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Items: 1 to 20 of 188

1.

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.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.

2.

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.

Database (Oxford). 2016 Feb 20;2016. pii: baw005. doi: 10.1093/database/baw005. Print 2016.

3.

Age-dependent impact of CaV 3.2 T-type calcium channel deletion on myogenic tone and flow-mediated vasodilatation in small arteries.

Mikkelsen MF, Björling K, Jensen LJ.

J Physiol. 2016 Jan 11. doi: 10.1113/JP271470. [Epub ahead of print]

PMID:
26752249
4.

No apparent role for T-type Ca(2+) channels in renal autoregulation.

Frandsen RH, Salomonsson M, Hansen PB, Jensen LJ, Braunstein TH, Holstein-Rathlou NH, Sorensen CM.

Pflugers Arch. 2016 Apr;468(4):541-50. doi: 10.1007/s00424-015-1770-9. Epub 2015 Dec 14.

PMID:
26658945
5.

SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.

Franceschini A, Lin J, von Mering C, Jensen LJ.

Bioinformatics. 2015 Nov 26. pii: btv696. [Epub ahead of print]

6.

Impact of microRNA-130a on the neutrophil proteome.

Pedersen CC, Refsgaard JC, Østergaard O, Jensen LJ, Heegaard NH, Borregaard N, Cowland JB.

BMC Immunol. 2015 Nov 25;16:70. doi: 10.1186/s12865-015-0134-8.

7.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D380-4. doi: 10.1093/nar/gkv1277. Epub 2015 Nov 20.

8.

Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics.

Refsgaard JC, Munk S, Jensen LJ.

Methods Mol Biol. 2016;1355:323-39. doi: 10.1007/978-1-4939-3049-4_22.

PMID:
26584936
9.

From Phosphosites to Kinases.

Munk S, Refsgaard JC, Olsen JV, Jensen LJ.

Methods Mol Biol. 2016;1355:307-21. doi: 10.1007/978-1-4939-3049-4_21.

PMID:
26584935
10.

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(D1):D286-93. doi: 10.1093/nar/gkv1248. Epub 2015 Nov 17.

11.

Avoiding abundance bias in the functional annotation of post-translationally modified proteins.

Schölz C, Lyon D, Refsgaard JC, Jensen LJ, Choudhary C, Weinert BT.

Nat Methods. 2015 Nov;12(11):1003-4. doi: 10.1038/nmeth.3621. No abstract available.

PMID:
26513550
12.

Soluble Receptor for Advanced Glycation End Product: A Biomarker for Acute Coronary Syndrome.

Jensen LJ, Flyvbjerg A, Bjerre M.

Biomed Res Int. 2015;2015:815942. doi: 10.1155/2015/815942. Epub 2015 Sep 30. Review.

13.

The SIDER database of drugs and side effects.

Kuhn M, Letunic I, Jensen LJ, Bork P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1075-9. doi: 10.1093/nar/gkv1075. Epub 2015 Oct 19.

14.

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.

J Proteome Res. 2015 Nov 6;14(11):4885-95. doi: 10.1021/acs.jproteome.5b00720. Epub 2015 Oct 28.

15.

Corrigendum: Worldwide variations in artificial skyglow.

Kyba CC, Tong KP, Bennie J, Birriel I, Birriel JJ, Cool A, Danielsen A, Davies TW, den Outer PN, Edwards W, Ehlert R, Falchi F, Fischer J, Giacomelli A, Giubbilini F, Haaima M, Hesse C, Heygster G, Hölker F, Inger R, Jensen LJ, Kuechly HU, Kuehn J, Langill P, Lolkema DE, Nagy M, Nievas M, Ochi N, Popow E, Posch T, Puschnig J, Ruhtz T, Schmidt W, Schwarz R, Schwope A, Spoelstra H, Tekatch A, Trueblood M, Walker CE, Weber M, Welch DL, Zamorano J, Gaston KJ.

Sci Rep. 2015 Aug 5;5:12180. doi: 10.1038/srep12180. No abstract available.

16.

HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases.

Palleja A, Jensen LJ.

PeerJ. 2015 Jun 30;3:e1057. doi: 10.7717/peerj.1057. eCollection 2015.

17.

Comprehensive comparison of large-scale tissue expression datasets.

Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ.

PeerJ. 2015 Jun 30;3:e1054. doi: 10.7717/peerj.1054. eCollection 2015.

18.

Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines.

Warrer P, Jensen PB, Aagaard L, Jensen LJ, Brunak S, Krag MH, Rossing P, Almdal T, Andersen HU, Hansen EH.

J Res Pharm Pract. 2015 Apr-Jun;4(2):64-72. doi: 10.4103/2279-042X.155753.

19.
20.

Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation.

Emdal KB, Pedersen AK, Bekker-Jensen DB, Tsafou KP, Horn H, Lindner S, Schulte JH, Eggert A, Jensen LJ, Francavilla C, Olsen JV.

Sci Signal. 2015 Apr 28;8(374):ra40. doi: 10.1126/scisignal.2005769.

PMID:
25921289
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