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Items: 1 to 50 of 218

1.

Role of age, Rho-kinase 2 expression, and G protein-mediated signaling in the myogenic response in mouse small mesenteric arteries.

Björling K, Joseph PD, Egebjerg K, Salomonsson M, Hansen JL, Ludvigsen TP, Jensen LJ.

Physiol Rep. 2018 Sep;6(17):e13863. doi: 10.14814/phy2.13863.

2.

Systems-wide Analysis of Serine ADP-Ribosylation Reveals Widespread Occurrence and Site-Specific Overlap with Phosphorylation.

Larsen SC, Hendriks IA, Lyon D, Jensen LJ, Nielsen ML.

Cell Rep. 2018 Aug 28;24(9):2493-2505.e4. doi: 10.1016/j.celrep.2018.07.083.

3.

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates.

Pan X, Wenzel A, Jensen LJ, Gorodkin J.

PLoS One. 2018 Aug 24;13(8):e0202369. doi: 10.1371/journal.pone.0202369. eCollection 2018.

4.

Site-specific characterization of endogenous SUMOylation across species and organs.

Hendriks IA, Lyon D, Su D, Skotte NH, Daniel JA, Jensen LJ, Nielsen ML.

Nat Commun. 2018 Jun 25;9(1):2456. doi: 10.1038/s41467-018-04957-4.

5.

Lack of tone in mouse small mesenteric arteries leads to outward remodeling, which can be prevented by prolonged agonist-induced vasoconstriction.

Klein A, Joseph PD, Christensen VG, Jensen LJ, Jacobsen JCB.

Am J Physiol Heart Circ Physiol. 2018 Sep 1;315(3):H644-H657. doi: 10.1152/ajpheart.00111.2018. Epub 2018 May 18.

PMID:
29775408
6.

TISSUES 2.0: an integrative web resource on mammalian tissue expression.

Palasca O, Santos A, Stolte C, Gorodkin J, Jensen LJ.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay003.

7.

Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting.

Mackie M, Rüther P, Samodova D, Di Gianvincenzo F, Granzotto C, Lyon D, Peggie DA, Howard H, Harrison L, Jensen LJ, Olsen JV, Cappellini E.

Angew Chem Int Ed Engl. 2018 Jun 18;57(25):7369-7374. doi: 10.1002/anie.201713020. Epub 2018 Apr 26.

8.

Unexplored therapeutic opportunities in the human genome.

Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G.

Nat Rev Drug Discov. 2018 May;17(5):377. doi: 10.1038/nrd.2018.52. Epub 2018 Mar 23.

PMID:
29567993
9.

Unexplored therapeutic opportunities in the human genome.

Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma'ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ, Zahoránszky-Köhalmi G.

Nat Rev Drug Discov. 2018 May;17(5):317-332. doi: 10.1038/nrd.2018.14. Epub 2018 Mar 23. Review. Erratum in: Nat Rev Drug Discov. 2018 Mar 23;:.

PMID:
29472638
10.

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.

Westergaard D, Stærfeldt HH, Tønsberg C, Jensen LJ, Brunak S.

PLoS Comput Biol. 2018 Feb 15;14(2):e1005962. doi: 10.1371/journal.pcbi.1005962. eCollection 2018 Feb.

11.

Long-term diet-induced hypertension in rats is associated with reduced expression and function of small artery SKCa, IKCa, and Kir2.1 channels.

Gradel AKJ, Salomonsson M, Sørensen CM, Holstein-Rathlou NH, Jensen LJ.

Clin Sci (Lond). 2018 Feb 28;132(4):461-474. doi: 10.1042/CS20171408. Print 2018 Feb 28.

PMID:
29436481
12.

LocText: relation extraction of protein localizations to assist database curation.

Cejuela JM, Vinchurkar S, Goldberg T, Prabhu Shankar MS, Baghudana A, Bojchevski A, Uhlig C, Ofner A, Raharja-Liu P, Jensen LJ, Rost B.

BMC Bioinformatics. 2018 Jan 17;19(1):15. doi: 10.1186/s12859-018-2021-9.

13.

Drug target ontology to classify and integrate drug discovery data.

Lin Y, Mehta S, Küçük-McGinty H, Turner JP, Vidovic D, Forlin M, Koleti A, Nguyen DT, Jensen LJ, Guha R, Mathias SL, Ursu O, Stathias V, Duan J, Nabizadeh N, Chung C, Mader C, Visser U, Yang JJ, Bologa CG, Oprea TI, Schürer SC.

J Biomed Semantics. 2017 Nov 9;8(1):50. doi: 10.1186/s13326-017-0161-x.

14.

miRandola 2017: a curated knowledge base of non-invasive biomarkers.

Russo F, Di Bella S, Vannini F, Berti G, Scoyni F, Cook HV, Santos A, Nigita G, Bonnici V, Laganà A, Geraci F, Pulvirenti A, Giugno R, De Masi F, Belling K, Jensen LJ, Brunak S, Pellegrini M, Ferro A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D354-D359. doi: 10.1093/nar/gkx854.

15.

Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification.

Mullari M, Lyon D, Jensen LJ, Nielsen ML.

J Proteome Res. 2017 Aug 4;16(8):2762-2772. doi: 10.1021/acs.jproteome.7b00042. Epub 2017 Jul 7.

PMID:
28648085
16.

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P.

Mol Biol Evol. 2017 Aug 1;34(8):2115-2122. doi: 10.1093/molbev/msx148.

17.

TIN-X: target importance and novelty explorer.

Cannon DC, Yang JJ, Mathias SL, Ursu O, Mani S, Waller A, Schürer SC, Jensen LJ, Sklar LA, Bologa CG, Oprea TI.

Bioinformatics. 2017 Aug 15;33(16):2601-2603. doi: 10.1093/bioinformatics/btx200.

18.

Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer.

Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV.

Cell Rep. 2017 Mar 28;18(13):3242-3256. doi: 10.1016/j.celrep.2017.03.015.

19.

Accurate Quantification of Site-specific Acetylation Stoichiometry Reveals the Impact of Sirtuin Deacetylase CobB on the E. coli Acetylome.

Weinert BT, Satpathy S, Hansen BK, Lyon D, Jensen LJ, Choudhary C.

Mol Cell Proteomics. 2017 May;16(5):759-769. doi: 10.1074/mcp.M117.067587. Epub 2017 Mar 2.

20.

miRNAs in human subcutaneous adipose tissue: Effects of weight loss induced by hypocaloric diet and exercise.

Kristensen MM, Davidsen PK, Vigelsø A, Hansen CN, Jensen LJ, Jessen N, Bruun JM, Dela F, Helge JW.

Obesity (Silver Spring). 2017 Mar;25(3):572-580. doi: 10.1002/oby.21765. Epub 2017 Feb 3.

21.

Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation.

Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML.

Nat Struct Mol Biol. 2017 Mar;24(3):325-336. doi: 10.1038/nsmb.3366. Epub 2017 Jan 23.

PMID:
28112733
22.

RAIN: RNA-protein Association and Interaction Networks.

Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J.

Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw167. Print 2017.

23.

T-type Ca2+ channels and autoregulation of local blood flow.

Jensen LJ, Nielsen MS, Salomonsson M, Sørensen CM.

Channels (Austin). 2017 May 4;11(3):183-195. doi: 10.1080/19336950.2016.1273997. Epub 2017 Jan 5. Review.

24.

Seqenv: linking sequences to environments through text mining.

Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E.

PeerJ. 2016 Dec 20;4:e2690. doi: 10.7717/peerj.2690. eCollection 2016.

25.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368. doi: 10.1093/nar/gkw937. Epub 2016 Oct 18.

26.

Pharos: Collating protein information to shed light on the druggable genome.

Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, Overington J, Patel J, Rouillard AD, Schürer S, Sheils T, Simeonov A, Sklar LA, Southall N, Ursu O, Vidovic D, Waller A, Yang J, Jadhav A, Oprea TI, Guha R.

Nucleic Acids Res. 2017 Jan 4;45(D1):D995-D1002. doi: 10.1093/nar/gkw1072. Epub 2016 Nov 29.

27.

Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls.

Belstrøm D, Jersie-Christensen RR, Lyon D, Damgaard C, Jensen LJ, Holmstrup P, Olsen JV.

PeerJ. 2016 Sep 14;4:e2433. doi: 10.7717/peerj.2433. eCollection 2016.

28.

Overview of the interactive task in BioCreative V.

Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN.

Database (Oxford). 2016 Sep 1;2016. pii: baw119. doi: 10.1093/database/baw119. Print 2016.

29.

Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells.

Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML.

Sci Signal. 2016 Aug 30;9(443):rs9. doi: 10.1126/scisignal.aaf7329.

PMID:
27577262
30.

Structure-based discovery of novel US28 small molecule ligands with different modes of action.

Lückmann M, Amarandi RM, Papargyri N, Jakobsen MH, Christiansen E, Jensen LJ, Pui A, Schwartz TW, Rosenkilde MM, Frimurer TM.

Chem Biol Drug Des. 2017 Mar;89(3):289-296. doi: 10.1111/cbdd.12848. Epub 2016 Sep 28.

PMID:
27569905
31.

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.

32.

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.

33.

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 Oct 15;594(20):5881-5898. doi: 10.1113/JP271470. Epub 2016 Feb 18.

34.

No apparent role for T-type Ca²⁺ 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
35.

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. 2016 Apr 1;32(7):1085-7. doi: 10.1093/bioinformatics/btv696. Epub 2015 Nov 26.

36.

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.

37.

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.

38.

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. Review.

PMID:
26584936
39.

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. Review.

PMID:
26584935
40.

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.

41.

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
42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.
50.

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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