Apr 29; 352(6285): 586-9. PubMed: 27126044.
Abstract + PDF
667.
Bacterial antisense RNAs are mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M
2016 Mar; 2(3): e1501363. PubMed: 26973873.
Abstract + PDF
666.
Gut Microbiota Linked to Sexual Preference and HIV Infection.
Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R
2016 Mar; 5: 135-46. PubMed: 27077120.
Abstract + PDF
665.
Spatiotemporal variation of mammalian protein complex stoichiometries.
Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M
2016 Mar 14; 17(1): 47. Epub 2016 Mar 14; PubMed: 26975353.
Abstract + PDF
664.
Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K, Consortium M, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O
2016 Jul 21; 535(7612): 376-81. Epub 2016 Jul 13; PubMed: 27409811.
Abstract + PDF
663.
Transcriptional interactions suggest niche segregation among microorganisms in the human gut.
Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AM, de Evgrafov MC, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O, MetaHit-Consortium , Sommer MO, Ehrlich SD, Sicheritz-Pontén T, Brunak S, Nielsen HB
2016 Aug 26; 1(11): 16152. PubMed: 27564131.
Abstract + PDF
662.
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D, Tara-Oceans-Coordinators , Bork P, Acinas SG, Wincker P, Sullivan MB
2016 Sep 29; 537(7622): 689-693. Epub 2016 Sep 21; PubMed: 27654921.
Abstract + PDF
661.
A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.
Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC
2016 Jun; 11(6): 1021-38. Epub 2016 May 5; PubMed: 27149326.
Abstract + PDF
660.
Benchmarking the next generation of homology inference tools.
Saripella GV, Sonnhammer EL, Forslund K
2016 Jun 1; [Epub ahead of print] PubMed: 27256311.
Abstract + PDF
659.
The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.
Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R
2016 Nov 21; 215(4): 543-558. PubMed: 27872256.
Abstract + PDF
658.
The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex.
Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW
2016; 11(1): e0146457. PubMed: 26745716.
Abstract + PDF
657.
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
2016 Jan 4; 44: D380-4. Epub 2015 Nov 20; PubMed: 26590256.
Abstract + PDF
656.
Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.
Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R
2016; 11(5): e0155362. PubMed: 27171425.
Abstract + PDF
655.
Global genetic capacity for mixotrophy in marine picocyanobacteria.
Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW
2016 Dec 3; 10(12): 2946-2957. PubMed: 27137127.
Abstract + PDF
654.
The exploration of network motifs as potential drug targets from post-translational regulatory networks.
Zhang XD, Song J, Bork P, Zhao XM
2016 Feb 8; 6: 20558. PubMed: 26853265.
Abstract + PDF
2015 31 publication(s).
653.
Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.
Betts MJ, Lu Q, Jiang Y, Drusko A, Wichmann O, Utz M, Valtierra-Gutiérrez IA, Schlesner M, Jaeger N, Jones DT, Pfister S, Lichter P, Eils R, Siebert R, Bork P, Apic G, Gavin AC, Russell RB
2015 Jan 30; 43(2): e10. Epub 2014 Nov 11; PubMed: 25392414.
Abstract + PDF
652.
Quest for Orthologs (QfO) entails Quest for Tree of Life (QfToL): in Search of the Gene Stream.
Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T, Quest for Orthologs Species tree working group
2015 Jul 1; 7(7): 1988-99. PubMed: 26133389.
Abstract + PDF
651.
Tara Oceans studies plankton at planetary scale. Introduction.
Bork P, Bowler C, De Vargas C, Gorsky G, Karsenti E, Wincker P
2015 May 22; 348(6237): 873. Epub 2015 May 21; PubMed: 25999501.
Abstract + PDF
650.
Patterns and ecological drivers of ocean viral communities.
Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, De Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB
2015 May 22; 348(6237): 1261498. PubMed: 25999515.
Abstract + PDF
649.
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images.
Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA
2015 Jul 15; 31(14): 2364-70. PubMed: 25792554.
Abstract
648.
Eukaryotic plankton diversity in the sunlit ocean.
De Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E.
2015 May 22; 348(6237): 1261605. PubMed: 25999516.
Abstract + PDF
647.
Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites.
Djuika CF, Huerta-Cepas J, Przyborski JM, Deil S, Sanchez CP, Doerks T, Bork P, Lanzer M, Deponte M
2015 Jan 5; 2(1): 5-13. PubMed: 28357258.
Abstract + PDF
646.
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT C, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
2015 Dec 10; 528(7581): 262-266. Epub 2015 Dec 2; PubMed: 26633628.
Abstract + PDF
645.
Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer.
2015 Apr-Jun; 2(2): e975080. PubMed: 27308430.
Abstract + PDF
644.
SMART: recent updates, new developments and status in 2015.
2015 Jan 28; 43: D257-60. Epub 2014 Oct 9; PubMed: 25300481.
Abstract + PDF
643.
Determinants of community structure in the global plankton interactome.
Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, De Vargas C, Raes J
2015 May 22; 348(6237): 1262073. PubMed: 25999517.
Abstract + PDF
642.
Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L
2015 Jan 21; 11(1): 780. PubMed: 25609650.
Abstract + PDF
641.
Histone deacetylase inhibitors cause the selective depletion of bromodomain containing proteins.
Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M
2015 May 9; 14(5): 1350-60. Epub 2015 Mar 9; PubMed: 25755299.
Abstract + PDF
640.
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
2015 Jan 28; 43: D494-502. Epub 2014 Oct 31; PubMed: 25361965.
Abstract + PDF
639.
The InterPro protein families database: the classification resource after 15 years.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD
2015 Jan 28; 43: D213-21. Epub 2014 Nov 26; PubMed: 25428371.
Abstract + PDF
638.
Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.
Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M
2015 Sep 23; 1(3): 224-37. Epub 2015 Sep 17; PubMed: 27135913.
Abstract + PDF
637.
Open science resources for the discovery and analysis of Tara Oceans data
Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Troublé R, Dimier C, Searson S, Acinas SG, Bork P, Boss E, Bowler C, De Vargas C, Follows M, Grimsley G, Hingamp P, Jaillon O, Karp-Boss L, Krzic U, Ogata H, Raes J, Reynaud EG, Sardet C, Sieracki M, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P
2015 May 26; 2: 1-16. PID: 680.
Abstract + PDF
636.
Open science resources for the discovery and analysis of Tara Oceans data.
Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Troublé R, Dimier C, Searson S, Tara Oceans Consortium Coordinators , Acinas SG, Bork P, Boss E, Bowler C, De Vargas C, Follows M, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Karp-Boss L, Karsenti E, Krzic U, Not F, Ogata H, Pesant S, Raes J, Reynaud EG, Sardet C, Sieracki M, Speich S, Stemmann L, Sullivan MB, Sunagawa S, Velayoudon D, Weissenbach J, Wincker P.
2015; 2: 150023. PubMed: 26029378.
Abstract + PDF
635.
Operon structure and cotranslational subunit association direct protein assembly in bacteria.
Shieh YW, Minguez P, Bork P, Auburger JJ, Guilbride DL, Kramer G, Bukau B
2015 Nov 6; 350(6261): 678-80. Epub 2015 Sep 24; PubMed: 26405228.
Abstract + PDF
634.
Structure and function of the global ocean microbiome.
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, De Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P
2015 May 22; 348(6237): 1261359. PubMed: 25999513.
Abstract + PDF
633.
Computational eco-systems biology in Tara Oceans: translating data into knowledge.
Sunagawa S, Karsenti E, Bowler C, Bork P
2015 May 21; 11(5): 809. PubMed: 25999085.
Abstract + PDF
632.
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C
2015 Jan 28; 43: D447-52. Epub 2014 Oct 28; PubMed: 25352553.
Abstract + PDF
631.
Shotgun metagenomes and multiple primer pairbarcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
Tedersoo L, Anslan S, Bahram M, Põlme S, Riit T, Liiv I, Kõljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K
2015 May 13; 10: 1-43. PID: 679.
Abstract + PDF
630.
Environmental characteristics of Agulhas rings affect interocean plankton transport.
Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Boss E, De Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D
2015 May 22; 348(6237): 1261447. PubMed: 25999514.
Abstract + PDF
629.
Temporal and technical variability of human gut metagenomes.
2015 Apr 8; 16(1): 73. Epub 2015 Apr 8; PubMed: 25888008.
Abstract + PDF
628.
In situ structural analysis of the human nuclear pore complex.
von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M
2015 Oct 1; 526(7571): 140-143. Epub 2015 Sep 23; PubMed: 26416747.
Abstract + PDF
627.
Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.
Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC
2015 Sep 1; 12(9): 1519-30. Epub 2015 Aug 20; PubMed: 26299969.
Abstract + PDF
626.
Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors.
Woerner SM, Tosti E, Yuan YP, Kloor M, Bork P, Edelmann W, Gebert J
2015 Nov 11; 54(11): 1376-86. Epub 2014 Sep 11; PubMed: 25213383.
Abstract + PDF
625.
Metabolic dependencies drive species co-occurrence in diverse microbial communities.
Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR
2015 May 19; 112(20): 6449-54. Epub 2015 May 4; PubMed: 25941371.
Abstract + PDF
624.
Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.
Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L
2015 Aug; 2(8): 968-84. PubMed: 26425705.
Abstract + PDF
623.
Inter-individual differences in the gene content of human gut bacterial species.
2015 Apr 21; 16(1): 82. Epub 2015 Apr 21; PubMed: 25896518.
Abstract + PDF
2014 24 publication(s).
622.
Addendum: Enterotypes of the human gut microbiome.
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT C, Weissenbach J, Ehrlich SD, Bork P
2014 Feb 27; 506(7489): 516. PubMed: 24572424.
Abstract + PDF
621.
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.
Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell S, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P
2014 Dec 16; 42(22): 13525-33. Epub 2014 Nov 14; PubMed: 25398899.
Abstract + PDF
620.
Blick zurück in die Zukunft der Bioinformatik
In: Laborjournal7-8 2014(7-8) pp.73-75. BID: 22.
Publisher:
Abstract + PDF
619.
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
2014 Jul; 10(7): e1003758. PubMed: 25077479.
PDF
618.
A fair comparison.
2014 Apr 28; 11(4): 359. PubMed: 24681719.
PDF
617.
Luminal signalling links cell communication to tissue architecture during organogenesis.
Durdu S, Iskar M, Revenu C, Schieber N, Kunze A, Bork P, Schwab Y, Gilmour D
2014 Nov 6; 515(7525): 120-4. Epub 2014 Oct 22; PubMed: 25337877.
Abstract + PDF
616.
Metagenomic insights into the human gut resistome and the forces that shape it.
2014 Mar 29; 36(3): 316-29. Epub 2014 Jan 29; PubMed: 24474281.
Abstract + PDF
615.
Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs.
Gallina AM, Bork P, Bordo D
2014 Feb; 27(2): 65-72. PubMed: 24436123.
Abstract + PDF
614.
SPI-23 of S. Derby: role in adherence and invasion of porcine tissues.
Hayward MR, AbuOun M, La Ragione RM, Tchórzewska MA, Cooley WA, Everest DJ, Petrovska L, Jansen VA, Woodward MJ
2014; 9(9): e107857. PubMed: 25238397.
Abstract
613.
LotuS: an efficient and user-friendly OTU processing pipeline.
2014 Sep 30; 2(1): 30. Epub 2014 Sep 30; PubMed: 27367037.
Abstract + PDF
612.
Correction: LotuS: an efficient and user-friendly OTU processing pipeline.
2014; 2: 37. PubMed: 25317332.
Abstract + PDF
611.
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P
2014 Jan 1; 42(Database issue): D401-7. Epub 2013 Nov 28; PubMed: 24293645.
Abstract + PDF
610.
An integrated catalog of reference genes in the human gut microbiome.
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD, MetaHIT C, Bork P, Wang J.
2014 Aug 6; 32(8): 834-41. Epub 2014 Jul 6; PubMed: 24997786.
Abstract + PDF
609.
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection.
Liehl P, Zuzarte-Luís V, Chan J, Zillinger T, Baptista F, Carapau D, Konert M, Hanson KK, Carret C, Lassnig C, Müller M, Kalinke U, Saeed M, Chora AF, Golenbock DT, Strobl B, Prudêncio M, Coelho LP, Kappe SH, Superti-Furga G, Pichlmair A, Vigário AM, Rice CM, Fitzgerald KA, Barchet W, Mota MM
2014 Jan; 20(1): 47-53. PubMed: 24362933.
Abstract
608.
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, De Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG
2014 Sep 18; 16(9): 2659-71. Epub 2013 Sep 18; PubMed: 24102695.
Abstract + PDF
607.
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T, MetaHIT C, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD
2014 Aug 6; 32(8): 822-8. Epub 2014 Jul 6; PubMed: 24997787.
Abstract + PDF
606.
eggNOG v4.0: nested orthology inference across 3686 organisms.
2014 Jan 1; 42(Database issue): D231-9. Epub 2013 Dec 1; PubMed: 24297252.
Abstract + PDF
605.
A quantitative liposome microarray to systematically characterize protein-lipid interactions.
Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin AC
2014 Jan 24; 11(1): 47-50. Epub 2013 Nov 24; PubMed: 24270602.
Abstract + PDF
604.
Immune escape and survival mechanisms in circulating tumor cells of colorectal cancer.
Steinert G, Schölch S, Niemietz T, Iwata N, García SA, Behrens B, Voigt AY, Kloor M, Benner A, Bork U, Rahbari NN, Büchler MW, Stoecklein NH, Weitz J, Koch M
2014 Mar 15; 74(6): 1694-704. PubMed: 24599131.
Abstract
603.
Association of high CD4-positive T cell infiltration with mutations in HLA class II-regulatory genes in microsatellite-unstable colorectal cancer.
Surmann EM, Voigt AY, Michel S, Bauer K, Reuschenbach M, Ferrone S, von Knebel Doeberitz M, Kloor M
2014 Dec 2; [Epub ahead of print] PubMed: 25445815.
Abstract
602.
A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation.
2014; 9(11): e111122. PubMed: 25369365.
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601.
Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene expression profiling.
van Noort V, Schölch S, Iskar M, Zeller G, Ostertag K, Schweitzer C, Werner K, Weitz J, Koch M, Bork P
2014 Oct 15; 74(20): 5690-9. Epub 2014 Jul 18; PubMed: 25038229.
Abstract + PDF
600.
Classification and quantification of bacteriophage taxa in human gut metagenomes.
Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P
2014 Jul 13; 8(7): 1391-402. Epub 2014 Mar 13; PubMed: 24621522.
Abstract + PDF
599.
Potential of fecal microbiota for early-stage detection of colorectal cancer.
Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P
2014 Nov 28; 10(11): 766. PubMed: 25432777.
Abstract + PDF
2013 20 publication(s).
598.
Evolution and functional cross-talk of protein post-translational modifications.
Beltrao P, Bork P, Krogan NJ, van Noort V
2013; 9(1): 714. PubMed: 24366814.
Abstract + PDF
597.
The microbiome explored: recent insights and future challenges.
Blaser M, Bork P, Fraser C, Knight R, Wang J
2013 Mar 4; 11(3): 213-7. Epub 2013 Feb 4; PubMed: 23377500.
Abstract + PDF
596.
Human monogenic disease genes have frequently functionally redundant paralogs.
2013 May; 9(5): e1003073. PubMed: 23696728.
Abstract + PDF
595.
Experimental characterization of the human non-sequence-specific nucleic acid interactome.
Duernberger G, Burckstummer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Muller AC, Schonegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J
2013 Jul 31; 14(7): R81. Epub 2013 Jul 31; PubMed: 23902751.
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594.
Country-specific antibiotic use practices impact the human gut resistome.
2013 Jul 29; 23(7): 1163-9. Epub 2013 Apr 8; PubMed: 23568836.
Abstract + PDF
593.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ
2013 Jan 1; 41: D808-15. Epub 2012 Nov 29; PubMed: 23203871.
Abstract + PDF
592.
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, Ferrera I, Sarmento H, Villar E, Lima-Mendez G, Faust K, Sunagawa S, Claverie JM, Moreau H, Desdevises Y, Bork P, Raes J, De Vargas C, Karsenti E, Kandels-Lewis S, Jaillon O, Not F, Pesant S, Wincker P, Ogata H
2013 Sep 11; 7(9): 1678-95. Epub 2013 Apr 11; PubMed: 23575371.
Abstract + PDF
591.
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC, Pepperkok R, van Noort V, Bork P
2013 Apr 30; 9: 662. PubMed: 23632384.
Abstract + PDF
590.
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.
Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV
2013 Mar 7; 195(5): 941-50. Epub 2012 Dec 7; PubMed: 23222723.
Abstract + PDF
589.
Systematic identification of proteins that elicit drug side effects.
Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P
2013 Apr 30; 9: 663. PubMed: 23632385.
Abstract + PDF
588.
Richness of human gut microbiome correlates with metabolic markers.
Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, MetaHIT Consortium , Bork P, Wang J, Ehrlich SD, Pedersen O
2013 Aug 29; 500(7464): 541-6. PubMed: 23985870.
Abstract + PDF
587.
Accurate and universal delineation of prokaryotic species.
2013 Sep 28; 10(9): 881-4. Epub 2013 Jul 28; PubMed: 23892899.
Abstract + PDF
586.
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
2013 Jan 1; 41: D306-11. Epub 2012 Nov 28; PubMed: 23193284.
Abstract + PDF
585.
Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.
Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M
2013 Mar 19; 9: 648. PubMed: 23511206.
Abstract + PDF
584.
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J
2013 Jan 1; 29(1): 132-4. Epub 2012 Nov 4; PubMed: 23129297.
Abstract + PDF
583.
Genomic variation landscape of the human gut microbiome.
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller AS, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P
2013 Jan 3; 493(7430): 45-50. Epub 2012 Dec 5; PubMed: 23222524.
Abstract + PDF
582.
Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.
Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP
2013 Mar 8; 339(6124): 1207-10. PubMed: 23471408.
Abstract
581.
Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P
2013 Dec 20; 10(12): 1196-9. Epub 2013 Oct 20; PubMed: 24141494.
Abstract + PDF
580.
Individuality and temporal stability of the human gut microbiome.
Sunagawa S, Schloissnig S, Arumugam M, Forslund K, Mitreva M, Tap J, Zhu A, Waller AS, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Typas A, Weinstock GM, Bork P
2013; 2(Suppl): 120. PubMed: 29805877.
Abstract + PDF
579.
Consistent mutational paths predict eukaryotic thermostability.
van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey CJ, Falk S, Mende DR, Sinning I, Hurt E, Bork P
2013 Jan 10; 13(1): 7. Epub 2013 Jan 10; PubMed: 23305080.
Abstract + PDF
2012 24 publication(s).
578.
Role for urea in nitrification by polar marine Archaea.
Alonso-Sáez L, Waller AS, Mende DR, Bakker K, Farnelid H, Yager PL, Lovejoy C, Tremblay JE, Potvin M, Heinrich F, Estrada M, Riemann L, Bork P, Pedrós-Alió C, Bertilsson S
2012 Oct 30; 109(44): 17989-94. Epub 2012 Oct 1; PubMed: 23027926.
Abstract + PDF
577.
OGEE: an online gene essentiality database.
2012 Jan 10; 40(Database issue): D901-6. Epub 2011 Nov 10; PubMed: 22075992.
Abstract + PDF
576.
Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age.
2012 Jul 7; 29(7): 1703-6. Epub 2012 Mar 7; PubMed: 22319151.
Abstract + PDF
575.
The Tenth Asia Pacific Bioinformatics Conference (APBC 2012).
Chen YP, Bork P
2012 Jan 17; 13 Suppl 1: I1. Epub 2012 Jan 17; PubMed: 22369290.
PDF
574.
Transcriptomic responses to darkness stress point to common coral bleaching mechanisms.
Desalvo MK, Estrada E, Sunagawa S, Medina M
2012; 31 (1): 215 - 228. PID: 567.
573.
Regarding the presence of membrane coat proteins in bacteria: Confusion? What confusion?
2012 Jan; 34(1): 38-9. PubMed: 22183969.
572.
Annotation of the M. tuberculosis Hypothetical Orfeome: Adding Functional Information to More than Half of the Uncharacterized Proteins.
2012; 7(4): e34302. PubMed: 22485162.
Abstract + PDF
571.
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments.
García-Alonso L, Alonso R, Vidal E, Amadoz A, de María A, Minguez P, Medina I, Dopazo J
2012 Jul 27; [Epub ahead of print] PubMed: 22844098.
Abstract
570.
A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL.
Haemmerling S, Behnisch W, Doerks T, Korbel JO, Bork P, Moog U, Hentze S, Grasshoff U, Bonin M, Rieß O, Janssen JW, Jauch A, Bartram CR, Reinhardt D, Koch KA, Bandapalli OR, Kulozik AE
2012 Apr 1; 157(2): 180-7. Epub 2012 Feb 1; PubMed: 22296450.
Abstract + PDF
569.
InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY
2012 Jan 1; 40: D306-12. Epub 2011 Nov 16; PubMed: 22096229.
Abstract + PDF
568.
The molecular basis of EPCAM expression loss in Lynch syndrome-associated tumors.
Huth C, Kloor M, Voigt AY, Bozukova G, Evers C, Gaspar H, Tariverdian M, Schirmacher P, von Knebel Doeberitz M, Bläker H
2012 Jun; 25(6): 911-6. PubMed: 22388758.
Abstract
567.
Drug discovery in the age of systems biology: the rise of computational approaches for data integration.
2012 Aug 5; 23(4): 609-16. Epub 2011 Dec 5; PubMed: 22153034.
Abstract + PDF
566.
Prevalence of mismatch repair-deficient crypt foci in Lynch syndrome: a pathological study.
Kloor M, Huth C, Voigt AY, Benner A, Schirmacher P, von Knebel Doeberitz M, Bläker H
2012 Jun; 13(6): 598-606. PubMed: 22552011.
Abstract
565.
STITCH 3: zooming in on protein-chemical interactions.
2012 Jan 1; 40: D876-80. Epub 2011 Nov 9; PubMed: 22075997.
Abstract + PDF
564.
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P
2012; 7(10): e47656. PubMed: 23082188.
Abstract + PDF
563.
SMART 7: recent updates to the protein domain annotation resource.
2012 Jan 3; 40(Database issue): D302-5. Epub 2011 Nov 3; PubMed: 22053084.
Abstract + PDF
562.
Assessment of metagenomic assembly using simulated next generation sequencing data.
Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P
2012; 7(2): e31386. PubMed: 22384016.
Abstract + PDF
561.
Deciphering a global network of functionally associated post-translational modifications.
Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P
2012 Jul 17; 8: 599. PubMed: 22806145.
Abstract + PDF
560.
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
2012 Jan 1; 40: D284-9. Epub 2011 Nov 16; PubMed: 22096231.
Abstract + PDF
559.
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.
van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC
2012 Feb 28; 8: 571. PubMed: 22373819.
Abstract + PDF
558.
Transcriptional analysis of a dehalococcoides-containing microbial consortium reveals prophage activation.
Waller AS, Hug LA, Mo K, Radford DR, Maxwell KL, Edwards EA
2012 Feb; 78(4): 1178-86. PubMed: 22179237.
Abstract
557.
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.
Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P
2012 May 8; 8: 581. PubMed: 22569339.
Abstract + PDF
556.
Transcription start site associated RNAs in bacteria.
Yus E, Güell M, Vivancos AP, Chen WH, Lluch-Senar M, Delgado J, Claude Gavin A, Bork P, Serrano L
2012 May 22; 8: 585. PubMed: 22617959.
Abstract + PDF
555.
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.
Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M
2012 Jul 19; 6(7): 1415-26. Epub 2012 Jan 19; PubMed: 22258098.
Abstract + PDF
2011 24 publication(s).
554.
The three-dimensional molecular structure of the desmosomal plaque.
Al-Amoudi A, Castaño-Diez D, Devos DP, Russell RB, Johnson GT, Frangakis AS
2011 Apr 19; 108(16): 6480-5. PubMed: 21464301.
Abstract
553.
Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile.
Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, Devos DP, Arumugam M, Bork P, Hurt E
2011 Jul 22; 146(2): 277-89. PubMed: 21784248.
Abstract + PDF
552.
Enterotypes of the human gut microbiome.
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Consortium M, Weissenbach J, Ehrlich SD, Bork P
2011 May 12; 473(7346): 174-80. Epub 2011 Apr 20; PubMed: 21508958.
Abstract + PDF
551.
Consider Context
2011 Mar 18; 144(6): 838. PID: 527.
PDF
550.
Network neighbors of drug targets contribute to drug side-effect similarity.
2011; 6(7): e22187. PubMed: 21765950.
Abstract + PDF
549.
The ecoresponsive genome of Daphnia pulex.
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL
2011 Feb 4; 331(6017): 555-61. PubMed: 21292972.
Abstract + PDF
548.
Universally distributed single-copy genes indicate a constant rate of horizontal transfer.
Creevey CJ, Doerks T, Fitzpatrick DA, Raes J, Bork P
2011; 6(8): e22099. PubMed: 21850220.
Abstract + PDF
547.
Identifying single copy orthologs in metazoa.
Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P
2011 Dec; 7(12): e1002269. PubMed: 22144877.
Abstract + PDF
546.
A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae.
Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C
2011 Jun; 10(6): M110.006478. PubMed: 21454883.
Abstract
545.
Analysis of the yeast nucleoporin Nup188 reveals a conserved S-like structure with similarity to karyopherins.
Flemming D, Devos DP, Schwarz J, Amlacher S, Lutzmann M, Hurt E
2011 Nov 22; [Epub ahead of print] PubMed: 22138091.
Abstract
544.
Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans.
Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM, Horvitz HR, Sternberg PW, Ringstad N
2011 Jan 4; 108(1): 254-9. PubMed: 21173231.
Abstract
543.
A Holistic Approach to Marine Eco-Systems Biology.
Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, Raes J, Sullivan M, Arendt D, Benzoni F, Claverie JM, Follows M, Gorsky G, Hingamp P, Iudicone D, Jaillon O, Kandels-Lewis S, Krzic U, Not F, Ogata H, Pesant S, Reynaud EG, Sardet C, Sieracki ME, Speich S, Velayoudon D, Weissenbach J, Wincker P, the Tara Oceans Consortium
2011 Oct; 9(10): e1001177. PubMed: 22028628.
Abstract + PDF
542.
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
2011 Jul 5; 39 Suppl 2: W475-8. Epub 2011 Apr 5; PubMed: 21470960.
Abstract + PDF
541.
Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties.
Minguez P, Dopazo J
2011; 6(3): e17474. PubMed: 21408226.
Abstract
540.
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
2011 Mar 15; 7: 473. PubMed: 21407210.
Abstract + PDF
539.
Codon adaptation-based control of protein expression in C. elegans.
Redemann S, Schloissnig S, Ernst S, Pozniakowsky A, Ayloo S, Hyman AA, Bringmann H
2011 Jan 30; [Epub ahead of print] PubMed: 21278743.
Abstract
538.
Transitional forms between the three domains of life and evolutionary implications.
Reynaud EG, Devos DP
2011 Nov 22; 278(1723): 3321-8. PubMed: 21920985.
Abstract
537.
Microbial Dysbiosis in Colorectal Cancer (CRC) Patients.
Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, Langella P, Corthier G, Van Nhieu JT, Furet JP
2011; 6(1): e16393. PubMed: 21297998.
Abstract
536.
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C
2011 Jan 2; 39: D561-8. Epub 2010 Nov 2; PubMed: 21045058.
Abstract + PDF
535.
Orthology prediction methods: A quality assessment using curated protein families.
2011 Oct 19; 33(10): 769-80. Epub 2011 Aug 19; PubMed: 21853451.
Abstract + PDF
534.
Rapid evolution of coral proteins responsible for interaction with the environment.
Voolstra CR, Sunagawa S, Matz MV, Bayer T, Aranda M, Buschiazzo E, Desalvo MK, Lindquist E, Szmant AM, Coffroth MA, Medina M
2011; 6(5): e20392. PubMed: 21633702.
Abstract
533.
iPath2.0: interactive pathway explorer.
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P
2011 Jul 5; 39 Suppl 2: W412-5. Epub 2011 May 5; PubMed: 21546551.
Abstract + PDF
532.
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, Desantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, Gil IS, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spor A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO
2011 May 6; 29(5): 415-20. Epub 2011 May 6; PubMed: 21552244.
Abstract + PDF
531.
Prediction of drug combinations by integrating molecular and pharmacological data.
2011 Dec; 7(12): e1002323. PubMed: 22219721.
Abstract + PDF
2010 29 publication(s).
530.
A method and server for predicting damaging missense mutations.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR
2010 Apr; 7(4): 248-9. PubMed: 20354512.
PDF
529.
Selection upon genome architecture: conservation of functional neighborhoods with changing genes.
Al-Shahrour F, Minguez P, Marqués-Bonet T, Gazave E, Navarro A, Dopazo J
2010; 6(10): e1000953. PubMed: 20949098.
Abstract
528.
SmashCommunity: A metagenomic annotation and analysis tool.
2010 Dec 1; 26(23): 2977-8. Epub 2010 Oct 19; PubMed: 20959381.
Abstract + PDF
527.
Ancient animal microRNAs and the evolution of tissue identity.
Christodoulou F, Raible F, Tomer R, Simakov O, Trachana K, Klaus S, Snyman H, Hannon GJ, Bork P, Arendt D
2010 Feb 25; 463(7284): 1084-8. Epub 2010 Jan 31; PubMed: 20118916.
Abstract + PDF
526.
Evolution. Intermediate steps.
Devos DP, Reynaud EG
2010 Nov 26; 330(6008): 1187-8. PubMed: 21109658.
525.
[Metagenomics of the intestinal microbiota: potential applications].
Dusko Ehrlich S, MetaHIT Consortium , Antolin M, Artiguenave F, Arumugam M, Batto JM, Bertalan M, Blottiere H, Bork P, Borruel N, Brechot C, Brunak S, Bruls T, Burgdorf KS, Cao J, Casellas F, Chervaux C, Colombel JF, Cultrone A, Doré J, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, Guarner F, Guchte Mv, Guedon E, Haimet F, Hansen T, Jamet A, Jian M, Juste C, Kaci G, Kleerebezem M, Knol J, Kristiansen K, Layec S, Le Roux K, Leclerc M, Le Paslier D, Levenez F, Li D, Li J, Li S, Li S, Li S, Li Y, Liang H, Mende D, Maguin E, Manichanh C, Minardi RM, Mrini C, Nielsen HB, Nielsen T, Oozeer R, Parkhill J, Pons N, Pedersen O, Pelletier E, Qin J, Raes J, Renault P, Rescigno M, Ruiqiang L, Sanchez N, Sicheritz-Ponten T, Tims S, Torrejon T, Turner K, Varela E, Vos Wd, Wang B, Wang J, Wang J, Weissenbach J, Winogradsky Y, Xie Y, Xu J, Yamada T, Yang H, Yu C, Zhang X, Zheng H, Zhu H, Zhou Y, Zoetendal E.
2010 Sep; 34 Suppl 1: S23-8. PubMed: 20889001.
Abstract
524.
Bioinformatics and molecular modeling in glycobiology.
Frank M, Schloissnig S
2010 Aug; 67(16): 2749-72. PubMed: 20364395.
Abstract
523.
Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers.
Furet JP, Kong LC, Tap J, Poitou C, Basdevant A, Bouillot JL, Mariat D, Corthier G, Doré J, Henegar C, Rizkalla S, Clément K
2010 Dec; 59(12): 3049-57. PubMed: 20876719.
Abstract
522.
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC
2010 Nov 30; 6: 430. PubMed: 21119626.
Abstract + PDF
521.
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium , Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH
2010 Dec 24; 330(6012): 1775-87. PubMed: 21177976.
Abstract + PDF
520.
High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM
2010 Mar 1; 11(3): R24. Epub 2010 Mar 1; PubMed: 20193063.
Abstract + PDF
519.
SmashCell: A software framework for the analysis of single-cell amplified genome sequences.
2010 Dec 1; 26(23): 2979-80. Epub 2010 Oct 21; PubMed: 20966005.
Abstract + PDF
518.
Systematic analysis of human protein complexes identifies chromosome segregation proteins.
Hutchins JR, Toyoda Y, Hegemann B, Poser I, Hériché JK, Sykora MM, Augsburg M, Hudecz O, Buschhorn BA, Bulkescher J, Conrad C, Comartin D, Schleiffer A, Sarov M, Pozniakovsky A, Slabicki MM, Schloissnig S, Steinmacher I, Leuschner M, Ssykor A, Lawo S, Pelletier L, Stark H, Nasmyth K, Ellenberg J, Durbin R, Buchholz F, Mechtler K, Hyman AA, Peters JM
2010 Apr 30; 328(5978): 593-9. PubMed: 20360068.
Abstract
517.
Drug-Induced Regulation of Target Expression.
2010 Sep 9; 6(9): . PubMed: 20838579.
Abstract + PDF
516.
Ontologies in quantitative biology: a basis for comparison, integration, and discovery.
2010 May 25; 8(5): e1000374. PubMed: 20520843.
Abstract + PDF
515.
A side effect resource to capture phenotypic effects of drugs.
2010; 6: 343. PubMed: 20087340.
Abstract + PDF
514.
STITCH 2: an interaction network database for small molecules and proteins.
2010 Jan 6; 38: D552-6. Epub 2009 Nov 6; PubMed: 19897548.
Abstract + PDF
513.
Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome.
Laubinger S, Zeller G, Henz SR, Buechel S, Sachsenberg T, Wang JW, Rätsch G, Weigel D
2010 Oct 12; 107(41): 17466-73. PubMed: 20870966.
Abstract
512.
Functional genomics and networks: new approaches in the extraction of complex gene modules.
Minguez P, Dopazo J
2010 Feb; 7(1): 55-63. PubMed: 20121476.
Abstract
511.
AQUA: Automated quality improvement for multiple sequence alignments.
Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P
2010 Jan 15; 26(2): 263-5. Epub 2009 Nov 19; PubMed: 19926669.
Abstract + PDF
510.
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
2010 Jan 9; 38: D190-5. Epub 2009 Nov 9; PubMed: 19900971.
Abstract + PDF
509.
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.
Nasonia Genome Working Group , Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA
2010 Jan 15; 327(5963): 343-8. PubMed: 20075255.
Abstract + PDF
508.
Visualization of multiple alignments, phylogenies and gene family evolution.
Procter JB, Thompson J, Letunic I, Creevey CJ, Jossinet F, Barton GJ
2010 Mar; 7(3 Suppl): S16-25. PubMed: 20195253.
Abstract + PDF
507.
A human gut microbial gene catalogue established by metagenomic sequencing.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J, MetaHIT Consortium
2010 Mar 4; 464(7285): 59-65. PubMed: 20203603.
Abstract + PDF
506.
A network of conserved co-occurring motifs for the regulation of alternative splicing.
Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P
2010 Dec 11; 38(22): 7916-26. Epub 2010 Aug 11; PubMed: 20702423.
Abstract + PDF
505.
Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.
Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G
2010 Nov; 20(11): 1605-12. PubMed: 20841432.
Abstract
504.
Evolution and regulation of cellular periodic processes: a role for paralogues.
2010 Mar 19; 11(3): 233-8. Epub 2010 Feb 19; PubMed: 20168326.
Abstract + PDF
503.
EUROCarbDB: An open-access platform for glycoinformatics.
von der Lieth CW, Ardá Freire A, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM
2010 Nov 23; [Epub ahead of print] PubMed: 21106561.
Abstract
502.
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.
Woerner SM, Yuan YP, Benner A, Korff S, von Knebel Doeberitz M, Bork P
2010 Jan 9; 38: D682-9. Epub 2009 Oct 9; PubMed: 19820113.
Abstract + PDF
2009 17 publication(s).
501.
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB
2009 Feb 3; 106(5): 1374-9. Epub 2009 Jan 22; PubMed: 19164758.
Abstract + PDF
500.
Transcriptome complexity in a genome-reduced bacterium.
Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L
2009 Nov 27; 326(5957): 1268-71. PubMed: 19965477.
Abstract + PDF
499.
InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C
2009 Jan 21; 37: D211-5. Epub 2008 Oct 21; PubMed: 18940856.
Abstract + PDF
498.
Repeatability of published microarray gene expression analyses.
Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, Falchi M, Furlanello C, Game L, Jurman G, Mangion J, Mehta T, Nitzberg M, Page GP, Petretto E, van Noort V
2009 Feb; 41(2): 149-155. PubMed: 19174838.
Abstract + PDF
497.
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
2009 Jan 21; 37: D412-6. Epub 2008 Oct 21; PubMed: 18940858.
Abstract + PDF
496.
Sequence-based feature prediction and annotation of proteins.
Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S
2009 Feb 2; 10(2): 206. Epub 2009 Feb 2; PubMed: 19226438.
Abstract + PDF
495.
ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny G, Texier VL, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington ED, Boue S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz MV, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D
2009 Mar 23; 93(3): 213-20. Epub 2008 Dec 24; PubMed: 19059335.
Abstract + PDF
494.
Proteome organization in a genome-reduced bacterium.
Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos DP, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC
2009 Nov 27; 326(5957): 1235-40. PubMed: 19965468.
Abstract + PDF
493.
SMART 6: recent updates and new developments.
2009 Jan 31; 37: D229-32. Epub 2008 Oct 31; PubMed: 18978020.
Abstract + PDF
492.
Reflect: augmented browsing for the life scientist.
Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R
2009 Jun; 27(6): 508-10. PubMed: 19513049.
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491.
OnTheFly: A Tool for automated document-based text annotation, data linking and network generation.
Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R
2009 Feb 17; 25(7): 977-8. PubMed: 19223449.
Abstract + PDF
490.
High frequency of LMAN1 abnormalities in colorectal tumors with microsatellite instability.
Roeckel N, Woerner SM, Kloor M, Yuan YP, Patsos G, Gromes R, Kopitz J, Gebert J
2009 Jan 1; 69(1): 292-9. PubMed: 19118014.
Abstract + PDF
489.
Microblogging the ISMB: a new approach to conference reporting.
Saunders N, Beltrão P, Jensen LJ, Jurczak D, Krause R, Kuhn M, Wu S
2009 Jan; 5(1): e1000263. PubMed: 19180175.
PDF
488.
Discovering functional novelty in metagenomes: examples from light-mediated processes.
2009 Jan 10; 191(1): 32-41. Epub 2008 Oct 10; PubMed: 18849420.
Abstract + PDF
487.
Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals.
Sunagawa S, Desalvo MK, Voolstra CR, Reyes-Bermudez A, Medina M
2009; 4(3): e4865. PubMed: 19283069.
Abstract
486.
Evolution of biomolecular networks - lessons from metabolic and protein interactions.
2009 Nov; 10(11): 791-803. PubMed: 19851337.
Abstract + PDF
485.
Impact of genome reduction on bacterial metabolism and its regulation.
Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L
2009 Nov 27; 326(5957): 1263-8. PubMed: 19965476.
Abstract + PDF
2008 33 publication(s).
484.
Drug target identification using side-effect similarity.
2008 Jul 11; 321(5886): 263-6. PubMed: 18621671. Media echos.
Abstract + PDF
483.
A computational screen for type I polyketide synthases in metagenomics shotgun data.
2008; 3(10): e3515. PubMed: 18953415.
Abstract + PDF
482.
A Nitrile Hydratase in the Eukaryote Monosiga brevicollis.
2008; 3(12): e3976. PubMed: 19096720.
Abstract + PDF
481.
Protein-protein interactions: analysis and prediction.
Frishman D, Albrecht M, Blankenburg H, Bork P, Harrington ED, Hermjakob H, Jensen LJ, Juan DA, Lengauer T, Pagel P, Schächter V, Valencia A
In: Frishman D and Valencia A (Editors): Modern genome annotation pp.353–412. BID: 20.
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480.
SuperTarget and Matador: resources for exploring drug-target relationships.
Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R
2008 Jan 16; 36: D919-22. Epub 2007 Oct 16; PubMed: 17942422.
Abstract + PDF
479.
Sircah: A tool for the detection and visualisation of alternative transcripts.
2008 Sep 1; 24(17): 1959-60. Epub 2008 Jul 17; PubMed: 18635569.
Abstract + PDF
478.
Predicting biological networks from genomic data.
2008 Apr 9; 582(8): 1251-8. Epub 2008 Feb 21; PubMed: 18294967.
Abstract + PDF
477.
4DXpress: a database for cross-species expression pattern comparisons.
Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong E, Wittbrodt J, Henrich T
2008 Jan 17; 36: D847-53. Epub 2007 Dec 17; PubMed: 17916571.
Abstract + PDF
476.
A Molecular Study of Microbe Transfer between Distant Environments.
2008 Jul 9; 3(7): e2607. PubMed: 18612393.
Abstract + PDF
475.
Biochemistry. Not comparable, but complementary.
2008 Oct 3; 322(5898): 56-7. PubMed: 18832636.
PDF
474.
Circular reasoning rather than cyclic expression.
Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P
2008 Jun 23; 9(6): 403. Epub 2008 Jun 23; PubMed: 18598377.
Abstract + PDF
473.
eggNOG: automated construction and annotation of orthologous groups of genes.
2008 Jan 16; 36: D250-4. Epub 2007 Oct 16; PubMed: 17942413.
Abstract + PDF
472.
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.
Kensche PR, van Noort V, Dutilh BE, Huynen MA
2008 Apr 22; 5(19): 151-70. PubMed: 17535793.
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471.
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D
2008 Feb 14; 451(7180): 783-8. PubMed: 18273011. Media echos.
Abstract + PDF
470.
Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.
Korff S, Woerner SM, Yuan YP, Bork P, von Knebel Doeberitz M, Gebert J
2008 Nov 10; 8(1): 329. Epub 2008 Nov 10; PubMed: 19000305.
Abstract + PDF
469.
Large-scale prediction of drug-target relationships.
2008 Apr 9; 582(8): 1283-90. Epub 2008 Feb 20; PubMed: 18291108.
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468.
STITCH: interaction networks of chemicals and proteins.
2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.
Abstract + PDF
467.
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P, Hugenholtz P
2008; 4: 198. PubMed: 18523433.
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466.
Comparative genomics of the Rab protein family in Apicomplexan parasites.
Langsley G, van Noort V, Carret C, Meissner M, de Villiers EP, Bishop R, Pain A
2008 Feb 8; 10(5): 462-70. PubMed: 18468471.
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465.
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.
Lasonder E, Janse CJ, van Gemert GJ, Mair GR, Vermunt AM, Douradinha BG, van Noort V, Huynen MA, Luty AJ, Kroeze H, Khan SM, Sauerwein RW, Waters AP, Mann M, Stunnenberg HG
2008 Oct; 4(10): e1000195. PubMed: 18974882.
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464.
iPath: interactive exploration of biochemical pathways and networks.
Letunic I, Yamada T, Kanehisa M, Bork P
2008 Mar 12; 33(3): 101-3. Epub 2008 Feb 13; PubMed: 18276143.
Abstract + PDF
463.
NetworKIN: a resource for exploring cellular phosphorylation networks.
Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T
2008 Jan 2; 36: D695-9. Epub 2007 Nov 2; PubMed: 17981841.
Abstract + PDF
462.
Linear motif atlas for phosphorylation-dependent signaling.
Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R
2008 Sep 2; 1(35): ra2. PubMed: 18765831.
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461.
KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M
2008 Jul 1; 36: W423-6. Epub 2008 May 13; PubMed: 18477636.
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460.
Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
Palleja A, Harrington ED, Bork P
2008 Jul 15; 9(1): 335. Epub 2008 Jul 15; PubMed: 18627618.
Abstract + PDF
459.
Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation.
Perotti C, Liu R, Parusel C, Boecher N, Schultz J, Bork P, Pfitzner E, Groner B, Shemanko C
2008 Nov 13; 10(6): R94. Epub 2008 Nov 13; PubMed: 19014541.
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458.
Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.
Pincus D, Letunic I, Bork P, Lim WA
2008 Jul 15; 105(28): 9680-4. Epub 2008 Jul 3; PubMed: 18599463. Media echos.
Abstract + PDF
457.
Selective maintenance of Drosophila tandemly-arranged duplicated genes during evolution.
Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M
2008 Dec 16; 9(12): R176. Epub 2008 Dec 16; PubMed: 19087263.
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456.
Molecular eco-systems biology: towards an understanding of community function.
2008 Sep 30; 6(9): 693-9. Epub 2008 Jun 30; PubMed: 18587409.
Abstract + PDF
455.
Enhanced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families.
Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R
2008 Jan 15; 407(1-2): 199-215. Epub 2007 Oct 15; PubMed: 17996400.
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454.
Non-random retention of protein-coding overlapping genes in Metazoa.
Solda' G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD
2008 Apr 16; 9(1): 174. Epub 2008 Apr 16; PubMed: 18416813.
Abstract + PDF
453.
The genome of the model beetle and pest Tribolium castaneum.
Tribolium Genome Sequencing Consortium , Project leader , Richards S, Principal investigators , Gibbs RA, Weinstock GM, White paper , Brown SJ, Denell R, Beeman RW, Gibbs R, Analysis leaders , Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, DNA sequence and global analysis: DNA sequencing , Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, EST sequencing , Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, genome assembly , Liu Y, Worley K, Weinstock G, G+C content , Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, repetitive DNA, transposons and telomeres , Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, gene prediction and consensus gene set , Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, global gene content analysis , Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Developmental processes and signalling pathways , Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Pest biology, senses, Medea and RNAi: ligand gated ion channels , Jones AK, Sattelle DB, oxidative phosphorylation , Ebert PR, P450 genes , Nelson D, Scott JG, Beeman RW, chitin and cuticular proteins , Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, digestive proteinases , Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, immunity , Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, neurohormones and GPCRs , Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, neuropeptide processing enzymes , Raible F, Bork P, opsins , Friedrich M, odorant receptors and gustatory receptors , Walden KK, Robertson HM, odorant binding and chemosensory proteins , Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Medea , Beeman RW, Lorenzen M, systemic RNAi , Tomoyasu Y, Miller SC, Grossmann D, Bucher G
2008 Apr 24; 452(7190): 949-55. Epub 2008 Mar 23; PubMed: 18362917.
Abstract + PDF
452.
metaTIGER: a metabolic evolution resource.
Whitaker JW, Letunic I, McConkey GA, Westhead DR
2008 Oct 25; 37: D531-8. PubMed: 18953037.
Abstract + PDF
2007 20 publication(s).
451.
Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris-A comparative view on 79 human genes.
Boettner M, Steffens C, von Mering C, Bork P, Stahl U, Lang C
2007 May 31; 130(1): 1-10. Epub 2007 Feb 28; PubMed: 17389146.
Abstract + PDF
450.
Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals.
Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE
2007 Jun 6; 26(11): 2658-69. Epub 2007 Apr 26; PubMed: 17464285.
Abstract + PDF
449.
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.
Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E
2007 Oct 15; 21(20): 2558-70. Epub 2007 Sep 27; PubMed: 17901217.
Abstract + PDF
448.
Cyclebase.org a comprehensive multi-organism online database of cell-cycle experiments.
Gauthier NP, Larsen ME, Wernersson R, Lichtenberg UD, Jensen LJ, Brunak S, Jensen TS
2007 Oct 16; 36: D854-9. PubMed: 17940094.
Abstract + PDF
447.
Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
2007 Aug 28; 104(35): 13913-8. Epub 2007 Aug 23; PubMed: 17717083.
Abstract + PDF
446.
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
Hooper SD, Boue S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P
2007; 3: 72. PubMed: 17224916.
Abstract + PDF
445.
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
2007 Jan 1; 23(1): 127-8. Epub 2006 Oct 18; PubMed: 17050570.
Abstract + PDF
444.
Evolution of Cell Cycle Control: Same Molecular Machines, Different Regulation.
Lichtenberg UD, Jensen TS, Brunak S, Bork P, Jensen LJ
2007 Aug 1; 6(15): 1819-25. Epub 2007 Jun 4; PubMed: 17671420.
Abstract + PDF
443.
Systematic Discovery of In Vivo Phosphorylation Networks.
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T
2007 Jun 29; 129(7): 1415-26. Epub 2007 Jun 14; PubMed: 17570479. Media echos.
Abstract + PDF
442.
New developments in the InterPro database.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C
2007 Jan; 35(Database issue): D224-8. PubMed: 17202162.
Abstract + PDF
441.
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
2007 Jul 15; 396(2): 215-25. Epub 2007 Mar 24; PubMed: 17467928.
Abstract + PDF
440.
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Perez-Iratxeta C, Bork P, Andrade-Navarro MA
2007 Jul 1; 35: W212-6. Epub 2007 May 3; PubMed: 17478516.
Abstract + PDF
439.
Get the most out of your metagenome: computational analysis of environmental sequence data.
2007 Oct 11; 10(5): 490-8. Epub 2007 Oct 23; PubMed: 17936679.
Abstract + PDF
438.
Protein function space: viewing the limits or limited by our view?
2007 Jun 14; 17(3): 362-9. Epub 2007 Jun 15; PubMed: 17574832.
Abstract + PDF
437.
Prediction of effective genome size in metagenomic samples.
2007 Jan 15; 8(1): R10. Epub 2007 Jan 15; PubMed: 17224063.
Abstract + PDF
436.
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer.
Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM
2007 Nov 30; 318(5855): 1449-52. Epub 2007 Oct 18; PubMed: 17947550.
Abstract + PDF
435.
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.
2007; 8(9): R197. PubMed: 17880677.
Abstract + PDF
434.
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments.
von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P
2007 Feb 23; 315(5815): 1126-30. Epub 2007 Feb 1; PubMed: 17272687. Media echos.
Abstract + PDF
433.
STRING 7--recent developments in the integration and prediction of protein interactions.
2007 Jan 10; 35: D358-62. Epub 2006 Nov 10; PubMed: 17098935.
Abstract + PDF
432.
Quantification of insect genome divergence.
2007 Jan 8; 23(1): 16-20. Epub 2006 Nov 9; PubMed: 17097187.
Abstract + PDF
2006 27 publication(s).
431.
An improved statistical method for detecting heterotachy in nucleotide sequences.
Baele G, Raes J, Van de Peer Y, Vansteelandt S
2006 Jul; 23(7): 1397-405. PubMed: 16672284.
Abstract + PDF
430.
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E
2006 Jul 15; 20(14): 1885-98. Epub 2006 Jun 30; PubMed: 16815998.
Abstract + PDF
429.
A global initiative on sharing avian flu data.
Bogner P, Capua I, Cox NJ, Lipman DJ, Aly MM, Auewarakul P, Baltimore D, Bork P, Brown I, Buchy P, Cameron G, Chen HL, Colwell R, Porceddu MC, Couacy-Hymann E, Czifra G, Ganguly NK, Gust ID, Doherty PC, Dulbecco R, Fejzic N, Garcia A, Gojobori T, Hargreaves S, Hashash EBS, Hay A, Joannis T, Johnson M, Jørgensen PH, Kida H, Koch G, Krnjaic D, Kurth R, Lamb RA, Lederberg J, Lim W, Lomlamthong Y, Maaetah H, Ali ASM, Marzuki S, Mettenleiter TC, Minta Z, Mishra AC, Muzio F, Naeem K, Osterhaus A, Pasick J, Peiris M, Perk S, Anh BQ, Ramishvili L, Ramzi ZS, Rojs OZ, Salzberg SL, Sánchez AS, Savic V, Senne D, Sulston J, Swayne DE, Tashiro M, Tufan M, Uzakbaev T, Van den Berg T, Varmus HE, Vitasek J, Webster RG, Wilbanks J, Yilmaz N, Zamora PA
2006 Aug 31; 442: 981. PID: 413.
Abstract + PDF
428.
Computational characterization of multiple Gag-like human proteins.
2006 Nov 15; 22(11): 585-9. Epub 2006 Sep 18; PubMed: 16979784.
Abstract + PDF
427.
Identification and analysis of evolutionarily cohesive functional modules in protein networks.
2006 Mar; 16(3): 374-82. Epub 2006 Jan 31; PubMed: 16449501.
Abstract + PDF
426.
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana.
Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y
2006; 7(2): R13. PubMed: 16507168.
Abstract + PDF
425.
Toward automatic reconstruction of a highly resolved tree of life.
2006 Mar 3; 311(5765): 1283-7. PubMed: 16513982. Media echos.
Abstract + PDF
424.
The TORNADO1 and TORNADO2 genes function in several patterning processes during early leaf development in Arabidopsis thaliana.
Cnops G, Neyt P, Raes J, Petrarulo M, Nelissen H, Malenica N, Luschnig C, Tietz O, Ditengou F, Palme K, Azmi A, Prinsen E, Van Lijsebettens M
2006 Apr; 18(4): 852-66. PubMed: 16531491.
Abstract + PDF
423.
Comparative analysis of environmental sequences: potential and challenges.
2006 Mar 29; 361(1467): 519-23. PubMed: 16524840.
Abstract + PDF
422.
Proteome survey reveals modularity of the yeast cell machinery.
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper SD, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G
2006 Mar 30; 440(7084): 631-6. Epub 2006 Jan 22; PubMed: 16429126. Media echos.
Abstract + PDF
421.
Insights into social insects from the genome of the honeybee Apis mellifera.
Honeybee Genome Sequencing Consortium , Weinstock GM, Robinson GE, Gibbs RA, Worley KC, Evans JD, Maleszka R, Robertson HM, Weaver DB, Beye M, Bork P, Elsik CG, Hartfelder K, Hunt GJ, Zdobnov EM, Amdam GV, Bitondi MMG, Collins AM, Cristino AS, Lattorff HMG, Lobo CH, Moritz RFA, Nunes FMF, Page RE, Simoes ZLP, Wheeler D, Carninci P, Fukuda S, Hayashizaki Y, Kai C, Kawai J, Sakazume N, Sasaki D, Tagami M, Albert S, Baggerman G, Beggs KT, Bloch G, Cazzamali G, Cohen M, Drapeau MD, Eisenhardt D, Emore C, Ewing MA, Fahrbach SE, Foret S, Grimmelikhuijzen CJP, Hauser F, Hummon AB, Huybrechts J, Jones AK, Kadowaki T, Kaplan N, Kucharski R, Leboulle G, Linial M, Littleton JT, Mercer AR, Richmond TA, Rodriguez-Zas SL, Rubin EB, Sattelle DB, Schlipalius D, Schoofs L, Shemesh Y, Sweedler JV, Velarde R, Verleyen P, Vierstraete E, Williamson MR, Ament SA, Brown SJ, Corona M, Dearden PK, Dunn WA, Elekonich MM, Fujiyuki T, Gattermeier I, Gempe T, Hasselmann M, Kadowaki T, Kage E, Kamikouchi A, Kubo T, Kucharski R, Kunieda T, Lorenzen M, Milshina NV, Morioka M, Ohashi K, Overbeek R, Ross CA, Schioett M, Shippy T, Takeuchi H, Toth AL, Willis JH, Wilson MJ, Gordon KHJ, Letunic I, Hackett K, Peterson J, Felsenfeld A, Guyer M, Solignac M, Agarwala R, Cornuet JM, Monnerot M, Mougel F, Reese JT, Vautrin D, Gillespie JJ, Cannone JJ, Gutell RR, Johnston JS, Eisen MB, Iyer VN, Iyer V, Kosarev P, Mackey AJ, Solovyev V, Souvorov A, Aronstein KA, Bilikova K, Chen YP, Clark AG, Decanini LI, Gelbart WM, Hetru C, Hultmark D, Imler JL, Jiang HB, Kanost M, Kimura K, Lazzaro BP, Lopez DL, Simuth J, Thompson GJ, Zou Z, de Jong P, Sodergren E, Csuros M, Milosavljevic A, Osoegawa K, Richards S, Shu CL, Duret L, Elhaik E, Graur D, Anzola JM, Campbell KS, Childs KL, Collinge D, Crosby MA, Dickens CM, Grametes LS, Grozinger CM, Jones PL, Jorda M, Ling X, Matthews BB, Miller J, Mizzen C, Peinado MA, Reid JG, Russo SM, Schroeder AJ, St Pierre SE, Wang Y, Zhou PL, Jiang HY, Kitts P, Ruef B, Venkatraman A, Zhang L, Aquino-Perez G, Whitfield CW, Behura SK, Berlocher SH, Sheppard WS, Smith DR, Suarez AV, Tsutsui ND, Wei XH, Wheeler D, Havlak P, Li BS, Liu Y, Sodergren E, Jolivet A, Lee S, Nazareth LV, Pu LL, Thorn R, Stolc V, Newman T, Samanta M, Tongprasit WA, Claudianos C, Berenbaum MR, Biswas S, de Graaf DC, Feyereisen R, Johnson RM, Oakeshott JG, Ranson H, Schuler MA, Muzny D, Chacko J, Davis C, Dinh H, Gill R, Hernandez J, Hines S, Hume J, Jackson L, Kovar C, Lewis L, Miner G, Morgan M, Nguyen N, Okwuonu G, Paul H, Santibanez J, Savery G, Svatek A, Villasana D, Wright R, Honeybee Genome Sequencing Consortium
2006 Oct 26; 443(7114): 931-49. PubMed: 17073008. Media echos.
Abstract + PDF
420.
Co-evolution of transcriptional and post-translational cell-cycle regulation.
Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P
2006 Oct 5; 443(7111): 594-7. Epub 2006 Sep 27; PubMed: 17006448. Media echos.
Abstract + PDF
419.
Literature mining for the biologist: from information retrieval to biological discovery.
Jensen LJ, Saric J, Bork P
2006 Feb; 7(2): 119-29. PubMed: 16418747.
Abstract + PDF
418.
SMART 5: domains in the context of genomes and networks.
Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P
2006 Jan 1; 34(Database issue): D257-60. PubMed: 16381859.
Abstract + PDF
417.
The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast.
Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bähler J
2006 Mar; 23(4): 261-77. PubMed: 16544289.
Abstract + PDF
416.
A novel MSH2 germline mutation in homozygous state in two brothers with colorectal cancers diagnosed at the age of 11 and 12 years.
Müller A, Schackert HK, Lange B, Rüschoff J, Füzesi L, Willert J, Burfeind P, Shah PK, Becker H, Epplen JT, Stemmler S
2006 Feb 1; 140(3): 195-9. PubMed: 16372347.
Abstract + PDF
415.
Literature and genome data mining for prioritizing disease-associated genes.
In: Discovering biomolecular mechanisms with computational biology. (Edited by F. Einsenhaber) pp.74-81. BID: 19.
ISBN: 0-387-34527-2 Publisher: Springer Science+Business Media, New York, New York, USA.
Abstract
414.
Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle.
Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM
2006 Oct 20; 2(10): e170. PubMed: 17054397.
Abstract + PDF
413.
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome.
Raible F, Tessmar-Raible K, Arboleda E, Kaller T, Bork P, Arendt D, Arnone MI
2006 Dec 1; 300(1): 461-75. Epub 2006 Sep 5; PubMed: 17067569.
Abstract + PDF
412.
Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors.
Rehwinkel J, Raes J, Izaurralde E
2006 Nov; 31(11): 639-46. PubMed: 17010613.
Abstract + PDF
411.
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development.
Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE
2006 Jun; 10(6): 797-807. PubMed: 16740481.
Abstract + PDF
410.
Extraction of regulatory gene/protein networks from Medline.
Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P
2006 Mar 15; 22(6): 645-50. Epub 2005 Jul 26; PubMed: 16046493.
Abstract + PDF
409.
LSAT: learning about alternative transcripts in MEDLINE.
2006 Apr 1; 22(7): 857-65. Epub 2006 Jan 12; PubMed: 16410322.
Abstract + PDF
408.
Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes.
2006 Jun 30; 2(6): e76. Epub 2006 May 16; PubMed: 16846249.
Abstract + PDF
407.
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
2006 Jul 1; 34(Web Server issue): W609-12. PubMed: 16845082.
Abstract + PDF
406.
Origin of replication in circular prokaryotic chromosomes.
Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW
2006 Feb; 8(2): 353-361. PubMed: 16423021.
Abstract + PDF
405.
Similar gene expression profiles do not imply similar tissue functions.
Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ
2006 Mar; 22(3): 132-8. Epub 2006 Feb 9; PubMed: 16480787.
Abstract + PDF
2005 35 publication(s).
404.
Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome.
Beysen D, Raes J, Leroy BP, Lucassen A, Yates JR, Clayton-Smith J, Ilyina H, Brooks SS, Christin-Maitre S, Fellous M, Fryns JP, Kim JR, Lapunzina P, Lemyre E, Meire F, Messiaen LM, Oley C, Splitt M, Thomson J, Van de Peer Y, Veitia RA, De Paepe A, De Baere E
2005 Aug; 77(2): 205-18. PubMed: 15962237.
Abstract
403.
Is there biological research beyond Systems Biology? A comparative analysis of terms.
2005; 1: 2005.0012. PubMed: 16729047.
PDF
402.
Towards cellular systems in 4D.
Bork P, Serrano L
2005 May 20; 121(4): 507-509. PubMed: 15907464.
PDF
401.
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G
2005 Jan; 15(1): 98-110. Epub 2004 December 8; PubMed: 15590940. Media echos.
Abstract + PDF
400.
Structural Genomics of human proteins - target selection and generation of a public catalog of expression clones.
Bussow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U
2005 Jul 5; 4: 21. Epub 2005 Jul 5; PubMed: 15998469.
Abstract + PDF
399.
Carbon isotopic fractionation during aerobic vinyl chloride degradation.
Chartrand MM, Waller AS, Mattes TE, Elsner M, Lacrampe-Couloume G, Gossett JM, Edwards EA, Lollar BS
2005 Feb 15; 39(4): 1064-70. PubMed: 15773478.
Abstract
398.
The WHy domain mediates the response to desiccation in plants and bacteria.
2005 Apr 15; 21(8): 1304-7. Epub 2004 Dec 14; PubMed: 15598830.
Abstract + PDF
397.
Complex genomic rearrangements lead to novel primate gene function.
2005 Mar; 15(3): 343-51. Epub 2005 Feb 14; PubMed: 15710750. Media echos.
Abstract + PDF
396.
Dynamic complex formation during the yeast cell cycle.
de Lichtenberg U, Jensen LJ, Brunak S, Bork P
2005 Feb 4; 307(5710): 724-7. PubMed: 15692050. Media echos.
Abstract + PDF
395.
Comparison of computational methods for the identification of cell cycle-regulated genes.
de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S
2005 Apr 1; 21(7): 1164-71. Epub 2004 Oct 28; PubMed: 15513999.
Abstract + PDF
394.
Environments shape the nucleotide composition of genomes.
2005 Dec; 6(12): 1208-13. PubMed: 16200051.
Abstract + PDF
393.
Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK
2005 Apr 7; 434(7034): 724-31. PubMed: 15815621.
Abstract + PDF
392.
Medusa: a simple tool for interaction graph analysis.
2005 Dec 15; 21(24): 4432-3. Epub 2005 Sep 27; PubMed: 16188923.
Abstract + PDF
391.
Re-analysis of data and its integration.
Jensen LJ, Steinmetz LM
2005 Mar 21; 579(8): 1802-7. PubMed: 15763555.
Abstract + PDF
390.
Systematic association of genes to phenotypes by genome and literature mining.
2005 May; 3(5): e134. Epub 2005 Apr 5; PubMed: 15799710. Media echos.
Abstract + PDF
389.
Computational Analysis of Modular Protein Architectures
Linding R, Letunic I, Gibson TJ, Bork P
In: Modular Protein Domains (Ed. Giovanni Cesareni, Mario Gimona, Marius Sudol, and Michael Yaffe)BID: 21.
ISBN: 3-527-30813-2 Publisher: Wiley-VCH Verlag GmbH & Co, KGaA Weinheim
Abstract + PDF
388.
Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases.
Mees A, Rock R, Ciccarelli FD, Leberfinger CB, Borawski JM, Bork P, Wiese S, Gessler M, Kerkhoff E
2005 Dec; 6(1): 79-85. Epub 2005 Aug 15; PubMed: 16099729.
Abstract + PDF
387.
Initial sequence of the chimpanzee genome and comparison with the human genome
Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang SP, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, Archidiacono N, Bork P, Butler J, Chang JL, Cheng Z, Chinwalla AT, deJong P, Delehaunty KD, Fronick CC, Fulton LL, Gilad Y, Glusman G, Gnerre S, Graves TA, Hayakawa T, Hayden KE, Huang X, Ji HK, Kent WJ, King MC, Kulbokas III EJ, Lee MK, Liu G, Lopez-Otin C, Makova KD, Man O, Mardis ER, Mauceli E, Miner TL, Nash WE, Nelson JO, Pääbo S, Patterson NJ, Pohl CS, Pollard KS, Prüfer K, Puente XS, Reich D, Rocchi M, Rosenbloom K, Ruvolo M, Richter DJ, Schaffner SF, Smit AFA, Smith SM, Suyama M, Taylor J, Torrents D, Tuzun E, Varki A, Velasco G, Ventura M, Wallis JW, Wendl MC, Wilson RK, Lander ES, Waterston RH
2005 09 1; 437: 69-87. PubMed: 16136131. Media echos.
Abstract + PDF
386.
InterPro, progress and status in 2005.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH
2005 Jan 1; 33(Database issue): D201-5. PubMed: 15608177.
Abstract + PDF
385.
G2D: A Tool for Mining Genes Associated with Disease.
2005 Aug 22; 6: 45. Epub 2005 Aug 22; PubMed: 16115313.
Abstract + PDF
384.
Functional divergence of proteins through frameshift mutations.
Raes J, Van de Peer Y
2005 Aug; 21(8): 428-31. PubMed: 15951050.
Abstract + PDF
383.
Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii.
Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, de Jong P, Weissenbach J, Bork P, Arendt D
2005 Nov 25; 310(5752): 1325-6. PubMed: 16311335. Media echos.
Abstract + PDF
382.
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.
Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E
RNA.
2005 Oct; 11(10): 1530-44. PubMed: 16199763.
Abstract + PDF
381.
Large-scale extraction of gene regulation for model organisms in an ontological context.
Saric J, Jensen LJ, Rojas I
2005; 5(1): 21-32. PubMed: 15972005.
Abstract + PDF
380.
Structural similarity to bridge sequence space: finding new families on the bridges.
Shah PK, Aloy P, Bork P, Russell RB
2005 May; 14(5): 1305-14. PubMed: 15840833.
Abstract + PDF
379.
Extraction of transcript diversity from scientific literature.
2005 Jun; 1(1): e10. Epub 2005 Jun 24; PubMed: 16103899.
Abstract + PDF
378.
Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.
2005 Oct 10; 579(24): 5281-6. PubMed: 16182294.
Abstract + PDF
377.
Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.
Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M
2005 Nov 21; 171(4): 627-40. Epub 2005 Nov 14; PubMed: 16286509.
Abstract + PDF
376.
DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
Tenhaken R, Doerks T, Bork P
2005 Jul 11; 6: 169. Epub 2005 Jul 11; PubMed: 16008837.
Abstract + PDF
375.
Comparative metagenomics of microbial communities.
Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM
2005 Apr 22; 308(5721): 554-7. PubMed: 15845853. Media echos.
Abstract + PDF
374.
Crystal ball. Systems biology: in the broadest sense of the word.
Ussery DW, de Lichtenberg U, Jensen LJ
2005 Apr; 7(4): 482-3. PubMed: 15816924.
PDF
373.
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
2005 Jan 1; 33(Database issue): D433-7. PubMed: 15608232.
Abstract + PDF
372.
Multiple reductive-dehalogenase-homologous genes are simultaneously transcribed during dechlorination by Dehalococcoides-containing cultures.
Waller AS, Krajmalnik-Brown R, Löffler FE, Edwards EA
2005 Dec; 71(12): 8257-64. PubMed: 16332811.
Abstract
371.
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
2005; 33(3): 946-54. PubMed: 15716312.
Abstract + PDF
370.
Consistency of genome-based methods in measuring Metazoan evolution.
2005 Jun 13; 579(15): 3355-61. Epub 2005 Apr 18; PubMed: 15943981.
Abstract + PDF
2004 24 publication(s).
369.
Structure-based assembly of protein complexes in yeast.
Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB
2004 Mar 26; 303(5666): 2026-9. PubMed: 15044803.
Abstract + PDF
368.
Protein interaction networks from yeast to human.
Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM
2004 Jun; 14(3): 292-9. PubMed: 15193308.
Abstract + PDF
367.
Genes and structures in context (editorial).
Bork P, Orengo C
2004 June; 14(3): 261-263. PID: 335.
PDF
366.
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gössling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Müller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E, Zimmer R
2004 Jan 22; 20(2): 268-70. PubMed: 14734319.
Abstract + PDF
365.
Global analysis of bacterial transcription factors to predict cellular target processes.
2004 Mar; 20(3): 126-31. PubMed: 15049306.
Abstract + PDF
364.
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
2004; 32(21): 6321-6. PubMed: 15576358.
Abstract + PDF
363.
RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export.
Forler D, Rabut G, Ciccarelli FD, Herold A, Köcher T, Niggeweg R, Bork P, Ellenberg J, Izaurralde E
2004 Feb; 24(3): 1155-67. PubMed: 14729961.
Abstract + PDF
362.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera , Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov EM, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium
2004 Apr 1; 428(6982): 493-521. PubMed: 15057822. Media echos.
Abstract + PDF
361.
Estimating rates of alternative splicing in mammals and invertebrates.
Harrington ED, Boue S, Valcarcel J, Reich JG, Bork P
2004 Sept; 36(9): 916 - 917. PID: 307.
PDF
360.
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R
2004 Feb; 22(2): 177-83. PubMed: 14755292.
Abstract + PDF
359.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RP, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MD, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WR, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SM, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK, International Chicken Genome Sequencing Consortium
2004 Dec 9; 432(7018): 695-716. PubMed: 15592404. Media echos.
Abstract + PDF
358.
Quality analysis and integration of large scale molecular data sets.
2004 Apr; 3(2): 51-56. PID: 308.
PDF
357.
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
2004 Jul 1; 32(Web Server issue): W445-8. PubMed: 15215427.
Abstract + PDF
356.
Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression.
Koehl A, Schmidt N, Rieger A, Pilgram SM, Letunic I, Bork P, Soto F, Friauf E, Nothwang HG
2004 Dec; 20(12): 3244-58. PubMed: 15610157.
Abstract + PDF
355.
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
2004 Jul; 22(7): 911-7. PubMed: 15229555.
Abstract + PDF
354.
Shared components of protein complexes--versatile building blocks or biochemical artefacts?
2004 Dec; 26(12): 1333-43. PubMed: 15551274.
Abstract + PDF
353.
SMART 4.0: towards genomic data integration.
2004 Jan 1; 32(Database issue): D142-4. PubMed: 14681379.
Abstract + PDF
352.
Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome.
Liska AJ, Popov AV, Sunyaev SR, Coughlin P, Habermann B, Shevchenko A, Bork P, Karsenti E, Shevchenko A
2004 Sep; 4(9): 2707-21. PubMed: 15352245.
Abstract + PDF
351.
Transgene methylation in mice reflects copy number but not expression level.
Pena RN, Webster J, Kwan S, Korbel JO, Whitelaw BA
2004 Mar; 26(3): 215-20. PubMed: 15004290.
Abstract
350.
Gene annotation from scientific literature using mappings between keyword systems.
Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA
2004 Sep 1; 20(13): 2084-91. Epub 2004 Apr 1; PubMed: 15059832.
Abstract + PDF
349.
Extracting regulatory gene expression networks from Pubmed.
Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P
2004; : 192-199. PID: 395.
PDF
348.
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
2004 Aug 12; 20(12): 1968-70. Epub 2004 Mar 22; PubMed: 15037510.
Abstract + PDF
347.
Perchlorate-reducing microorganisms isolated from contaminated sites.
Waller AS, Cox EE, Edwards EA
2004 May; 6(5): 517-27. PubMed: 15049925.
Abstract
346.
PASBio: predicate-argument structures for event extraction in molecular biology.
Wattarujeekrit T, Shah PK, Collier N
2004 Oct 19; 5: 155. PubMed: 15494078.
Abstract + PDF
2003 30 publication(s).
345.
Current Perspectives.
In: Bioinformatics and genomes. (M. Andrade eds.) pp.1-227. BID: 14.
Publisher: Horizon Scientific Press, UK
344.
Alternative splicing and evolution.
2003 Nov; 25(11): 1031-4. PubMed: 14579243.
Abstract + PDF
343.
The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold.
Ciccarelli FD, Bork P, Kerkhoff E
2003 Jul; 28(7): 349-52. PubMed: 12877999.
PDF
342.
The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
Ciccarelli FD, Izaurralde E, Bork P
2003 Dec 19; 4: 64. Epub 2003 Dec 19; PubMed: 14687415.
Abstract + PDF
341.
The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia.
Ciccarelli FD, Proukakis C, Patel H, Cross H, Azam S, Patton MA, Bork P, Crosby AH
2003 Apr; 81(4): 437-41. PubMed: 12676568.
Abstract + PDF
340.
Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways.
Gatfield D, Unterholzner L, Ciccarelli FD, Bork P, Izaurralde E
2003 Aug 1; 22(15): 3960-70. PubMed: 12881430.
Abstract + PDF
339.
The DNA sequence of human chromosome 7.
Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK
2003 Jul 10; 424(6945): 157-64. PubMed: 12853948. Media echos.
Abstract + PDF
338.
Function prediction and protein networks.
2003 Apr; 15(2): 191-8. PubMed: 12648675.
Abstract + PDF
337.
Evaluation of annotation strategies using an entire genome sequence.
Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos DP, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA
2003 Apr 12; 19(6): 717-26. PubMed: 12691983.
Abstract + PDF
336.
Bioinformatics in the post-sequence era.
Kanehisa M, Bork P
2003 Mar; 33 Suppl: 305-10. PubMed: 12610540.
Abstract + PDF
335.
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
2003 Oct 12; 19(15): 1901-8. PubMed: 14555622.
Abstract + PDF
334.
Increase of functional diversity by alternative splicing.
Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev SR
2003 Mar; 19(3): 124-8. PubMed: 12615003.
Abstract + PDF
333.
Protein disorder prediction: implications for structural proteomics.
Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB
2003 Nov; 11(11): 1453-9. PubMed: 14604535.
Abstract + PDF
332.
Systematic discovery of analogous enzymes in thiamin biosynthesis.
Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P
2003 Jul; 21(7): 790-5. Epub 2003 Jun 8; PubMed: 12794638.
Abstract + PDF
331.
High rate of gene displacement in vitamine biosynthetic pathways.
Morett E, Saab-Rincon G, Merino E, Bork P, Rajan E, Olvera L, Olvera M
In: Bioinformatics and genomes. (M. Andrade eds.) pp. 69-79. BID: 3.
Publisher: Horizon Sci. Press
PDF
330.
The InterPro Database, 2003 brings increased coverage and new features.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM
2003 Jan 1; 31(1): 315-8. PubMed: 12520011.
Abstract + PDF
329.
The way we write.
2003 May; 4(5): 446-51. PubMed: 12728240.
PDF
328.
A protocol for the update of references to scientific literature in biological databases.
2003; 2(3): 189-91. PubMed: 15130808.
Abstract + PDF
327.
Update on XplorMed: A web server for exploring scientific literature.
2003 Jul 1; 31(13): 3866-8. PubMed: 12824439.
Abstract + PDF
326.
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ
2003 Jul 1; 31(13): 3625-30. PubMed: 12824381.
Abstract + PDF
325.
Metabolites: a helping hand for pathway evolution?
2003 Jun; 28(6): 336-41. PubMed: 12826406.
Abstract + PDF
324.
Information extraction from full text scientific articles: where are the keywords?
2003 May 29; 4: 20. Epub 2003 May 29; PubMed: 12775220.
Abstract + PDF
323.
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes.
Shevchenko A, Sunyaev SR, Liska A, Bork P, Shevchenko A
2003; 211: 221-34. PubMed: 12489434.
PDF
322.
Impact of selection, mutation rate and genetic drift on human genetic variation.
Sunyaev SR, Kondrashov FA, Bork P, Ramensky VE
2003 Dec 15; 12(24): 3325-30. Epub 2003 Oct 21; PubMed: 14570704.
Abstract + PDF
321.
Pseudogenes and Genomes.
In: Bioinformatics and genomes. (M. Andrade eds.) pp.197-209. BID: 4.
Publisher: Horizon Sci. Press
PDF
320.
A genome-wide survey of human pseudogenes.
2003 Dec; 13(12): 2559-67. PubMed: 14656963.
Abstract + PDF
319.
STRING: a database of predicted functional associations between proteins.
2003 Jan 1; 31(1): 258-61. PubMed: 12519996.
Abstract + PDF
318.
Genome evolution reveals biochemical networks and functional modules.
von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P
2003 Dec 23; 100(26): 15428-33. Epub 2003 Dec 12; PubMed: 14673105.
Abstract + PDF
317.
The human genome: genes, pseudogenes, and variation on chromosome 7.
Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK
PDF
316.
Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes.
Woerner SM, Benner A, Sutter C, Schiller M, Yuan YP, Keller G, Bork P, Doeberitz MK, Gebert JF
2003 Apr 17; 22(15): 2226-35. PubMed: 12700659.
Abstract + PDF
2002 43 publication(s).
315.
A complex prediction: three-dimensional model of the yeast exosome.
Aloy P, Ciccarelli FD, Leutwein C, Gavin AC, Superti-Furga G, Bork P, Bottcher B, Russell RB
2002 Jul; 3(7): 628-35. PubMed: 12101094.
Abstract + PDF
314.
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
2002 Aug 15; 3(9): RESEARCH0047. Epub 2002 Aug 15; PubMed: 12225586.
Abstract + PDF
313.
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
Bordo D, Bork P
2002 Aug; 3(8): 741-6. PubMed: 12151332.
Abstract + PDF
312.
Comparative analysis of protein interaction networks.
2002; 18 Suppl 2: S64. PubMed: 12385984.
Abstract + PDF
311.
Alternative splicing and genome complexity.
Brett D, Pospisil H, Valcárcel J, Reich J, Bork P
2002 Jan; 30(1): 29-30. Epub 2001 Dec 17; PubMed: 11743582.
Abstract + PDF
310.
Immunity-related genes and gene families in Anopheles gambiae.
Christophides GK, Zdobnov EM, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, Levashina EA, Loukeris TG, Lycett G, Meister S, Michel K, Moita LF, Müller HM, Osta MA, Paskewitz SM, Reichhart JM, Rzhetsky A, Troxler L, Vernick KD, Vlachou D, Volz J, von Mering C, Xu J, Zheng L, Bork P, Kafatos FC
2002 Oct 4; 298(5591): 159-65. PubMed: 12364793.
Abstract + PDF
309.
CASH--a beta-helix domain widespread among carbohydrate-binding proteins.
2002 Feb; 27(2): 59-62. PubMed: 11852237.
Abstract + PDF
308.
AMOP, a protein module alternatively spliced in cancer cells.
2002 Mar; 27(3): 113-5. PubMed: 11893501.
Abstract + PDF
307.
Protein domain analysis in the era of complete genomes.
2002 Feb 20; 513(1): 129-34. PubMed: 11911892.
Abstract + PDF
306.
Genome and protein evolution in eukaryotes.
2002 Feb; 6(1): 39-45. PubMed: 11827821.
Abstract + PDF
305.
Sequence analysis of multidomain proteins: past perspectives and future directions.
Copley RR, Ponting CP, Schultz J, Bork P
2002; 61: 75-98. PubMed: 12461821.
PDF
304.
Comparative Genome Analysis of the Mollicutes.
Dandekar T, Snel B, Schmidt S, Lathe W, Suyama M, Huynen M, Bork P
In: Molecular Biology and Pathogenicity of Mycoplasmas. (Razin and Herrmann, eds.) pp.255-278. BID: 5.
Publisher: Kluwer Academic/Plenum Publishers, New York
PDF
303.
Systematic identification of novel protein domain families associated with nuclear functions.
2002 Jan; 12(1): 47-56. PubMed: 11779830.
Abstract + PDF
302.
BSD: a novel domain in transcription factors and synapse-associated proteins.
Doerks T, Huber S, Buchner E, Bork P
2002 Apr; 27(4): 168-70. PubMed: 11943536.
Abstract + PDF
301.
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ
2002 Jan 1; 30(1): 387-91. PubMed: 11752345.
Abstract + PDF
300.
Functional organization of the yeast proteome by systematic analysis of protein complexes.
Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G
2002 Jan 10; 415(6868): 141-7. PubMed: 11805826. Media echos.
Abstract + PDF
299.
HSPG modification by the secreted enzyme Notum shapes the Wingless morphogen gradient.
Giráldez AJ, Copley RR, Cohen SM
2002 May; 2(5): 667-76. PubMed: 12015973.
Abstract + PDF
298.
The genome sequence of the malaria mosquito Anopheles gambiae.
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL
2002 Oct 4; 298(5591): 129-49. PubMed: 12364791.
Abstract + PDF
297.
Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes.
Kloor M, Bork P, Duwe A, Klaes R, von Knebel Doeberitz M, Ridder R
2002 Dec 12; 1579(2-3): 219-24. PubMed: 12427560.
Abstract + PDF
296.
On the regulation of transcription in eukaryotes and methods for finding DNA regulatory elements using bioinformatics.
In: Sitzungsberichte der Gesellschaft Naturforschender Freunde zu Berlin. (Walter Sudhaus)41 pp.57-66. BID: 6.
Publisher: Goecke & Evers, Keltern
295.
SHOT: a web server for the construction of genome phylogenies.
2002 Mar; 18(3): 158-62. PubMed: 11858840.
Abstract + PDF
294.
Common exon duplication in animals and its role in alternative splicing.
2002 Jun 15; 11(13): 1561-7. PubMed: 12045209.
Abstract + PDF
293.
Recent improvements to the SMART domain-based sequence annotation resource.
Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P
2002 Jan 1; 30(1): 242-4. PubMed: 11752305.
Abstract + PDF
292.
Predicting protein cellular localization using a domain projection method.
Mott R, Schultz J, Bork P, Ponting CP
2002 Aug; 12(8): 1168-74. PubMed: 12176924.
Abstract + PDF
291.
InterPro: an integrated documentation resource for protein families, domains and functional sites.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ, InterPro Consortium
2002 Sep; 3(3): 225-35. PubMed: 12230031.
Abstract + PDF
290.
A self-organizing model for the development of orientation selectivity and ocular dominance patterns in the visual nervous system.
Muro EM, Andrade MA, Morán F
2002; 12: 319-332. PID: 336.
289.
SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia.
Patel H, Cross H, Proukakis C, Hershberger R, Bork P, Ciccarelli FD, Patton MA, McKusick VA, Crosby AH
2002 Aug; 31(4): 347-8. Epub 2002 Jul 22; PubMed: 12134148.
Abstract + PDF
288.
Worldwide scientific publishing activity.
2002 Jul 26; 297(5581): 519. PubMed: 12143877.
PDF
287.
Exploring MEDLINE abstracts with XplorMed.
2002 Jun; 38(6): 381-9. PubMed: 12532176.
Abstract
286.
Association of genes to genetically inherited diseases using data mining.
2002 Jul; 31(3): 316-9. Epub 2002 May 13; PubMed: 12006977.
Abstract + PDF
285.
Computing fuzzy associations for the analysis of biological literature.
2002 Jun; 32(6): 1380-2, 1384-5. PubMed: 12074170.
Abstract + PDF
284.
Human non-synonymous SNPs: server and survey.
2002 Sep 1; 30(17): 3894-900. PubMed: 12202775.
Abstract + PDF
283.
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F
2002 Oct 29; 99(22): 14422-7. Epub 2002 Oct 15; PubMed: 12381787.
Abstract + PDF
282.
A versatile structural domain analysis server using profile weight matrices.
2002 Mar-Apr; 42(2): 405-7. PubMed: 11911710.
Abstract + PDF
281.
Conservation of gene co-regulation in prokaryotes and eukaryotes.
2002 Oct 1; 20(10): 410. PID: 338.
Abstract + PDF
280.
The identification of functional modules from the genomic association of genes.
2002 Apr 30; 99(9): 5890-5. PubMed: 11983890.
Abstract + PDF
279.
Genomes in flux: the evolution of archaeal and proteobacterial gene content.
2002 Jan; 12(1): 17-25. PubMed: 11779827.
Abstract + PDF
278.
Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae.
Thomasova D, Ton LQ, Copley RR, Zdobnov EM, Wang X, Hong YS, Sim C, Bork P, Kafatos FC, Collins FH
2002 Jun 11; 99(12): 8179-84. PubMed: 12060762.
Abstract + PDF
277.
Proteinkomplexe und Netzwerke: Neue Herausforderungen für die Proteomik.
2002; 2: 2-4. PID: 310.
PDF
276.
Teamed up for transcription.
2002 Jun 20; 417(6891): 797-8. PubMed: 12075329.
PDF
275.
Comparative assessment of large-scale data sets of protein-protein interactions.
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P
2002 May 23; 417(6887): 399-403. Epub 2002 May 8; PubMed: 12000970.
Abstract + PDF
274.
Initial sequencing and comparative analysis of the mouse genome.
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES, Mouse Genome Sequencing Consortium
2002 Dec 5; 420(6915): 520-62. PubMed: 12466850. Media echos.
Abstract + PDF
273.
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P
2002 Oct 4; 298(5591): 149-59. PubMed: 12364792.
Abstract + PDF
2001 29 publication(s).
272.
A combination of the F-box motif and kelch repeats defines a large Arabidopsis family of F-box proteins.
Andrade MA, González-Guzmán M, Serrano R, Rodríguez PL
2001 Jul; 46(5): 603-14. PubMed: 11516153.
Abstract
271.
Simulation of plasticity in the adult visual cortex.
Andrade MA, Muro EM, Morán F
2001 Jun; 84(6): 445-51. PubMed: 11417056.
Abstract
270.
Protein repeats: structures, functions, and evolution.
2001; 134(2-3): 117-31. PubMed: 11551174.
Abstract + PDF
269.
Comparison of ARM and HEAT protein repeats.
Andrade MA, Petosa C, O'Donoghue SI, Müller CW, Bork P
2001 May 25; 309(1): 1-18. PubMed: 11491282.
Abstract + PDF
268.
The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival.
Becker S, Gehrsitz A, Bork P, Buchner S, Buchner E
2001 Jan 10; 262(1-2): 15-22. PubMed: 11179663.
Abstract + PDF
267.
The draft sequences. Filling in the gaps.
Bork P, Copley R
2001 Feb 15; 409(6822): 818-20. PubMed: 11236994.
PDF
266.
Genome speak.
Bork P, Copley R
2001 Feb 15; 409(6822): 815. PubMed: 11241984.
PDF
265.
Sialidase-like Asp-boxes: sequence-similar structures within different protein folds.
Copley RR, Russell RB, Ponting CP
2001 Feb; 10(2): 285-92. PubMed: 11266614.
Abstract + PDF
264.
Trends in Biochemical Systems (Review).
2001; 26: 637-637. PID: 314.
263.
Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches.
Dandekar T, Du F, Schirmer RH, Schmidt S
2001 Dec; 26(1): 15-21. PubMed: 11765847.
Abstract + PDF
262.
DDT -- a novel domain in different transcription and chromosome remodeling factors.
Doerks T, Copley R, Bork P
2001 Mar; 26(3): 145-6. PubMed: 11246006.
Abstract + PDF
261.
Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes.
2001 Jan; 14(1): 17-25. PubMed: 11287675.
Abstract + PDF
260.
Inversions and the dynamics of eukaryotic gene order.
2001 Jun; 17(6): 304-6. PubMed: 11377779.
Abstract + PDF
259.
The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Huynen MA, Snel B, Bork P, Gibson TJ
2001 Oct 1; 10(21): 2463-8. PubMed: 11689493.
Abstract + PDF
258.
Genome sequences and great expectations.
Iliopoulos I, Tsoka S, Andrade MA, Janssen P, Audit B, Tramontano A, Valencia A, Leroy C, Sander C, Ouzounis CA
2001; 2(1): INTERACTIONS0001. PubMed: 11178275.
Abstract + PDF
257.
Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Iyer LM, Aravind L, Bork P, Hofmann K, Mushegian AR, Zhulin IB, Koonin EV
2001; 2(12): RESEARCH0051. Epub 2001 Nov 13; PubMed: 11790254.
Abstract + PDF
256.
The Spir actin organizers are involved in vesicle transport processes.
Kerkhoff E, Simpson JC, Leberfinger CB, Otto IM, Doerks T, Bork P, Rapp UR, Raabe T, Pepperkok R
2001 Dec 11; 11(24): 1963-8. PubMed: 11747823.
Abstract + PDF
255.
Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, Levine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J, International Human Genome Sequencing Consortium
2001 Feb 15; 409(6822): 860-921. PubMed: 11237011. Media echos.
Abstract + PDF
254.
Evolution of tuf genes: ancient duplication, differential loss and gene conversion.
2001 Aug 3; 502(3): 113-6. PubMed: 11583110.
Abstract + PDF
253.
Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens.
Linnebacher M, Gebert J, Rudy W, Woerner S, Yuan YP, Bork P, von Knebel Doeberitz M
2001 Jul 1; 93(1): 6-11. PubMed: 11391614.
Abstract + PDF
252.
XplorMed: a tool for exploring MEDLINE abstracts.
2001 Sep; 26(9): 573-5. PubMed: 11551795.
Abstract + PDF
251.
Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.
Ponting CP, Mott R, Bork P, Copley RR
2001 Dec; 11(12): 1996-2008. PubMed: 11731489.
Abstract + PDF
250.
Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35].
Schultz J, Jones T, Bork P, Sheer D, Blencke S, Steyrer S, Wellbrock U, Bevec D, Ullrich A, Wallasch C
2001 Feb 1; 71(3): 368-70. PubMed: 11170754.
Abstract + PDF
249.
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Shevchenko A, Sunyaev SR, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG
2001 May 1; 73(9): 1917-26. PubMed: 11354471.
Abstract + PDF
248.
Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms.
2001 Feb; 11(1): 125-30. PubMed: 11179902.
Abstract + PDF
247.
Prediction of deleterious human alleles.
Sunyaev SR, Ramensky VE, Koch I, Lathe WC, Kondrashov AS, Bork P
2001 Mar 15; 10(6): 591-7. PubMed: 11230178.
Abstract + PDF
246.
Evolution of prokaryotic gene order: genome rearrangements in closely related species.
2001 Jan; 17(1): 10-3. PubMed: 11163906.
Abstract + PDF
245.
When genetic distance matters: measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species.
Wang R, Zheng L, Touré YT, Dandekar T, Kafatos FC
2001 Sep 11; 98(19): 10769-74. PubMed: 11553812.
Abstract + PDF
244.
Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.
Woerner SM, Gebert J, Yuan YP, Sutter C, Ridder R, Bork P, von Knebel Doeberitz M
2001 Jul 1; 93(1): 12-9. PubMed: 11391615.
Abstract + PDF
2000 38 publication(s).
243.
Automated extraction of information in molecular biology.
2000 Jun 30; 476(1-2): 12-7. PubMed: 10878241.
Abstract + PDF
242.
Homology-based method for identification of protein repeats using statistical significance estimates.
Andrade MA, Ponting CP, Gibson TJ, Bork P
2000 May 5; 298(3): 521-37. PubMed: 10772867.
Abstract + PDF
241.
Powers and pitfalls in sequence analysis: the 70% hurdle.
2000 Apr; 10(4): 398-400. PubMed: 10779480.
PDF
240.
Genome and proteome informatics.
Bork P, Eisenberg D
2000; 10(3): 341-342. PID: 318.
PDF
239.
Comparitve genome analysis: Exploiting the contect of genes to infer evolution and predict function
Bork P, Snel B, Lehmann G, Suyama M, Dandekar T, Lathe III, Huynen M
In: Comparitive Genomics pp.281-294. BID: 18.
ISBN: 0-7923-6583-6 Publisher: Kluwer Academic Publishers Printed in the Netherlands
Abstract + PDF
238.
EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
Brett D, Hanke J, Lehmann G, Haase S, Delbrück S, Krueger S, Reich J, Bork P
2000 May 26; 474(1): 83-6. PubMed: 10828456.
Abstract + PDF
237.
EST analysis online: WWW tools for detection of SNPs and alternative splice forms.
Brett D, Lehmann G, Hanke J, Gross S, Reich J, Bork P
2000 Sep; 16(9): 416-8. PubMed: 10973071.
PDF
236.
HGBASE: a database of SNPs and other variations in and around human genes.
Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F
2000 Jan 1; 28(1): 356-60. PubMed: 10592273.
Abstract + PDF
235.
Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways.
2000 Nov 3; 303(4): 627-41. PubMed: 11054297.
Abstract + PDF
234.
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar T, Huynen MA, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P
2000 Sep 1; 28(17): 3278-88. PubMed: 10954595.
Abstract + PDF
233.
Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines.
Dimopoulos G, Casavant TL, Chang S, Scheetz T, Roberts C, Donohue M, Schultz J, Benes V, Bork P, Ansorge W, Soares MB, Kafatos FC
2000 Jun 6; 97(12): 6619-24. PubMed: 10841561.
Abstract + PDF
232.
L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7.
Doerks T, Bork P, Kamberov E, Makarova O, Muecke S, Margolis B
2000 Jul; 25(7): 317-8. PubMed: 10871881.
PDF
231.
GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
Doerks T, Strauss M, Brendel M, Bork P
2000 Oct; 25(10): 483-5. PubMed: 11050430.
PDF
230.
Automated annotation of GPI anchor sites: case study C. elegans.
2000 Jul; 25(7): 340-1. PubMed: 10871885.
PDF
229.
Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.
Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlü N, Bork P, Hyman AA
2000 Nov 16; 408(6810): 331-6. PubMed: 11099034.
Abstract + PDF
228.
TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture.
Herold A, Suyama M, Rodrigues JP, Braun IC, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E
2000 Dec; 20(23): 8996-9008. PubMed: 11073998.
Abstract + PDF
227.
The GeneQuiz web server: protein functional analysis through the Web.
Hoersch S, Leroy C, Brown NP, Andrade MA, Sander C
2000 Jan; 25(1): 33-5. PubMed: 10637611.
226.
Gene and context: integrative approaches to genome analysis.
2000; 54: 345-79. PubMed: 10829232.
225.
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences.
2000 Aug; 10(8): 1204-10. PubMed: 10958638.
Abstract + PDF
224.
Exploitation of gene context.
2000 Jun; 10(3): 366-70. PubMed: 10851194.
Abstract + PDF
223.
Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.
Isaksson A, Landegren U, Syvänen AC, Bork P, Stein C, Ortigao F, Brookes AJ
2000 Feb; 8(2): 154-6. PubMed: 10757651.
Abstract + PDF
222.
The 3'-untranslated region of the human estrogen receptor alpha gene mediates rapid messenger ribonucleic acid turnover.
Kenealy MR, Flouriot G, Sonntag-Buck V, Dandekar T, Brand H, Gannon F
2000 Aug; 141(8): 2805-13. PubMed: 10919266.
Abstract + PDF
221.
Gene context conservation of a higher order than operons.
2000 Oct; 25(10): 474-9. PubMed: 11050428.
Abstract + PDF
220.
The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization.
Otto IM, Raabe T, Rennefahrt UE, Bork P, Rapp UR, Kerkhoff E
2000 Mar 23; 10(6): 345-8. PubMed: 10744979.
Abstract + PDF
219.
Evolution of domain families.
2000; 54: 185-244. PubMed: 10829229.
PDF
218.
SMART: a web-based tool for the study of genetically mobile domains.
2000 Jan 1; 28(1): 231-4. PubMed: 10592234.
Abstract + PDF
217.
More than 1,000 putative new human signalling proteins revealed by EST data mining.
2000 Jun; 25(2): 201-4. PubMed: 10835637.
Abstract + PDF
216.
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.
2000 Mar; 18(3): 326-32. PubMed: 10700151.
Abstract + PDF
215.
Genome evolution. Gene fusion versus gene fission.
2000 Jan; 16(1): 9-11. PubMed: 10637623.
PDF
214.
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Snel B, Lehmann G, Bork P, Huynen MA
2000 Sep 15; 28(18): 3442-4. PubMed: 10982861.
Abstract + PDF
213.
REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export.
Stutz F, Bachi A, Doerks T, Braun IC, Séraphin B, Wilm M, Bork P, Izaurralde E
RNA.
2000 Apr; 6(4): 638-50. PubMed: 10786854.
Abstract + PDF
212.
Individual variation in protein-coding sequences of human genome.
Sunyaev SR, Hanke J, Brett D, Aydin A, Zastrow I, Lathe WC, Bork P, Reich J
2000; 54: 409-37. PubMed: 10829234.
PDF
211.
SNP frequencies in human genes an excess of rare alleles and differing modes of selection.
2000 Aug; 16(8): 335-7. PubMed: 10904261.
PDF
210.
Towards a structural basis of human non-synonymous single nucleotide polymorphisms.
2000 May; 16(5): 198-200. PubMed: 10782110.
PDF
209.
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.
Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P
2000 Jul; 1(1): 53-8. PubMed: 11256625.
Abstract + PDF
208.
NAIL-Network Analysis Interface for Linking HMMER results.
2000 Jul; 16(7): 656-7. PubMed: 11038338.
Abstract + PDF
207.
DNA recognition, strand selectivity, and cleavage mode during integrase family site-specific recombination.
Tribble G, Ahn YT, Lee J, Dandekar T, Jayaram M
2000 Jul 21; 275(29): 22255-67. PubMed: 10748094.
Abstract + PDF
206.
A mitochondrial ancestry of the hydrogenosomes of Nyctotherus ovalis.
van Hoek AH, Akhmanova AS, Huynen MA, Hackstein JH
2000 Jan; 17(1): 202-6. PubMed: 10666720.
PDF
1999 44 publication(s).
205.
Position-specific annotation of protein function based on multiple homologs.
Abstract
204.
Automated genome sequence analysis and annotation.
Andrade MA, Brown NP, Leroy C, Hoersch S, de Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C
1999 May; 15(5): 391-412. PubMed: 10366660.
Abstract + PDF
203.
Functional classes in the three domains of life.
Andrade MA, Ouzounis C, Sander C, Tamames J, Valencia A
1999 Nov; 49(5): 551-7. PubMed: 10552036.
Abstract + PDF
202.
Applying logic programming to derive novel functional information of genomes.
In: lecture notes in computer sciences: Practical aspects of declarative languages. (Gupta, G.)1551 pp.275-289. BID: 7.
Publisher: Springer, New York
201.
A lipid-binding domain in Wnt: a case of mistaken identity?
Barnes MR, Russell RB, Copley RR, Ponting CP, Bork P, Cumberledge S, Reichsman F, Moore HM
1999 Oct 7; 9(19): R717-9. PubMed: 10531014.
PDF
200.
Automatic extraction of biological information from scientific text: protein-protein interactions.
Blaschke C, Andrade MA, Ouzounis C, Valencia A
Abstract
199.
Bioinformatik (editorial).
1999; 3: 172. PID: 302.
PDF
198.
Genome Comparsions to Monitor Molecular Evolution.
In: Microbial Evolution and Infection. (Goebel, U.B., Ruf, B.R.) pp.80-92. BID: 8.
Publisher: Einhorn-Presse Verlag Reinbek
197.
Domains in plexins: links to integrins and transcription factors.
Bork P, Doerks T, Springer TA, Snel B
1999 Jul; 24(7): 261-3. PubMed: 10390613.
PDF
196.
A point of entry into genomics. (book review).
1999 Nov 1; 23(3): 273. PID: 300.
PDF
195.
The gene for X-linked anhidrotic ectodermal dysplasia encodes a TNF-like domain.
1999 Apr; 77(4): 361-3. PubMed: 10353440.
194.
Phospholipases A2 and Wnts are unlikely to share a common ancestor.
Copley RR, Ponting CP, Bork P
1999 Oct 7; 9(19): R718-9. PubMed: 10712041.
PDF
193.
Protein families in multicellular organisms.
Copley RR, Schultz J, Ponting CP, Bork P
1999 Jun; 9(3): 408-15. PubMed: 10361098.
Abstract + PDF
192.
Analyzing the interplay between secondary and tertiary structure predictions in folding simulations with a genetic algorithm.
1999; 5: 78-89. PID: 341.
191.
Pathway alignment: application to the comparative analysis of glycolytic enzymes.
1999 Oct 1; 343 Pt 1: 115-24. PubMed: 10493919.
Abstract + PDF
190.
Prediction of potential GPI-modification sites in proprotein sequences.
1999 Sep 24; 292(3): 741-58. PubMed: 10497036.
Abstract + PDF
189.
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
1999 Jul-Aug; 15(7-8): 528-35. PubMed: 10487860.
Abstract + PDF
188.
Aligning sequences
Gibson TJ, Bork P
In: Encyclopedia of Molecular Biology (Ed. Thomas E. Creighton) pp.2320-2324. BID: 9.
ISBN: 0-471-15302-8 Publisher: John Wiley & Sons, Inc. A Wiley-Interscience Publication
Abstract + PDF
187.
Alternative splicing of human genes: more the rule than the exception?
Hanke J, Brett D, Zastrow I, Aydin A, Delbrück S, Lehmann G, Luft F, Reich J, Bork P
1999 Oct; 15(10): 389-90. PubMed: 10498933.
PDF
186.
Associative database of protein sequences.
Hanke J, Lehmann G, Bork P, Reich JG
1999 Sep; 15(9): 741-8. PubMed: 10498774.
Abstract + PDF
185.
Variation and evolution of the citric-acid cycle: a genomic perspective.
1999 Jul; 7(7): 281-91. PubMed: 10390638.
Abstract + PDF
184.
Lateral Gene Transfer, Genome Surveys and the Phylogeny of Prokaryotes.
1999 Nov 19; 286(5444): 1443. PID: 293.
Abstract + PDF
183.
Microinjected glutathione reductase crystals as indicators of the redox status in living cells.
Keese MA, Saffrich R, Dandekar T, Becker K, Schirmer RH
1999 Mar 26; 447(2-3): 135-8. PubMed: 10214933.
Abstract
182.
Mice lacking bombesin receptor subtype-3 develop metabolic defects and obesity (Condensation and commentary).
Kelly L, Sharma K, Dandekar T
1999; 12: 223-228. PID: 342.
181.
Fold recognition using sequence and secondary structure information.
Koretke KK, Russell RB, Copley RR, Lupas AN
1999; Suppl 3: 141-8. PubMed: 10526363.
Abstract
180.
Refined genetic algorithm simulations to model proteins.
König R, Dandekar T
1999; 5: 317-324. PID: 343.
179.
Improving genetic algorithms for protein folding simulations by systematic crossover.
König R, Dandekar T
1999 Apr; 50(1): 17-25. PubMed: 10235648.
Abstract
178.
The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins.
Liu Z, Macias MJ, Bottomley MJ, Stier G, Linge JP, Nilges M, Bork P, Sattler M
1999 Dec 15; 7(12): 1557-66. PubMed: 10647186.
Abstract + PDF
177.
Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster.
Liu Z, Song D, Kramer A, Martin AC, Dandekar T, Schneider-Mergener J, Bautz EK, Dübel S
1999; 12(2): 103-11. PubMed: 10398401.
Abstract
176.
A novel transactivation domain in parkin.
1999 Jun; 24(6): 229-31. PubMed: 10366851.
PDF
175.
Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures.
Müller SA, Sasaki T, Bork P, Wolpensinger B, Schulthess T, Timpl R, Engel A, Engel J
1999 Aug 27; 291(4): 801-13. PubMed: 10452890.
Abstract + PDF
174.
The mahogany protein is a receptor involved in suppression of obesity.
Nagle DL, McGrail SH, Vitale J, Woolf EA, Dussault BJ, DiRocco L, Holmgren L, Montagno J, Bork P, Huszar D, Fairchild-Huntress V, Ge P, Keilty J, Ebeling C, Baldini L, Gilchrist J, Burn P, Carlson GA, Moore KJ
1999 Mar 11; 398(6723): 148-52. PubMed: 10086355.
Abstract + PDF
173.
Pore-forming peptides of Entamoeba dispar. Similarity and divergence to amoebapores in structure, expression and activity.
Nickel R, Ott C, Dandekar T, Leippe M
1999 Nov; 265(3): 1002-7. PubMed: 10518795.
Abstract
172.
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Ponting CP, Aravind L, Schultz J, Bork P, Koonin EV
1999 Jun 18; 289(4): 729-45. PubMed: 10369758.
Abstract + PDF
171.
No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho.
Ponting CP, Bork P, Schultz J, Aravind L
1999 May; 24(5): 177-8. PubMed: 10322430.
PDF
170.
A latrophilin/CL-1-like GPS domain in polycystin-1.
Ponting CP, Hofmann K, Bork P
1999 Aug 26; 9(16): R585-8. PubMed: 10469603.
PDF
169.
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Ponting CP, Schultz J, Milpetz F, Bork P
1999 Jan 1; 27(1): 229-32. PubMed: 9847187.
Abstract + PDF
168.
Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering.
1999 Feb; 17(2): 53-60. PubMed: 10087604.
Abstract
167.
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
Smalla M, Schmieder P, Kelly M, Ter Laak A, Krause G, Ball L, Wahl M, Bork P, Oschkinat H
1999 Oct; 8(10): 1954-61. PubMed: 10548040.
Abstract + PDF
166.
Genome phylogeny based on gene content.
1999 Jan; 21(1): 108-10. PubMed: 9916801.
Abstract + PDF
165.
Quality-of-life assessment in the old using the WHOQOL 100: differences between patients with senile dementia and patients with cancer.
Struttmann T, Fabro M, Romieu G, de Roquefeuil G, Touchon J, Dandekar T, Ritchie K
1999 Sep; 11(3): 273-9. PubMed: 10547127.
Abstract
164.
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.
Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN
1999 May; 12(5): 387-94. PubMed: 10360979.
Abstract
163.
Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.
Sunyaev SR, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P
1999 Nov; 77(11): 754-60. PubMed: 10619435.
Abstract + PDF
162.
Neutral evolution of mutational robustness.
van Nimwegen E, Crutchfield JP, Huynen MA
1999 Aug 17; 96(17): 9716-20. PubMed: 10449760.
Abstract
1998 41 publication(s).
161.
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Andrade MA, Valencia A
1998; 14(7): 600-7. PubMed: 9730925.
Abstract
160.
Automated Pair-wise Comparisons of Microbial Genomes.
Bansal AK, Bork P, Stuckey P
PDF
159.
Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins.
Beckmann G, Hanke J, Bork P, Reich JG
1998 Feb 6; 275(5): 725-30. PubMed: 9480764.
Abstract + PDF
158.
Predicting function: from genes to genomes and back.
1998 Nov 6; 283(4): 707-25. PubMed: 9790834.
Abstract + PDF
157.
Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases.
1998 Feb; 76(2): 77-9. PubMed: 9500672.
PDF
156.
Sequences and Topology. Deriving biological knowledge from genomic sequence. (editorial overview)
Bork P, Eisenberg D
1998; 8: 331-332. PID: 348.
PDF
155.
Predicting functions from protein sequences--where are the bottlenecks?
Bork P, Koonin EV
1998 Apr; 18(4): 313-8. PubMed: 9537411.
Abstract + PDF
154.
Frame: detection of genomic sequencing errors.
Brown NP, Sander C, Bork P
1998; 14(4): 367-71. PubMed: 9632832.
Abstract + PDF
153.
Homology-based gene prediction using neural nets.
1998 Dec 15; 265(2): 269-74. PubMed: 9882402.
Abstract + PDF
152.
Structural Basis for the Binding of a Globular Antifreeze Protein to Ice (Review).
Dandekar T, Argos P
1998; 11: 229-232. PID: 349.
151.
Determination of the Fold of the Core Protein of Hepatitis B Virus by Electron Cryomicroscopy (Review).
Dandekar T, Argos P
1998; 11: 161-165. PID: 350.
150.
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Dandekar T, Beyer K, Bork P, Kenealy MR, Pantopoulos K, Hentze M, Sonntag-Buck V, Flouriot G, Gannon F, Schreiber S
1998; 14(3): 271-8. PubMed: 9614270.
Abstract + PDF
149.
Regulatory RNA.
Dandekar T, Sharma K
In: Regulatory RNA. (Hardcover) pp.1-262. BID: 10.
ISBN: 3-540-64343-5 Publisher: Springer Verlag, Heidelberg, Germany
148.
Conservation of gene order: a fingerprint of proteins that physically interact.
1998 Sep; 23(9): 324-8. PubMed: 9787636.
Abstract + PDF
147.
Protein annotation: detective work for function prediction.
Doerks T, Bairoch A, Bork P
1998 Jun; 14(6): 248-50. PubMed: 9635409.
PDF
146.
Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase.
1998 Dec; 11(12): 1155-61. PubMed: 9930665.
Abstract
145.
Stops Genejockeys being taken for a ride.
1998; 8: 377-378. PID: 351.
144.
Wanted: subcellular localization of proteins based on sequence.
1998 Apr; 8(4): 169-70. PubMed: 9695832.
PDF
143.
Sequence and Structure of Proteins.
In: Recombinant proteins, monoclonal antibodies and theraeutic genes (series Biotechnology, 2nd. Edition). (Rehm, H.-J. Reed, G+A. Mountain, U. Ney and D. Schomburg)5a pp.43-86. BID: 11.
Publisher: Wiley-VCH Weinheim
PDF
142.
The modelling of metabolic systems. Structure, control and optimality.
Heinrich R, Schuster S
1998; 47(1-2): 61-77. PubMed: 9715751.
Abstract
141.
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Hofacker IL, Fekete M, Flamm C, Huynen MA, Rauscher S, Stolorz PE, Stadler PF
1998 Aug 15; 26(16): 3825-36. PubMed: 9685502.
Abstract
140.
Measuring genome evolution.
1998 May 26; 95(11): 5849-56. PubMed: 9600883.
Abstract + PDF
139.
Differential genome analysis applied to the species-specific features of Helicobacter pylori.
1998 Apr 10; 426(1): 1-5. PubMed: 9598967.
Abstract + PDF
138.
Homology-based fold predictions for Mycoplasma genitalium proteins.
1998 Jul 17; 280(3): 323-6. PubMed: 9665839.
Abstract + PDF
137.
The frequency distribution of gene family sizes in complete genomes.
Huynen MA, van Nimwegen E
1998 May; 15(5): 583-9. PubMed: 9580988.
Abstract
136.
Isolation and molecular characterization of a surface-bound proteinase of Entamoeba histolytica.
Jacobs T, Bruchhaus I, Dandekar T, Tannich E, Leippe M
1998 Jan; 27(2): 269-76. PubMed: 9484883.
Abstract
135.
Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries.
Kharrat A, Millevoi S, Baraldi E, Ponting CP, Bork P, Pastore A
1998 Jun 11; 1385(1): 157-64. PubMed: 9630596.
Abstract + PDF
134.
Control analysis of metabolic systems involving quasi-equilibrium reactions.
Kholodenko BN, Schuster S, Garcia J, Westerhoff HV, Cascante M
1998 Mar 2; 1379(3): 337-52. PubMed: 9545597.
Abstract
133.
Mitochondria as an important factor in the maintenance of constant amplitudes of cytosolic calcium oscillations.
Marhl M, Schuster S, Brumen M
1998 Apr; 2(3): 125-32. PubMed: 12369585.
Abstract
132.
Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC.
1998 Aug 14; 433(1-2): 108-12. PubMed: 9738943.
Abstract + PDF
131.
Processing of the precursors to small nucleolar RNAs and rRNAs requires common components.
Petfalski E, Dandekar T, Henry Y, Tollervey D
1998 Mar; 18(3): 1181-9. PubMed: 9488433.
Abstract
130.
SMART, a simple modular architecture research tool: identification of signaling domains.
Schultz J, Milpetz F, Bork P, Ponting CP
1998 May 26; 95(11): 5857-64. PubMed: 9600884.
Abstract + PDF
129.
Elementary Modes Analysis Illustrated with Human Red Cell Metabolism.
Schuster S, Fell DA, Pfeiffer T, Dandekar T, Bork P
In: BioThermoKinetics in the Post Genomic Era. (C. Larsson, I.-L. Pahlman and L. Gustafsson, eds.) pp.332-339. BID: 12.
Publisher: Chalmers, Goeteborg
128.
Influence of Calcium Binding to Proteins on Calcium Oscillations and ER Membrane Potential Oscillations. A Mathematical Model.
Schuster S, Marhl M, Brumen M, Heinrich R
In: Information Processing in Cells and Tissues. (R. Paton and M. Holcombe) pp.137-150. BID: 13.
Publisher: Plenum Press, New York
127.
Modelling the interrelation between the transmembrane potential and pH difference across membranes with electrogenic proton transport upon build-up of the proton-motive force.
Schuster S, Ouhabi R, Rigoulet M, Mazat JP
1998; 45: 181-192. PID: 357.
126.
Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis.
Schwirzke M, Gnirke A, Bork P, Tarin D, Weidle UH
1998 May-Jun; 18(3A): 1409-21. PubMed: 9673349.
Abstract + PDF
125.
Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?
Sunyaev SR, Eisenhaber F, Argos P, Kuznetsov EN, Tumanyan VG
1998 May 15; 31(3): 225-46. PubMed: 9593195.
Abstract
124.
Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
Trelles O, Andrade MA, Valencia A, Zapata EL, Carazo JM
1998 Jun; 14(5): 439-51. PubMed: 9682057.
Abstract
123.
Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues.
Willeke F, Ridder R, Bork P, Klaes R, Mechtersheimer G, Schwarzbach M, Zimmer D, Kloor M, Lehnert T, Herfarth C, von Knebel Doeberitz M
1998 Dec; 23(4): 195-200. PubMed: 9869447.
Abstract + PDF
122.
Towards detection of orthologues in sequence databases.
Yuan YP, Eulenstein O, Vingron M, Bork P
1998; 14(3): 285-9. PubMed: 9614272.
Abstract + PDF
121.
A pyrimidine-rich exonic splicing suppressor binds multiple RNA splicing factors and inhibits spliceosome assembly.
Zheng ZM, Huynen MA, Baker CC
1998 Nov 24; 95(24): 14088-93. PubMed: 9826658.
Abstract
1997 26 publication(s).
120.
RNA ligands selected by cleavage stimulation factor contain distinct sequence motifs that function as downstream elements in 3'-end processing of pre-mRNA.
Beyer K, Dandekar T, Keller W
1997 Oct 17; 272(42): 26769-79. PubMed: 9334264.
Abstract + PDF
119.
Bioinformatics and molecular medicine--introduction and call for papers.
1997 Jan; 75(1): 3-4. PubMed: 9020378.
PDF
118.
Comparative genome analysis: From sequences to functions.
1997; 34: 21-23. PID: 361.
PDF
117.
A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins.
Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV
1997 Jan; 11(1): 68-76. PubMed: 9034168.
Abstract + PDF
116.
Cytoplasmic signalling domains: the next generation.
Bork P, Schultz J, Ponting CP
1997 Aug; 22(8): 296-8. PubMed: 9270302.
Abstract + PDF
115.
Artificial neural network method for predicting the specificity of GalNAc-transferase.
Cai YD, Yu H, Chou KC
1997 Oct; 16(7): 689-700. PubMed: 9330227.
Abstract
114.
Probabilistic evaluation of similarity between pairs of three-dimensional structures utilizing temperature factors.
Carugo O, Eisenhaber F
1997 Oct 1; 30(5): 547-549. PID: 299.
113.
Free radicals and memory loss.
1997; 3: 71-73. PID: 368.
112.
Improving protein structure prediction by new strategies, experimental insights and the genetic algorithm.
1997; 3: 312-314. PID: 367.
111.
Applying experimental data to protein fold prediction with the genetic algorithm.
Dandekar T, Argos P
1997 Aug; 10(8): 877-93. PubMed: 9415438.
Abstract
110.
Computational methods for the prediction of protein folds.
Dandekar T, König R
1997 Nov 14; 1343(1): 1-15. PubMed: 9428653.
109.
Molecular modeling of amoebapore and NK-lysin: a four-alpha-helix bundle motif of cytolytic peptides from distantly related organisms.
Dandekar T, Leippe M
1997; 2(1): 47-52. PubMed: 9080198.
Abstract
108.
Genome maps 8. Building gene families. Wall chart.
Green EA, Pietrokovski S, Henikoff S, Bork P, Attwood T, Hood L, Bairoch A
1997 Oct 24; 278(5338): 615-30. PubMed: 9381172.
107.
A novel class of RanGTP binding proteins.
Görlich D, Dabrowski M, Bischoff FR, Kutay U, Bork P, Hartmann E, Prehn S, Izaurralde E
1997 Jul 14; 138(1): 65-80. PubMed: 9214382.
Abstract + PDF
106.
On the classification and evolution of protein modules.
1997 Jul; 16(5): 545-51. PubMed: 9246642.
Abstract + PDF
105.
The Sequence Alerting Server--a new WEB server.
1997 Dec; 13(6): 619-20. PubMed: 9475991.
Abstract + PDF
104.
Gene families: the taxonomy of protein paralogs and chimeras.
Henikoff S, Greene EA, Pietrokovski S, Bork P, Attwood TK, Hood L
1997 Oct 24; 278(5338): 609-14. PubMed: 9381171.
Abstract + PDF
103.
Differential genome display.
1997 Oct; 13(10): 389-90. PubMed: 9351339.
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102.
Assessing the reliability of RNA folding using statistical mechanics.
Huynen MA, Gutell R, Konings D
1997 Apr 18; 267(5): 1104-12. PubMed: 9150399.
Abstract
101.
A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases.
Morozov VM, Mushegian AR, Koonin EV, Bork P
1997 Nov; 22(11): 417-8. PubMed: 9397680.
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100.
Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs.
Mushegian AR, Bassett DE, Boguski MS, Bork P, Koonin EV
1997 May 27; 94(11): 5831-6. PubMed: 9159160.
Abstract + PDF
99.
SPRY domains in ryanodine receptors (Ca(2+)-release channels).
1997 Jun; 22(6): 193-4. PubMed: 9204703.
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98.
The breast cancer gene product TSG101: a regulator of ubiquitination?
Ponting CP, Cai YD, Bork P
1997 Jul; 75(7): 467-9. PubMed: 9253709.
Abstract + PDF
97.
Probing Flp: a new approach to analyze the structure of a DNA recognizing protein by combining the genetic algorithm, mutagenesis and non-canonical DNA target sites.
Saxena P, Whang I, Voziyanov Y, Harkey C, Argos P, Jayaram M, Dandekar T
1997 Jul 18; 1340(2): 187-204. PubMed: 9252106.
Abstract
96.
SAM as a protein interaction domain involved in developmental regulation.
Schultz J, Ponting CP, Hofmann K, Bork P
1997 Jan; 6(1): 249-53. PubMed: 9007998.
Abstract + PDF
95.
Secreted fringe-like signaling molecules may be glycosyltransferases.
Yuan YP, Schultz J, Mlodzik M, Bork P
1997 Jan 10; 88(1): 9-11. PubMed: 9019410.
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1996 33 publication(s).
94.
On exon shuffling and other mechanisms of domain rearrangements.
1996; 15: 311-12. PID: 370.
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93.
Sperm-egg binding protein or proto-oncogene?
1996 Mar 8; 271(5254): 1431-2; author reply 1434-5. PubMed: 8596918.
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92.
Von Genomsequenzen zu Proteinfunktionen.
1996; 5: 20-26. PID: 369.
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91.
Go hunting in sequence databases but watch out for the traps.
Bork P, Bairoch A
1996 Oct; 12(10): 425-7. PubMed: 8909140.
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90.
Internal repeats in the BRCA2 protein sequence.
Bork P, Blomberg N, Nilges M
1996 May; 13(1): 22-3. PubMed: 8673099.
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89.
The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues.
1996 Jul; 5(7): 1421-5. PubMed: 8819174.
Abstract + PDF
88.
Structure and distribution of modules in extracellular proteins.
Bork P, Downing AK, Kieffer B, Campbell ID
1996 May; 29(2): 119-67. PubMed: 8870072.
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87.
Applying motif and profile searches.
Bork P, Gibson TJ
1996; 266: 162-84. PubMed: 8743684.
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86.
Protein sequence motifs.
Bork P, Koonin EV
1996 Jun; 6(3): 366-76. PubMed: 8804823.
Abstract + PDF
85.
Nahua indian medicinal plants (Mexico): Inhibitory activity on NF-κB as an anti-inflammatory model and antibacterial effects.
Bork PM, Schmitz ML, Weimann C, Kist M, Heinrich M
1996 Nov; 3(3): 263-9. PubMed: 23195081.
Abstract
84.
Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions.
Dandekar T, Argos P
1996 Mar 1; 256(3): 645-60. PubMed: 8604145.
Abstract
83.
Hydrophobic regions on protein surfaces. Derivation of the solvation energy from their area distribution in crystallographic protein structures.
1996 Aug; 5(8): 1676-86. PubMed: 8844856.
Abstract
82.
Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation.
Eisenhaber F, Argos P
1996 Dec; 9(12): 1121-33. PubMed: 9010925.
Abstract
81.
Prediction of secondary structural content of proteins from their amino acid composition alone. II. The paradox with secondary structural class.
Eisenhaber F, Frömmel C, Argos P
1996 Jun; 25(2): 169-79. PubMed: 8811733.
Abstract
80.
Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytic vector decomposition methods.
Eisenhaber F, Imperiale F, Argos P, Frömmel C
1996 Jun; 25(2): 157-68. PubMed: 8811732.
Abstract
79.
Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction.
Gibson TJ, Koonin EV, Musco G, Pastore A, Bork P
1996 Nov; 19(11): 465-8. PubMed: 8931268.
Abstract + PDF
78.
Self-organizing hierarchic networks for pattern recognition in protein sequence.
Hanke J, Beckmann G, Bork P, Reich JG
1996 Jan; 5(1): 72-82. PubMed: 8771198.
Abstract + PDF
77.
On the classification of modular proteins.
Henrissat B, Bork P
1996 Sep; 9(9): 725-6. PubMed: 8888136.
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76.
Exploring phenotype space through neutral evolution.
1996 Sep; 43(3): 165-9. PubMed: 8703081.
Abstract
75.
Rate of killing of HIV-infected T cells and disease progression.
Huynen MA, Neumann AU
1996 Jun 28; 272(5270): 1962. PubMed: 8658174.
74.
Base pairing probabilities in a complete HIV-1 RNA.
Huynen MA, Perelson A, Vieira WA, Stadler PF
1996; 3(2): 253-74. PubMed: 8811486.
Abstract
73.
Smoothness within ruggedness: the role of neutrality in adaptation.
Huynen MA, Stadler PF, Fontana W
1996 Jan 9; 93(1): 397-401. PubMed: 8552647.
Abstract
72.
BRCA1 protein products ... Functional motifs...
Koonin EV, Altschul SF, Bork P
1996 Jul; 13(3): 266-8. PubMed: 8673121.
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71.
Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes.
Koonin EV, Bork P
1996 Apr; 21(4): 128-9. PubMed: 8701468.
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70.
Non-orthologous gene displacement.
Koonin EV, Mushegian AR, Bork P
1996 Sep; 12(9): 334-6. PubMed: 8855656.
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69.
Structural motifs of the PKD1 protein.
Löhning C, Pohlschmidt M, Glücksmann-Kuis MA, Duyk G, Bork P, Schneider MO, Reeders ST, Frischauf AM
1996; 11 Suppl 6: 2-4. PubMed: 9044318.
Abstract + PDF
68.
[Structure-activity analysis of amino acid sequences using the Internet]
1996; 30(2): 387-93. PubMed: 8724771.
67.
Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome.
Nagle DL, Karim MA, Woolf EA, Holmgren L, Bork P, Misumi DJ, McGrail SH, Dussault BJ, Perou CM, Boissy RE, Duyk GM, Spritz RA, Moore KJ
1996 Nov; 14(3): 307-11. PubMed: 8896560.
Abstract + PDF
66.
Comparison of CD45 extracellular domain sequences from divergent vertebrate species suggests the conservation of three fibronectin type III domains.
Okumura M, Matthews RJ, Robb B, Litman GW, Bork P, Thomas ML
1996 Aug 15; 157(4): 1569-75. PubMed: 8759740.
Abstract + PDF
65.
Pleckstrin's repeat performance: a novel domain in G-protein signaling?
Ponting CP, Bork P
1996 Jul; 21(7): 245-6. PubMed: 8755244.
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64.
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli.
Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV
1996 Mar 1; 6(3): 279-91. PubMed: 8805245.
Abstract + PDF
63.
Principles of helix-helix packing in proteins: the helical lattice superposition model.
Walther D, Eisenhaber F, Argos P
1996 Jan 26; 255(3): 536-53. PubMed: 8568896.
Abstract
62.
Identification of residues within the SHC phosphotyrosine binding/phosphotyrosine interaction domain crucial for phosphopeptide interaction.
Yajnik V, Blaikie P, Bork P, Margolis B
1996 Jan 26; 271(4): 1813-6. PubMed: 8567619.
Abstract + PDF
1995 12 publication(s).
61.
HEAT repeats in the Huntington's disease protein.
1995 Oct; 11(2): 115-6. PubMed: 7550332.
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60.
Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
Bork P, Gellerich J, Groth H, Hooft R, Martin F
1995 Feb; 4(2): 268-74. PubMed: 7757015.
Abstract + PDF
59.
The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction.
Bork P, Holm L, Koonin EV, Sander C
1995 Jul; 22(3): 259-66. PubMed: 7479698.
Abstract + PDF
58.
A phosphotyrosine interaction domain.
Bork P, Margolis B
1995 Mar 10; 80(5): 693-4. PubMed: 7534213.
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57.
Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology.
Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM
1995 Jun; 16(5): 955-67. PubMed: 7476192.
Abstract + PDF
56.
Ready for a motif submission? A proposed checklist.
Bork P, Ouzounis C, McEntyre J
1995 Mar; 20(3): 104. PubMed: 7709426.
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55.
The SEA module: a new extracellular domain associated with O-glycosylation.
Bork P, Patthy L
1995 Jul; 4(7): 1421-5. PubMed: 7670383.
Abstract + PDF
54.
Challenging times for bioinformatics.
Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C
1995 Aug 24; 376(6542): 647-8. PubMed: 7651513.
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53.
Polycystic kidney disease: the complete structure of the PKD1 gene and its protein. The International Polycystic Kidney Disease Consortium.
Glücksmann-Kuis MA, Tayber O, Woolf EA, Bougueleret L, Deng NH, Alperin GD, Iris F, Lakey N, Duyk G, Schneider MC, Geng L, Zhang F, Zhao ZH, Torosian S, Zhou J, Reeders ST, Bork P, Pohlschmidt M, Löhning C, Kraus B, Nowicka U, Leung ALS, Frischauf AM
1995 Apr 21; 81(2): 289-98. PubMed: 7736581.
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52.
New protein functions in yeast chromosome VIII.
Ouzounis C, Bork P, Casari G, Sander C
1995 Nov; 4(11): 2424-8. PubMed: 8563640.
Abstract + PDF
51.
Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain.
Sudol M, Bork P, Einbond A, Kastury K, Druck T, Negrini M, Huebner K, Lehman D
1995 Jun 16; 270(24): 14733-41. PubMed: 7782338.
Abstract + PDF
50.
Characterization of a novel protein-binding module--the WW domain.
Sudol M, Chen HI, Bougeret C, Einbond A, Bork P
1995 Aug 1; 369(1): 67-71. PubMed: 7641887.
Abstract + PDF
1994 13 publication(s).
49.
Drosophila kelch motif is derived from a common enzyme fold.
Bork P, Doolittle RF
1994 Mar 11; 236(5): 1277-82. PubMed: 8126718.
Abstract + PDF
48.
The immunoglobulin fold. Structural classification, sequence patterns and common core.
Bork P, Holm L, Sander C
1994 Sep 30; 242(4): 309-20. PubMed: 7932691.
Abstract + PDF
47.
A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity.
Bork P, Koonin EV
1994 Dec; 20(4): 347-55. PubMed: 7731953.
Abstract + PDF
46.
A new family of carbon-nitrogen hydrolases.
Bork P, Koonin EV
1994 Aug; 3(8): 1344-6. PubMed: 7987228.
Abstract + PDF
45.
Sequenzvergleiche in der Genomanalyse
Bork P, Ouzounis C, Casari G, Sander C, Gillevet PM
44.
The WW domain: a signalling site in dystrophin?
Bork P, Sudol M
1994 Dec; 19(12): 531-3. PubMed: 7846762.
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43.
FMN- or DNA-binding?
Koonin EV, Bork P
1994 Jun; 19(6): 234-5. PubMed: 8073499.
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42.
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
Koonin EV, Bork P, Sander C
1994 Jun 11; 22(11): 2166-7. PubMed: 7518079.
Abstract + PDF
41.
Yeast chromosome III: new gene functions.
Koonin EV, Bork P, Sander C
1994 Feb 1; 13(3): 493-503. PubMed: 8313894.
Abstract + PDF
40.
Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain--study of a diverse, ancient protein superfamily using motif search and structural modeling.
Koonin EV, Mushegian AR, Tatusov RL, Altschul SF, Bryant SH, Bork P, Valencia A
1994 Nov; 3(11): 2045-54. PubMed: 7703850.
Abstract + PDF
39.
Tracing the spread of fibronectin type III domains in bacterial glycohydrolases.
Little E, Bork P, Doolittle RF
1994 Dec; 39(6): 631-43. PubMed: 7528812.
Abstract + PDF
38.
The modular structure of NifU proteins.
Ouzounis C, Bork P, Sander C
1994 May; 19(5): 199-200. PubMed: 8048161.
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37.
GeneQuiz: a workbench for sequence analysis.
Scharf M, Schneider R, Casari G, Bork P, Valencia A, Ouzounis C, Sander C
Abstract + PDF
1993 17 publication(s).
36.
An adhesive domain detected in functionally diverse receptors.
Beckmann G, Bork P
1993 Feb; 18(2): 40-1. PubMed: 8387703.
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35.
Entschlüsselung von Proteinfunktion mit Hilfe des Computers: Erkennung und Interpretation entfernter Sequenzähnlichkeiten.
In: Informatik aktuell - Informatik in den Biowissenschaften, (eds. Ralf Hofestädt, Fritz Krückeberg, Thomas Lengauer) pp.67-78. BID: 16.
Publisher: Springer Verlag
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34.
The modular architecture of a new family of growth regulators related to connective tissue growth factor.
1993 Jul 26; 327(2): 125-30. PubMed: 7687569.
Abstract + PDF
33.
Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally?
1993 Dec; 17(4): 363-74. PubMed: 8108379.
Abstract + PDF
32.
Monitoring the Evolution of Protein Modules by Sequence Analysis
In: Futura Informationen aus dem Boehringer Ingelheim Fonds4 pp.45-47. BID: 17.
ISBN: 01796372 Publisher:
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31.
A trefoil domain in the major rabbit zona pellucida protein.
1993 Apr; 2(4): 669-70. PubMed: 8518738.
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30.
The CUB domain. A widespread module in developmentally regulated proteins.
Bork P, Beckmann G
1993 May 20; 231(2): 539-45. PubMed: 8510165.
Abstract + PDF
29.
Fibronectin type III modules in the receptor phosphatase CD45 and tapeworm antigens.
Bork P, Doolittle RF
1993 Jul; 2(7): 1185-7. PubMed: 8358302.
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28.
An expanding family of helicases within the 'DEAD/H' superfamily.
Bork P, Koonin EV
1993 Feb 11; 21(3): 751-2. PubMed: 8382805.
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27.
A hybrid protein kinase-RNase in an interferon-induced pathway?
Bork P, Sander C
1993 Nov 15; 334(2): 149-52. PubMed: 7693513.
Abstract + PDF
26.
Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases.
Bork P, Sander C, Valencia A
1993 Jan; 2(1): 31-40. PubMed: 8382990.
Abstract + PDF
25.
Epidermal growth factor-like modules.
Campbell ID, Bork P
1993; 3: 385-92. PID: 374.
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24.
Evolutionarily mobile modules in proteins.
Doolittle RF, Bork P
1993 Oct; 269(4): 50-6. PubMed: 8235550.
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23.
Prokaryotic members of a new family of putative helicases with similarity to transcription activator SNF2.
Kolstø AB, Bork P, Kvaløy K, Lindback T, Grønstadt A, Kristensen T, Sander C
1993 Mar 20; 230(2): 684-8. PubMed: 8464078.
Abstract + PDF
22.
Molecular modelling of the Norrie disease protein predicts a cystine knot growth factor tertiary structure.
Meitinger T, Meindl A, Bork P, Rost B, Sander C, Haasemann M, Murken J
1993 Dec; 5(4): 376-80. PubMed: 8298646.
Abstract + PDF
21.
Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily.
Reizer J, Reizer A, Saier MH, Bork P, Sander C
1993 Jul; 18(7): 247-8. PubMed: 8212131.
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20.
A fast, sensitive pattern-matching approach for protein sequences.
Rohde K, Bork P
1993 Apr; 9(2): 183-9. PubMed: 8481821.
Abstract + PDF
1992 9 publication(s).
19.
Mobile modules and motifs.
1992; 2: 413-21. PID: 373.
18.
The modular architecture of vertebrate collagens.
1992 Jul 27; 307(1): 49-54. PubMed: 1639194.
Abstract + PDF
17.
Proposed acquisition of an animal protein domain by bacteria.
Bork P, Doolittle RF
1992 Oct 1; 89(19): 8990-4. PubMed: 1409594.
Abstract + PDF
16.
Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.
Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E
1992 Dec; 1(12): 1677-90. PubMed: 1304897.
Abstract + PDF
15.
What's in a genome?
Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E
1992 Jul 23; 358(6384): 287. PubMed: 1641000.
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14.
A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
Bork P, Sander C
1992 Apr 6; 300(3): 237-40. PubMed: 1313375.
Abstract + PDF
13.
An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.
Bork P, Sander C, Valencia A
1992 Aug 15; 89(16): 7290-4. PubMed: 1323828.
Abstract + PDF
12.
A module of the DnaJ heat shock proteins found in malaria parasites.
Bork P, Sander C, Valencia A, Bukau B
1992 Apr; 17(4): 129. PubMed: 1585456.
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11.
Cloning of a gene from Bacillus cereus with homology to the mreB gene from Escherichia coli.
Narahara A, Naterstad K, Kristensen T, Lopez R, Bork P, Kolstø AB
1992 Dec 1; 122(1): 181-5. PubMed: 1452027.
Abstract + PDF
1991 5 publication(s).
10.
Shuffled domains in extracellular proteins.
1991 Jul 29; 286(1-2): 47-54. PubMed: 1864378.
Abstract + PDF
9.
Complement components C1r/C1s, bone morphogenic protein 1 and Xenopus laevis developmentally regulated protein UVS.2 share common repeats.
1991 Apr 22; 282(1): 9-12. PubMed: 2026272.
Abstract + PDF
8.
On alpha-helices terminated by glycine. 2. Recognition by sequence patterns.
Bork P, Preissner R
1991 Oct 31; 180(2): 666-72. PubMed: 1953738.
Abstract + PDF
7.
More von Willebrand factor type A domains? Sequence similarities with malaria thrombospondin-related anonymous protein, dihydropyridine-sensitive calcium channel and inter-alpha-trypsin inhibitor.
Bork P, Rohde K
1991 Nov 1; 279 ( Pt 3): 908-10. PubMed: 1659389.
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6.
On alpha-helices terminated by glycine. 1. Identification of common structural features.
Preissner R, Bork P
1991 Oct 31; 180(2): 660-5. PubMed: 1953737.
Abstract + PDF
1990 3 publication(s).
5.
Erkennung und Nutzung von Eigenschaftensmustern in Proteinsequenzen
In: Dissertation A, Universität LeipzigBID: 15.
Publisher: -
4.
Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach.
Bork P, Grunwald C
1990 Jul 31; 191(2): 347-58. PubMed: 2384083.
Abstract + PDF
3.
Sequence similarities between tryptophan synthase beta subunit and other pyridoxal-phosphate-dependent enzymes.
Bork P, Rohde K
1990 Sep 28; 171(3): 1319-25. PubMed: 2222447.
Abstract + PDF
1989 2 publication(s).
2.
Recognition of functional regions in primary structures using a set of property patterns.
1989 Oct 23; 257(1): 191-5. PubMed: 2806560.
Abstract + PDF
1.
A method for property pattern searches in protein sequence databases, demonstrated by detection of GTP binding sites.
Bork P, Grunwald C
1989; 129: 231-240. PID: 304.
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