Publications of P. Bork in the journal "Nucleic Acids Res".

Publications of P. Bork in the journal "Nucleic Acids Res".

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2024 1 publication(s).
85.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Pedro Coelho L, Bork P
Nucleic Acids Res.
2024 Jan 5; 52: D777-D783. PubMed: 37897342.
Abstract + PDF
2023 4 publication(s).
84.
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
Nucleic Acids Res.
2023 Jan 6; 51: D760-D766. PubMed: 36408900.
Abstract + PDF
83.
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
Nucleic Acids Res.
2023 Jan 6; 51: D389-D394. PubMed: 36399505.
Abstract + PDF
82.
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
Nucleic Acids Res.
2023 Jan 6; 51: D418-D427. PubMed: 36350672.
Abstract + PDF
81.
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
Nucleic Acids Res.
2023 Jan 6; 51: D638-D646. PubMed: 36370105.
Abstract + PDF
2022 1 publication(s).
80.
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
Nucleic Acids Res.
2022 Apr 8; 50(6): 3155-3168. PubMed: 35323968.
Abstract + PDF
2021 6 publication(s).
79.
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
Nucleic Acids Res.
2021 Jan 8; 49(D1): D344-D354. PubMed: 33156333.
Abstract + PDF
78.
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
Nucleic Acids Res.
2021 Jan 8; 49(D1): D998-D1003. PubMed: 33084874.
Abstract + PDF
77.
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.
Letunic I, Bork P
Nucleic Acids Res.
2021 Jul 2; 49(W1): W293-W296. PubMed: 33885785.
Abstract + PDF
76.
SMART: recent updates, new developments and status in 2020.
Nucleic Acids Res.
2021 Jan 8; 49(D1): D458-D460. PubMed: 33104802.
Abstract + PDF
75.
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
Nucleic Acids Res.
2021 Oct 11; 49(18): 10800. PubMed: 34530444.
PDF
74.
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
Nucleic Acids Res.
2021 Jan 8; 49(D1): D605-D612. PubMed: 33237311.
Abstract + PDF
2020 1 publication(s).
73.
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Nucleic Acids Res.
2020 Jan 8; 48: D621-D625. PubMed: 31647096.
Abstract + PDF
2019 4 publication(s).
72.
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
Nucleic Acids Res.
2019 Jan 8; 47: D309-D314. PubMed: 30418610.
Abstract + PDF
71.
Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Letunic I, Bork P
Nucleic Acids Res.
2019 Jul 2; 47: W256-W259. PubMed: 30931475.
Abstract + PDF
70.
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
Nucleic Acids Res.
2019 Jan 8; 47: D351-D360. PubMed: 30398656.
Abstract + PDF
69.
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
Nucleic Acids Res.
2019 Jan 8; 47: D607-D613. PubMed: 30476243.
Abstract + PDF
2018 3 publication(s).
68.
iPath3.0: interactive pathways explorer v3.
Darzi Y, Letunic I, Bork P, Yamada T
Nucleic Acids Res.
2018 Jul 2; 46: W510-W513. PubMed: 29718427.
Abstract + PDF
67.
MVP: a microbe-phage interaction database.
Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH
Nucleic Acids Res.
2018 Jan 4; 46: D700-D707. PubMed: 29177508.
Abstract + PDF
66.
20 years of the SMART protein domain annotation resource.
Letunic I, Bork P
Nucleic Acids Res.
2018 Jan 4; 46: D493-D496. PubMed: 29040681.
Abstract + PDF
2017 4 publication(s).
65.
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
Nucleic Acids Res.
2017 Jan 4; 45(D1): D940-D944. PubMed: 27799467.
Abstract + PDF
64.
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
Nucleic Acids Res.
2017 Jan 4; 45(D1): D190-D199. PubMed: 27899635.
Abstract + PDF
63.
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Nucleic Acids Res.
2017 Jan 4; 45(D1): D529-D534. PubMed: 28053165.
Abstract + PDF
62.
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
Nucleic Acids Res.
2017 Jan 4; 45(D1): D362-D368. PubMed: 27924014.
Abstract + PDF
2016 5 publication(s).
61.
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
Nucleic Acids Res.
2016 Feb 18; 44(3): 1192-202. Epub 2016 Jan 14; PubMed: 26773059.
Abstract + PDF
60.
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
Nucleic Acids Res.
2016 Jan 4; 44: D286-93. Epub 2015 Nov 17; PubMed: 26582926.
Abstract + PDF
59.
The SIDER database of drugs and side effects.
Nucleic Acids Res.
2016 Jan 4; 44: D1075-9. Epub 2015 Oct 19; PubMed: 26481350.
Abstract + PDF
58.
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
Letunic I, Bork P
Nucleic Acids Res.
2016 Jul 8; 44: W242-5. Epub 2016 Apr 19; PubMed: 27095192.
Abstract + PDF
57.
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Nucleic Acids Res.
2016 Jan 4; 44: D380-4. Epub 2015 Nov 20; PubMed: 26590256.
Abstract + PDF
2015 5 publication(s).
56.
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
Nucleic Acids Res.
2015 Jan 30; 43(2): e10. Epub 2014 Nov 11; PubMed: 25392414.
Abstract + PDF
55.
SMART: recent updates, new developments and status in 2015.
Nucleic Acids Res.
2015 Jan 28; 43: D257-60. Epub 2014 Oct 9; PubMed: 25300481.
Abstract + PDF
54.
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res.
2015 Jan 28; 43: D494-502. Epub 2014 Oct 31; PubMed: 25361965.
Abstract + PDF
53.
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
Nucleic Acids Res.
2015 Jan 28; 43: D213-21. Epub 2014 Nov 26; PubMed: 25428371.
Abstract + PDF
52.
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
Nucleic Acids Res.
2015 Jan 28; 43: D447-52. Epub 2014 Oct 28; PubMed: 25352553.
Abstract + PDF
2014 3 publication(s).
51.
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
Nucleic Acids Res.
2014 Dec 16; 42(22): 13525-33. Epub 2014 Nov 14; PubMed: 25398899.
Abstract + PDF
50.
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
Nucleic Acids Res.
2014 Jan 1; 42(Database issue): D401-7. Epub 2013 Nov 28; PubMed: 24293645.
Abstract + PDF
49.
eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res.
2014 Jan 1; 42(Database issue): D231-9. Epub 2013 Dec 1; PubMed: 24297252.
Abstract + PDF
2013 2 publication(s).
48.
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
Nucleic Acids Res.
2013 Jan 1; 41: D808-15. Epub 2012 Nov 29; PubMed: 23203871.
Abstract + PDF
47.
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
Nucleic Acids Res.
2013 Jan 1; 41: D306-11. Epub 2012 Nov 28; PubMed: 23193284.
Abstract + PDF
2012 5 publication(s).
46.
OGEE: an online gene essentiality database.
Nucleic Acids Res.
2012 Jan 10; 40(Database issue): D901-6. Epub 2011 Nov 10; PubMed: 22075992.
Abstract + PDF
45.
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
Nucleic Acids Res.
2012 Jan 1; 40: D306-12. Epub 2011 Nov 16; PubMed: 22096229.
Abstract + PDF
44.
STITCH 3: zooming in on protein-chemical interactions.
Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P
Nucleic Acids Res.
2012 Jan 1; 40: D876-80. Epub 2011 Nov 9; PubMed: 22075997.
Abstract + PDF
43.
SMART 7: recent updates to the protein domain annotation resource.
Nucleic Acids Res.
2012 Jan 3; 40(Database issue): D302-5. Epub 2011 Nov 3; PubMed: 22053084.
Abstract + PDF
42.
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res.
2012 Jan 1; 40: D284-9. Epub 2011 Nov 16; PubMed: 22096231.
Abstract + PDF
2011 3 publication(s).
41.
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
Letunic I, Bork P
Nucleic Acids Res.
2011 Jul 5; 39 Suppl 2: W475-8. Epub 2011 Apr 5; PubMed: 21470960.
Abstract + PDF
40.
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
Nucleic Acids Res.
2011 Jan 2; 39: D561-8. Epub 2010 Nov 2; PubMed: 21045058.
Abstract + PDF
39.
iPath2.0: interactive pathway explorer.
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P
Nucleic Acids Res.
2011 Jul 5; 39 Suppl 2: W412-5. Epub 2011 May 5; PubMed: 21546551.
Abstract + PDF
2010 4 publication(s).
38.
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
Nucleic Acids Res.
2010 Jan 6; 38: D552-6. Epub 2009 Nov 6; PubMed: 19897548.
Abstract + PDF
37.
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Nucleic Acids Res.
2010 Jan 9; 38: D190-5. Epub 2009 Nov 9; PubMed: 19900971.
Abstract + PDF
36.
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
Nucleic Acids Res.
2010 Dec 11; 38(22): 7916-26. Epub 2010 Aug 11; PubMed: 20702423.
Abstract + PDF
35.
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
Nucleic Acids Res.
2010 Jan 9; 38: D682-9. Epub 2009 Oct 9; PubMed: 19820113.
Abstract + PDF
2009 3 publication(s).
34.
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
Nucleic Acids Res.
2009 Jan 21; 37: D211-5. Epub 2008 Oct 21; PubMed: 18940856.
Abstract + PDF
33.
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
Nucleic Acids Res.
2009 Jan 21; 37: D412-6. Epub 2008 Oct 21; PubMed: 18940858.
Abstract + PDF
32.
SMART 6: recent updates and new developments.
Nucleic Acids Res.
2009 Jan 31; 37: D229-32. Epub 2008 Oct 31; PubMed: 18978020.
Abstract + PDF
2008 6 publication(s).
31.
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
Nucleic Acids Res.
2008 Jan 16; 36: D919-22. Epub 2007 Oct 16; PubMed: 17942422.
Abstract + PDF
30.
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
Nucleic Acids Res.
2008 Jan 17; 36: D847-53. Epub 2007 Dec 17; PubMed: 17916571.
Abstract + PDF
29.
eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic Acids Res.
2008 Jan 16; 36: D250-4. Epub 2007 Oct 16; PubMed: 17942413.
Abstract + PDF
28.
STITCH: interaction networks of chemicals and proteins.
Nucleic Acids Res.
2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.
Abstract + PDF
27.
NetworKIN: a resource for exploring cellular phosphorylation networks.
Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T
Nucleic Acids Res.
2008 Jan 2; 36: D695-9. Epub 2007 Nov 2; PubMed: 17981841.
Abstract + PDF
26.
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
Nucleic Acids Res.
2008 Jul 1; 36: W423-6. Epub 2008 May 13; PubMed: 18477636.
Abstract + PDF
2007 3 publication(s).
25.
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
Nucleic Acids Res.
2007 Jan; 35(Database issue): D224-8. PubMed: 17202162.
Abstract + PDF
24.
Update of the G2D tool for prioritization of gene candidates to inherited diseases.
Perez-Iratxeta C, Bork P, Andrade-Navarro MA
Nucleic Acids Res.
2007 Jul 1; 35: W212-6. Epub 2007 May 3; PubMed: 17478516.
Abstract + PDF
23.
STRING 7--recent developments in the integration and prediction of protein interactions.
Nucleic Acids Res.
2007 Jan 10; 35: D358-62. Epub 2006 Nov 10; PubMed: 17098935.
Abstract + PDF
2006 2 publication(s).
22.
SMART 5: domains in the context of genomes and networks.
Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P
Nucleic Acids Res.
2006 Jan 1; 34(Database issue): D257-60. PubMed: 16381859.
Abstract + PDF
21.
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Nucleic Acids Res.
2006 Jul 1; 34(Web Server issue): W609-12. PubMed: 16845082.
Abstract + PDF
2005 3 publication(s).
20.
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
Nucleic Acids Res.
2005 Jan 1; 33(Database issue): D201-5. PubMed: 15608177.
Abstract + PDF
19.
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res.
2005 Jan 1; 33(Database issue): D433-7. PubMed: 15608232.
Abstract + PDF
18.
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.
Nucleic Acids Res.
2005; 33(3): 946-54. PubMed: 15716312.
Abstract + PDF
2004 3 publication(s).
17.
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes.
Nucleic Acids Res.
2004; 32(21): 6321-6. PubMed: 15576358.
Abstract + PDF
16.
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Nucleic Acids Res.
2004 Jul 1; 32(Web Server issue): W445-8. PubMed: 15215427.
Abstract + PDF
15.
SMART 4.0: towards genomic data integration.
Nucleic Acids Res.
2004 Jan 1; 32(Database issue): D142-4. PubMed: 14681379.
Abstract + PDF
2003 4 publication(s).
14.
The InterPro Database, 2003 brings increased coverage and new features.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R, Zdobnov EM
Nucleic Acids Res.
2003 Jan 1; 31(1): 315-8. PubMed: 12520011.
Abstract + PDF
13.
Update on XplorMed: A web server for exploring scientific literature.
Perez-Iratxeta C, Pérez AJ, Bork P, Andrade MA
Nucleic Acids Res.
2003 Jul 1; 31(13): 3866-8. PubMed: 12824439.
Abstract + PDF
12.
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ
Nucleic Acids Res.
2003 Jul 1; 31(13): 3625-30. PubMed: 12824381.
Abstract + PDF
11.
STRING: a database of predicted functional associations between proteins.
Nucleic Acids Res.
2003 Jan 1; 31(1): 258-61. PubMed: 12519996.
Abstract + PDF
2002 3 publication(s).
10.
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.
Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ
Nucleic Acids Res.
2002 Jan 1; 30(1): 387-91. PubMed: 11752345.
Abstract + PDF
9.
Recent improvements to the SMART domain-based sequence annotation resource.
Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P
Nucleic Acids Res.
2002 Jan 1; 30(1): 242-4. PubMed: 11752305.
Abstract + PDF
8.
Human non-synonymous SNPs: server and survey.
Nucleic Acids Res.
2002 Sep 1; 30(17): 3894-900. PubMed: 12202775.
Abstract + PDF
2000 4 publication(s).
7.
HGBASE: a database of SNPs and other variations in and around human genes.
Brookes AJ, Lehväslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, Bork P, Ortigao F
Nucleic Acids Res.
2000 Jan 1; 28(1): 356-60. PubMed: 10592273.
Abstract + PDF
6.
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar T, Huynen MA, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P
Nucleic Acids Res.
2000 Sep 1; 28(17): 3278-88. PubMed: 10954595.
Abstract + PDF
5.
SMART: a web-based tool for the study of genetically mobile domains.
Schultz J, Copley RR, Doerks T, Ponting CP, Bork P
Nucleic Acids Res.
2000 Jan 1; 28(1): 231-4. PubMed: 10592234.
Abstract + PDF
4.
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
Snel B, Lehmann G, Bork P, Huynen MA
Nucleic Acids Res.
2000 Sep 15; 28(18): 3442-4. PubMed: 10982861.
Abstract + PDF
1999 1 publication(s).
3.
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Ponting CP, Schultz J, Milpetz F, Bork P
Nucleic Acids Res.
1999 Jan 1; 27(1): 229-32. PubMed: 9847187.
Abstract + PDF
1994 1 publication(s).
2.
A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?
Koonin EV, Bork P, Sander C
Nucleic Acids Res.
1994 Jun 11; 22(11): 2166-7. PubMed: 7518079.
Abstract + PDF
1993 1 publication(s).
1.
An expanding family of helicases within the 'DEAD/H' superfamily.
Bork P, Koonin EV
Nucleic Acids Res.
1993 Feb 11; 21(3): 751-2. PubMed: 8382805.
PDF