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Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Campillos M, von Mering C, Jensen LJ, Bork P. Campillos M, et al. Among authors: jensen lj. Genome Res. 2006 Mar;16(3):374-82. doi: 10.1101/gr.4336406. Epub 2006 Jan 31. Genome Res. 2006. PMID: 16449501 Free PMC article.
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. Muller J, et al. Among authors: jensen lj. Nucleic Acids Res. 2010 Jan;38(Database issue):D190-5. doi: 10.1093/nar/gkp951. Epub 2009 Nov 9. Nucleic Acids Res. 2010. PMID: 19900971 Free PMC article.
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. von Mering C, et al. Among authors: jensen lj. Science. 2007 Feb 23;315(5815):1126-30. doi: 10.1126/science.1133420. Epub 2007 Feb 1. Science. 2007. PMID: 17272687
Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Harrington ED, et al. Among authors: jensen lj. Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13913-8. doi: 10.1073/pnas.0702636104. Epub 2007 Aug 23. Proc Natl Acad Sci U S A. 2007. PMID: 17717083 Free PMC article.
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. Szklarczyk D, et al. Among authors: jensen lj. Nucleic Acids Res. 2016 Jan 4;44(D1):D380-4. doi: 10.1093/nar/gkv1277. Epub 2015 Nov 20. Nucleic Acids Res. 2016. PMID: 26590256 Free PMC article.
Drug target identification using side-effect similarity.
Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Campillos M, et al. Among authors: jensen lj. Science. 2008 Jul 11;321(5886):263-6. doi: 10.1126/science.1158140. Science. 2008. PMID: 18621671
Large-scale prediction of drug-target relationships.
Kuhn M, Campillos M, González P, Jensen LJ, Bork P. Kuhn M, et al. Among authors: jensen lj. FEBS Lett. 2008 Apr 9;582(8):1283-90. doi: 10.1016/j.febslet.2008.02.024. Epub 2008 Feb 20. FEBS Lett. 2008. PMID: 18291108 Review.
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. Shah PK, et al. Among authors: jensen lj. Gene. 2008 Jan 15;407(1-2):199-215. doi: 10.1016/j.gene.2007.10.012. Epub 2007 Oct 15. Gene. 2008. PMID: 17996400
eggNOG: automated construction and annotation of orthologous groups of genes.
Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. Jensen LJ, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D250-4. doi: 10.1093/nar/gkm796. Epub 2007 Oct 16. Nucleic Acids Res. 2008. PMID: 17942413 Free PMC article.
Literature mining for the biologist: from information retrieval to biological discovery.
Jensen LJ, Saric J, Bork P. Jensen LJ, et al. Nat Rev Genet. 2006 Feb;7(2):119-29. doi: 10.1038/nrg1768. Nat Rev Genet. 2006. PMID: 16418747 Review.
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