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Ontologies in quantitative biology: a basis for comparison, integration, and discovery.
Jensen LJ, Bork P. Jensen LJ, et al. Among authors: bork p. PLoS Biol. 2010 May 25;8(5):e1000374. doi: 10.1371/journal.pbio.1000374. PLoS Biol. 2010. PMID: 20520843 Free PMC article.
Literature mining for the biologist: from information retrieval to biological discovery.
Jensen LJ, Saric J, Bork P. Jensen LJ, et al. Among authors: bork p. Nat Rev Genet. 2006 Feb;7(2):119-29. doi: 10.1038/nrg1768. Nat Rev Genet. 2006. PMID: 16418747 Review.
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. Szklarczyk D, et al. Among authors: bork p. Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. doi: 10.1093/nar/gkq973. Epub 2010 Nov 2. Nucleic Acids Res. 2011. PMID: 21045058 Free PMC article.
Drug discovery in the age of systems biology: the rise of computational approaches for data integration.
Iskar M, Zeller G, Zhao XM, van Noort V, Bork P. Iskar M, et al. Among authors: bork p. Curr Opin Biotechnol. 2012 Aug;23(4):609-16. doi: 10.1016/j.copbio.2011.11.010. Epub 2011 Dec 5. Curr Opin Biotechnol. 2012. PMID: 22153034 Review.
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. Kuhn M, et al. Among authors: bork p. Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28. Nucleic Acids Res. 2014. PMID: 24293645 Free PMC article.
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. Szklarczyk D, et al. Among authors: bork p. Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003. Epub 2014 Oct 28. Nucleic Acids Res. 2015. PMID: 25352553 Free PMC article.
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; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. Altenhoff AM, et al. Among authors: bork p. Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4. Nat Methods. 2016. PMID: 27043882 Free PMC article.
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. Szklarczyk D, et al. Among authors: bork p. Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. doi: 10.1093/nar/gkw937. Epub 2016 Oct 18. Nucleic Acids Res. 2017. PMID: 27924014 Free PMC article.
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. Pedersen HK, et al. Among authors: bork p. Nat Protoc. 2018 Dec;13(12):2781-2800. doi: 10.1038/s41596-018-0064-z. Nat Protoc. 2018. PMID: 30382244
eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. Powell S, et al. Among authors: bork p. Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253. Epub 2013 Dec 1. Nucleic Acids Res. 2014. PMID: 24297252 Free PMC article.
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