Publications of P. Bork

Publications of P. Bork

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2023 6 publication(s).
694.
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
693.
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
692.
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
691.
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
690.
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
689.
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 Feb 25; [Epub ahead of print] PubMed: 36849086.
Abstract
2022 19 publication(s).
688.
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
687.
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.
Abstract + PDF
686.
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.
Abstract + PDF
685.
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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684.
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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683.
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.
Khedkar S, Smyshlyaev G, Letunic I, Maistrenko OM, Coelho LP, Orakov A, Forslund SK, Hildebrand F, Luetge M, Schmidt TSB, Barabas O, Bork P
2022 Apr 8; 50(6): 3155-3168. PubMed: 35323968.
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682.
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.
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681.
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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680.
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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679.
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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678.
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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677.
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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676.
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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675.
Dissecting the intracellular pancreatic tumor microbiome at single-cell level.
Schmidt TSB, Bork P
2022 Oct 10; 40(10): 1083-1085. PubMed: 36179685.
Abstract
674.
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.
Abstract + PDF
673.
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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672.
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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671.
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.
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670.
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 34 publication(s).
669.
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.
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668.
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.
Abstract + PDF
667.
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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666.
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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665.
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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664.
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.
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663.
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.
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662.
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.
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661.
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.
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660.
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.
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659.
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.
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658.
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.
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657.
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.
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656.
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.
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655.
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
654.
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.
Letunic I, Bork P
2021 Jul 2; 49(W1): W293-W296. PubMed: 33885785.
Abstract + PDF
653.
SMART: recent updates, new developments and status in 2020.
2021 Jan 8; 49(D1): D458-D460. PubMed: 33104802.
Abstract + PDF
652.
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
651.
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
650.
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
649.
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
648.
GUNC: detection of chimerism and contamination in prokaryotic genomes.
2021 Jun 13; 22(1): 178. PubMed: 34120611.
Abstract + PDF
647.
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
646.
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
645.
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.
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644.
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
643.
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
642.
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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641.
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
640.
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
639.
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
638.
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
637.
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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636.
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.
Abstract + PDF
2020 15 publication(s).
635.
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.
Abstract + PDF
634.
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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633.
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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632.
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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631.
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
2020 May 11; 14(5): 1247-1259. PubMed: 32047279.
Abstract + PDF
630.
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
629.
(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
628.
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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627.
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
626.
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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625.
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.
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624.
Tara Oceans: towards global ocean ecosystems biology.
Sunagawa S, Acinas SG, Bork P, Bowler C
2020 Aug 12; 18(8): 428-445. PubMed: 32398798.
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623.
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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622.
Diversity within species: interpreting strains in microbiomes.
2020 Sep 4; 18(9): 491-506. PubMed: 32499497.
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621.
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.
Abstract + PDF
2019 26 publication(s).
620.
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.
PDF
619.
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.
PDF
618.
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
617.
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
616.
[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
615.
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
614.
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.
Abstract + PDF
613.
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.
Abstract + PDF
612.
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.
Abstract + PDF
611.
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
610.
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
609.
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
608.
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
607.
Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Letunic I, Bork P
2019 Jul 2; 47: W256-W259. PubMed: 30931475.
Abstract + PDF
606.
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
605.
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
604.
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
603.
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
602.
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
601.
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
600.
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
599.
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.
Abstract + PDF
598.
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.
Abstract + PDF
597.
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.
Abstract + PDF
596.
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.
Abstract + PDF
595.
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.
Abstract + PDF
2018 27 publication(s).
594.
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.
Abstract + PDF
593.
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.
Abstract + PDF
592.
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.
PDF
591.
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.
PDF
590.
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.
Abstract + PDF
589.
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.
Abstract + PDF
588.
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.
Abstract + PDF
587.
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
586.
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
585.
iPath3.0: interactive pathways explorer v3.
Darzi Y, Letunic I, Bork P, Yamada T
2018 Jul 2; 46: W510-W513. PubMed: 29718427.
Abstract + PDF
584.
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
583.
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
582.
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
581.
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
580.
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
579.
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
578.
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
577.
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
576.
20 years of the SMART protein domain annotation resource.
Letunic I, Bork P
2018 Jan 4; 46: D493-D496. PubMed: 29040681.
Abstract + PDF
575.
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
574.
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
573.
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
572.
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
571.
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
570.
The Human Gut Microbiome: From Association to Modulation.
2018 Mar 8; 172(6): 1198-1215. PubMed: 29522742.
Abstract + PDF
569.
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
568.
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 25 publication(s).
567.
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
566.
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
565.
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
564.
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
563.
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
562.
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
561.
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
560.
Subspecies in the global human gut microbiome.
2017 Dec 14; 13(12): 960. PubMed: 29242367.
Abstract + PDF
559.
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
558.
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
557.
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
556.
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
555.
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
2017 Aug 1; 34(8): 2115-2122. PubMed: 28460117.
Abstract + PDF
554.
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
553.
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
552.
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
551.
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
550.
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
549.
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
2017 Jan 4; 45(D1): D529-D534. PubMed: 28053165.
Abstract + PDF
548.
Bioinformatics Analysis of Functional Associations of PTMs.
Minguez P, Bork P
2017; 1558: 303-320. PubMed: 28150244.
Abstract + PDF
547.
RTK: efficient rarefaction analysis of large datasets.
Saary P, Forslund K, Bork P, Hildebrand F
2017 Aug 15; 33(16): 2594-2595. PubMed: 28398468.
Abstract + PDF
546.
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
545.
[Microbial Biomarkers for Early Cancer Detection].
2017 Feb; 142(4): 267-274. PubMed: 28235227.
Abstract + PDF
544.
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
543.
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 26 publication(s).
542.
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
541.
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
540.
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
539.
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
538.
CART - a chemical annotation retrieval toolkit.
2016 Sep 15; 32(18): 2869-71. Epub 2016 Jun 2; PubMed: 27256313.
Abstract + PDF
537.
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
536.
ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas J, Serra F, Bork P
2016 Jun 26; 33(6): 1635-8. Epub 2016 Feb 26; PubMed: 26921390.
Abstract + PDF
535.
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P
2016 Jan 4; 44: D286-93. Epub 2015 Nov 17; PubMed: 26582926.
Abstract + PDF
534.
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
533.
The SIDER database of drugs and side effects.
2016 Jan 4; 44: D1075-9. Epub 2015 Oct 19; PubMed: 26481350.
Abstract + PDF
532.
MOCAT2: a metagenomic assembly, annotation and profiling framework.
2016 Aug 15; 32(16): 2520-3. Epub 2016 Apr 8; PubMed: 27153620.
Abstract + PDF
531.
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Letunic I, Bork P
2016 Jul 8; 44: W242-5. Epub 2016 Apr 19; PubMed: 27095192.
Abstract + PDF
530.
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
529.
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
528.
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
527.
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
526.
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
525.
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
524.
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
523.
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
522.
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
521.
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
520.
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
519.
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
518.
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
517.
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 30 publication(s).
516.
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
515.
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
514.
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
513.
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
512.
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
511.
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
510.
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
509.
Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer.
2015 Apr-Jun; 2(2): e975080. PubMed: 27308430.
Abstract + PDF
508.
SMART: recent updates, new developments and status in 2015.
2015 Jan 28; 43: D257-60. Epub 2014 Oct 9; PubMed: 25300481.
Abstract + PDF
507.
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.
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506.
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
505.
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
504.
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
503.
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
502.
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
501.
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
500.
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
499.
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
498.
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
497.
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
496.
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
495.
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
494.
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
493.
Temporal and technical variability of human gut metagenomes.
2015 Apr 8; 16(1): 73. Epub 2015 Apr 8; PubMed: 25888008.
Abstract + PDF
492.
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
491.
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
490.
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
489.
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
488.
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
487.
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 20 publication(s).
486.
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
485.
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
484.
Blick zurück in die Zukunft der Bioinformatik
Bork P
In: Laborjournal7-8 2014(7-8) pp.73-75. BID: 22.
Publisher:
Abstract + PDF
483.
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
2014 Jul; 10(7): e1003758. PubMed: 25077479.
PDF
482.
A fair comparison.
2014 Apr 28; 11(4): 359. PubMed: 24681719.
PDF
481.
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
480.
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
479.
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
478.
LotuS: an efficient and user-friendly OTU processing pipeline.
Hildebrand F, Tadeo R, Voigt AY, Bork P, Raes J
2014 Sep 30; 2(1): 30. Epub 2014 Sep 30; PubMed: 27367037.
Abstract + PDF
477.
Correction: LotuS: an efficient and user-friendly OTU processing pipeline.
Hildebrand F, Tito RY, Voigt AY, Bork P, Raes J
2014; 2: 37. PubMed: 25317332.
Abstract + PDF
476.
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
475.
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
474.
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
473.
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
472.
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
471.
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
470.
A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation.
2014; 9(11): e111122. PubMed: 25369365.
Abstract + PDF
469.
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
468.
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
467.
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 19 publication(s).
466.
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
465.
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
464.
Human monogenic disease genes have frequently functionally redundant paralogs.
2013 May; 9(5): e1003073. PubMed: 23696728.
Abstract + PDF
463.
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.
Abstract + PDF
462.
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
461.
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
460.
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
459.
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
458.
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
457.
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
456.
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
455.
Accurate and universal delineation of prokaryotic species.
2013 Sep 28; 10(9): 881-4. Epub 2013 Jul 28; PubMed: 23892899.
Abstract + PDF
454.
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
453.
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
452.
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
451.
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
450.
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
449.
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
448.
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 18 publication(s).
447.
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
446.
OGEE: an online gene essentiality database.
2012 Jan 10; 40(Database issue): D901-6. Epub 2011 Nov 10; PubMed: 22075992.
Abstract + PDF
445.
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
444.
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
443.
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
442.
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
441.
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
440.
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
439.
STITCH 3: zooming in on protein-chemical interactions.
Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P
2012 Jan 1; 40: D876-80. Epub 2011 Nov 9; PubMed: 22075997.
Abstract + PDF
438.
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
437.
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
436.
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
435.
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
434.
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
433.
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
432.
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
431.
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
430.
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 15 publication(s).
429.
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
428.
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
427.
Consider Context
Bork P
2011 Mar 18; 144(6): 838. PID: 527.
PDF
426.
Network neighbors of drug targets contribute to drug side-effect similarity.
2011; 6(7): e22187. PubMed: 21765950.
Abstract + PDF
425.
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
424.
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
423.
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
422.
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
421.
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
Letunic I, Bork P
2011 Jul 5; 39 Suppl 2: W475-8. Epub 2011 Apr 5; PubMed: 21470960.
Abstract + PDF
420.
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
2011 Mar 15; 7: 473. PubMed: 21407210.
Abstract + PDF
419.
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
418.
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
417.
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
416.
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
415.
Prediction of drug combinations by integrating molecular and pharmacological data.
2011 Dec; 7(12): e1002323. PubMed: 22219721.
Abstract + PDF
2010 18 publication(s).
414.
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
413.
SmashCommunity: A metagenomic annotation and analysis tool.
2010 Dec 1; 26(23): 2977-8. Epub 2010 Oct 19; PubMed: 20959381.
Abstract + PDF
412.
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
411.
[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
410.
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
409.
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
408.
SmashCell: A software framework for the analysis of single-cell amplified genome sequences.
Harrington ED, Arumugam M, Raes J, Bork P, Relman DA
2010 Dec 1; 26(23): 2979-80. Epub 2010 Oct 21; PubMed: 20966005.
Abstract + PDF
407.
Drug-Induced Regulation of Target Expression.
2010 Sep 9; 6(9): . PubMed: 20838579.
Abstract + PDF
406.
Ontologies in quantitative biology: a basis for comparison, integration, and discovery.
Jensen LJ, Bork P
2010 May 25; 8(5): e1000374. PubMed: 20520843.
Abstract + PDF
405.
A side effect resource to capture phenotypic effects of drugs.
2010; 6: 343. PubMed: 20087340.
Abstract + PDF
404.
STITCH 2: an interaction network database for small molecules and proteins.
Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P
2010 Jan 6; 38: D552-6. Epub 2009 Nov 6; PubMed: 19897548.
Abstract + PDF
403.
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
402.
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
401.
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
400.
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
399.
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
398.
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
397.
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 11 publication(s).
396.
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
395.
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
394.
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
393.
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey CJ, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C
2009 Jan 21; 37: D412-6. Epub 2008 Oct 21; PubMed: 18940858.
Abstract + PDF
392.
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
391.
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
390.
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
389.
SMART 6: recent updates and new developments.
2009 Jan 31; 37: D229-32. Epub 2008 Oct 31; PubMed: 18978020.
Abstract + PDF
388.
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
387.
Evolution of biomolecular networks - lessons from metabolic and protein interactions.
Yamada T, Bork P
2009 Nov; 10(11): 791-803. PubMed: 19851337.
Abstract + PDF
386.
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 29 publication(s).
385.
Drug target identification using side-effect similarity.
Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P
2008 Jul 11; 321(5886): 263-6. PubMed: 18621671. Media echos.
Abstract + PDF
384.
A computational screen for type I polyketide synthases in metagenomics shotgun data.
Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P
2008; 3(10): e3515. PubMed: 18953415.
Abstract + PDF
383.
A Nitrile Hydratase in the Eukaryote Monosiga brevicollis.
2008; 3(12): e3976. PubMed: 19096720.
Abstract + PDF
382.
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.
ISBN: 978-3-211-75122-0 Publisher: Springer
381.
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
380.
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
379.
Predicting biological networks from genomic data.
2008 Apr 9; 582(8): 1251-8. Epub 2008 Feb 21; PubMed: 18294967.
Abstract + PDF
378.
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
377.
A Molecular Study of Microbe Transfer between Distant Environments.
2008 Jul 9; 3(7): e2607. PubMed: 18612393.
Abstract + PDF
376.
Biochemistry. Not comparable, but complementary.
Jensen LJ, Bork P
2008 Oct 3; 322(5898): 56-7. PubMed: 18832636.
PDF
375.
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
374.
eggNOG: automated construction and annotation of orthologous groups of genes.
2008 Jan 16; 36: D250-4. Epub 2007 Oct 16; PubMed: 17942413.
Abstract + PDF
373.
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
372.
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
371.
Large-scale prediction of drug-target relationships.
Kuhn M, Campillos M, González P, Jensen LJ, Bork P
2008 Apr 9; 582(8): 1283-90. Epub 2008 Feb 20; PubMed: 18291108.
Abstract + PDF
370.
STITCH: interaction networks of chemicals and proteins.
2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.
Abstract + PDF
369.
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.
Abstract + PDF
368.
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
367.
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
366.
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.
Abstract + PDF
365.
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.
Abstract + PDF
364.
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
363.
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.
Abstract + PDF
362.
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
361.
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.
Abstract + PDF
360.
Molecular eco-systems biology: towards an understanding of community function.
Raes J, Bork P
2008 Sep 30; 6(9): 693-9. Epub 2008 Jun 30; PubMed: 18587409.
Abstract + PDF
359.
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.
Abstract + PDF
358.
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
357.
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
2007 18 publication(s).
356.
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
355.
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
354.
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
353.
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
352.
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
351.
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic I, Bork P
2007 Jan 1; 23(1): 127-8. Epub 2006 Oct 18; PubMed: 17050570.
Abstract + PDF
350.
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
349.
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
348.
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
347.
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
Pachkov M, Dandekar T, Korbel JO, Bork P, Schuster S
2007 Jul 15; 396(2): 215-25. Epub 2007 Mar 24; PubMed: 17467928.
Abstract + PDF
346.
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
345.
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
344.
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
343.
Prediction of effective genome size in metagenomic samples.
2007 Jan 15; 8(1): R10. Epub 2007 Jan 15; PubMed: 17224063.
Abstract + PDF
342.
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
341.
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
340.
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
339.
Quantification of insect genome divergence.
Zdobnov EM, Bork P
2007 Jan 8; 23(1): 16-20. Epub 2006 Nov 9; PubMed: 17097187.
Abstract + PDF
2006 20 publication(s).
338.
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
337.
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
336.
Computational characterization of multiple Gag-like human proteins.
2006 Nov 15; 22(11): 585-9. Epub 2006 Sep 18; PubMed: 16979784.
Abstract + PDF
335.
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
334.
Toward automatic reconstruction of a highly resolved tree of life.
2006 Mar 3; 311(5765): 1283-7. PubMed: 16513982. Media echos.
Abstract + PDF
333.
Comparative analysis of environmental sequences: potential and challenges.
2006 Mar 29; 361(1467): 519-23. PubMed: 16524840.
Abstract + PDF
332.
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.
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331.
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.
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330.
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.
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329.
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.
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328.
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.
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327.
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
326.
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.
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325.
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
324.
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
323.
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
322.
LSAT: learning about alternative transcripts in MEDLINE.
Shah PK, Bork P
2006 Apr 1; 22(7): 857-65. Epub 2006 Jan 12; PubMed: 16410322.
Abstract + PDF
321.
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.
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320.
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
2006 Jul 1; 34(Web Server issue): W609-12. PubMed: 16845082.
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319.
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 28 publication(s).
318.
Is there biological research beyond Systems Biology? A comparative analysis of terms.
Bork P
2005; 1: 2005.0012. PubMed: 16729047.
PDF
317.
Towards cellular systems in 4D.
Bork P, Serrano L
2005 May 20; 121(4): 507-509. PubMed: 15907464.
PDF
316.
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.
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315.
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
314.
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
313.
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
312.
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.
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311.
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
310.
Environments shape the nucleotide composition of genomes.
2005 Dec; 6(12): 1208-13. PubMed: 16200051.
Abstract + PDF
309.
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.
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308.
Medusa: a simple tool for interaction graph analysis.
Hooper SD, Bork P
2005 Dec 15; 21(24): 4432-3. Epub 2005 Sep 27; PubMed: 16188923.
Abstract + PDF
307.
Systematic association of genes to phenotypes by genome and literature mining.
2005 May; 3(5): e134. Epub 2005 Apr 5; PubMed: 15799710. Media echos.
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306.
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
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305.
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.
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304.
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.
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303.
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
302.
G2D: A Tool for Mining Genes Associated with Disease.
Perez-Iratxeta C, Wjst M, Bork P, Andrade MA
2005 Aug 22; 6: 45. Epub 2005 Aug 22; PubMed: 16115313.
Abstract + PDF
301.
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
300.
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
299.
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
298.
Extraction of transcript diversity from scientific literature.
2005 Jun; 1(1): e10. Epub 2005 Jun 24; PubMed: 16103899.
Abstract + PDF
297.
Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.
2005 Oct 10; 579(24): 5281-6. PubMed: 16182294.
Abstract + PDF
296.
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
295.
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
294.
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
293.
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
2005 Jan 1; 33(Database issue): D433-7. PubMed: 15608232.
Abstract + PDF
292.
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
2005; 33(3): 946-54. PubMed: 15716312.
Abstract + PDF
291.
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 21 publication(s).
290.
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
289.
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
288.
Genes and structures in context (editorial).
Bork P, Orengo C
2004 June; 14(3): 261-263. PID: 335.
PDF
287.
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
286.
Global analysis of bacterial transcription factors to predict cellular target processes.
2004 Mar; 20(3): 126-31. PubMed: 15049306.
Abstract + PDF
285.
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
2004; 32(21): 6321-6. PubMed: 15576358.
Abstract + PDF
284.
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
283.
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
282.
Estimating rates of alternative splicing in mammals and invertebrates.
Harrington ED, Boue S, Valcarcel J, Reich JG, Bork P