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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.
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.
COMPARTMENTS: unification and visualization of protein subcellular localization evidence.
Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. Binder JX, et al. Among authors: jensen lj. Database (Oxford). 2014 Feb 25;2014:bau012. doi: 10.1093/database/bau012. Print 2014. Database (Oxford). 2014. PMID: 24573882 Free PMC article.
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
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 S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G. Gavin AC, et al. Among authors: jensen lj. Nature. 2006 Mar 30;440(7084):631-6. doi: 10.1038/nature04532. Epub 2006 Jan 22. Nature. 2006. PMID: 16429126
Evolution and regulation of cellular periodic processes: a role for paralogues.
Trachana K, Jensen LJ, Bork P. Trachana K, et al. Among authors: jensen lj. EMBO Rep. 2010 Mar;11(3):233-8. doi: 10.1038/embor.2010.9. Epub 2010 Feb 19. EMBO Rep. 2010. PMID: 20168326 Free PMC article.
Biochemistry. Not comparable, but complementary.
Jensen LJ, Bork P. Jensen LJ, et al. Science. 2008 Oct 3;322(5898):56-7. doi: 10.1126/science.1164801. Science. 2008. PMID: 18832636 No abstract available.
STITCH: interaction networks of chemicals and proteins.
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. Kuhn M, et al. Among authors: jensen lj. Nucleic Acids Res. 2008 Jan;36(Database issue):D684-8. doi: 10.1093/nar/gkm795. Epub 2007 Dec 15. Nucleic Acids Res. 2008. PMID: 18084021 Free PMC article.
Co-evolution of transcriptional and post-translational cell-cycle regulation.
Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P. Jensen LJ, et al. Among authors: jensen ts. Nature. 2006 Oct 5;443(7111):594-7. doi: 10.1038/nature05186. Epub 2006 Sep 27. Nature. 2006. PMID: 17006448
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.
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