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Ontologies in quantitative biology: a basis for comparison, integration, and discovery.
Jensen LJ, Bork P. Jensen LJ, et al. PLoS Biol. 2010 May 25;8(5):e1000374. doi: 10.1371/journal.pbio.1000374. PLoS Biol. 2010. PMID: 20520843 Free PMC article.
Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation.
Weinert BT, Wagner SA, Horn H, Henriksen P, Liu WR, Olsen JV, Jensen LJ, Choudhary C. Weinert BT, et al. Among authors: jensen lj. Sci Signal. 2011 Jul 26;4(183):ra48. doi: 10.1126/scisignal.2001902. Sci Signal. 2011. PMID: 21791702
Are graph databases ready for bioinformatics?
Have CT, Jensen LJ. Have CT, et al. Among authors: jensen lj. Bioinformatics. 2013 Dec 15;29(24):3107-8. doi: 10.1093/bioinformatics/btt549. Epub 2013 Oct 17. Bioinformatics. 2013. PMID: 24135261 Free PMC article.
DISEASES: text mining and data integration of disease-gene associations.
Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ. Pletscher-Frankild S, et al. Among authors: jensen lj. Methods. 2015 Mar;74:83-9. doi: 10.1016/j.ymeth.2014.11.020. Epub 2014 Dec 5. Methods. 2015. PMID: 25484339
Protein-protein interaction databases.
Szklarczyk D, Jensen LJ. Szklarczyk D, et al. Among authors: jensen lj. Methods Mol Biol. 2015;1278:39-56. doi: 10.1007/978-1-4939-2425-7_3. Methods Mol Biol. 2015. PMID: 25859942
Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow.
Deshmukh AS, Cox J, Jensen LJ, Meissner F, Mann M. Deshmukh AS, et al. Among authors: jensen lj. J Proteome Res. 2015 Nov 6;14(11):4885-95. doi: 10.1021/acs.jproteome.5b00720. Epub 2015 Oct 28. J Proteome Res. 2015. PMID: 26457550
Avoiding abundance bias in the functional annotation of post-translationally modified proteins.
Schölz C, Lyon D, Refsgaard JC, Jensen LJ, Choudhary C, Weinert BT. Schölz C, et al. Among authors: jensen lj. Nat Methods. 2015 Nov;12(11):1003-4. doi: 10.1038/nmeth.3621. Nat Methods. 2015. PMID: 26513550 No abstract available.
From Phosphosites to Kinases.
Munk S, Refsgaard JC, Olsen JV, Jensen LJ. Munk S, et al. Among authors: jensen lj. Methods Mol Biol. 2016;1355:307-21. doi: 10.1007/978-1-4939-3049-4_21. Methods Mol Biol. 2016. PMID: 26584935 Review.
Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics.
Refsgaard JC, Munk S, Jensen LJ. Refsgaard JC, et al. Among authors: jensen lj. Methods Mol Biol. 2016;1355:323-39. doi: 10.1007/978-1-4939-3049-4_22. Methods Mol Biol. 2016. PMID: 26584936 Review.
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.
Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C, Jensen LJ. Pafilis E, et al. Among authors: jensen lj. Database (Oxford). 2016 Feb 20;2016:baw005. doi: 10.1093/database/baw005. Print 2016. Database (Oxford). 2016. PMID: 26896844 Free PMC article.
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