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Comparing 22 Popular Phosphoproteomics Pipelines for Peptide Identification and Site Localization.

Locard-Paulet M, Bouyssié D, Froment C, Burlet-Schiltz O, Jensen LJ.

J Proteome Res. 2020 Feb 4. doi: 10.1021/acs.jproteome.9b00679. [Epub ahead of print]


Hyperglycemia-induced transcriptional regulation of ROCK1 and TGM2 expression is involved in small artery remodeling in obese diabetic Göttingen Minipigs.

Ludvigsen TP, Olsen LH, Pedersen HD, Christoffersen BØ, Jensen LJ.

Clin Sci (Lond). 2019 Dec 20;133(24):2499-2516. doi: 10.1042/CS20191066.


SnapShot: S-Phase Entry and Exit.

Burgess A, Vuong J, Marzec KA, Nicolai de Lichtenberg U, O'Donoghue SI, Jensen LJ.

Cell. 2019 Oct 17;179(3):802-802.e1. doi: 10.1016/j.cell.2019.09.031.


Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites.

Lundby A, Franciosa G, Emdal KB, Refsgaard JC, Gnosa SP, Bekker-Jensen DB, Secher A, Maurya SR, Paul I, Mendez BL, Kelstrup CD, Francavilla C, Kveiborg M, Montoya G, Jensen LJ, Olsen JV.

Cell. 2019 Oct 3;179(2):543-560.e26. doi: 10.1016/j.cell.2019.09.008.


Transcriptome analysis in patients with temporal lobe epilepsy.

Kjær C, Barzaghi G, Bak LK, Goetze JP, Yde CW, Woldbye D, Pinborg LH, Jensen LJ.

Brain. 2019 Oct 1;142(10):e55. doi: 10.1093/brain/awz265. No abstract available.


ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.

Tagore S, Gorohovski A, Jensen LJ, Frenkel-Morgenstern M.

PLoS Comput Biol. 2019 Aug 22;15(8):e1007239. doi: 10.1371/journal.pcbi.1007239. eCollection 2019 Aug.


Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types.

Hjaltelin JX, Izarzugaza JMG, Jensen LJ, Russo F, Westergaard D, Brunak S.

NPJ Syst Biol Appl. 2019 Aug 7;5:27. doi: 10.1038/s41540-019-0104-5. eCollection 2019.


CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision.

Junge A, Jensen LJ.

Bioinformatics. 2020 Jan 1;36(1):264-271. doi: 10.1093/bioinformatics/btz490.


Effect of TRPA1 activator allyl isothiocyanate (AITC) on rat dural and pial arteries.

Hansted AK, Bhatt DK, Olesen J, Jensen LJ, Jansen-Olesen I.

Pharmacol Rep. 2019 Aug;71(4):565-572. doi: 10.1016/j.pharep.2019.02.015. Epub 2019 Feb 21.


Improving Peptide-Spectrum Matching by Fragmentation Prediction Using Hidden Markov Models.

Kirik U, Refsgaard JC, Jensen LJ.

J Proteome Res. 2019 Jun 7;18(6):2385-2396. doi: 10.1021/acs.jproteome.8b00499. Epub 2019 May 22.


Design, implementation, and operation of a rapid, robust named entity recognition web service.

Pletscher-Frankild S, Jensen LJ.

J Cheminform. 2019 Mar 8;11(1):19. doi: 10.1186/s13321-019-0344-9.


A Guide to Dictionary-Based Text Mining.

Cook HV, Jensen LJ.

Methods Mol Biol. 2019;1939:73-89. doi: 10.1007/978-1-4939-9089-4_5.


Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism.

Cuesta-Astroz Y, Santos A, Oliveira G, Jensen LJ.

Front Immunol. 2019 Feb 13;10:212. doi: 10.3389/fimmu.2019.00212. eCollection 2019.


STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV.

Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131.


Quantitative metaproteomics of medieval dental calculus reveals individual oral health status.

Jersie-Christensen RR, Lanigan LT, Lyon D, Mackie M, Belstrøm D, Kelstrup CD, Fotakis AK, Willerslev E, Lynnerup N, Jensen LJ, Cappellini E, Olsen JV.

Nat Commun. 2018 Nov 20;9(1):4744. doi: 10.1038/s41467-018-07148-3.


Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.

Doncheva NT, Morris JH, Gorodkin J, Jensen LJ.

J Proteome Res. 2019 Feb 1;18(2):623-632. doi: 10.1021/acs.jproteome.8b00702. Epub 2018 Dec 5.


An Integrative Approach to Virus-Host Protein-Protein Interactions.

Cook HV, Jensen LJ.

Methods Mol Biol. 2018;1819:175-196. doi: 10.1007/978-1-4939-8618-7_8.


eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. doi: 10.1093/nar/gky1085.


WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

Pan X, Xiong K, Anthon C, Hyttel P, Freude KK, Jensen LJ, Gorodkin J.

Genes (Basel). 2018 Nov 6;9(11). pii: E536. doi: 10.3390/genes9110536.


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/bay028. No abstract available.


Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.

Pan X, Jensen LJ, Gorodkin J.

Bioinformatics. 2019 May 1;35(9):1494-1502. doi: 10.1093/bioinformatics/bty859.


Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000.

Sinha S, Eisenhaber B, Jensen LJ, Kalbuaji B, Eisenhaber F.

Proteomics. 2018 Nov;18(21-22):e1800093. doi: 10.1002/pmic.201800093. Epub 2018 Oct 30.


Viruses.STRING: A Virus-Host Protein-Protein Interaction Database.

Cook HV, Doncheva NT, Szklarczyk D, von Mering C, Jensen LJ.

Viruses. 2018 Sep 23;10(10). pii: E519. doi: 10.3390/v10100519.


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.


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.


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.


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.


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.


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. Erratum in: Database (Oxford). 2018 Jan 1;2018:.


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.


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.


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;:.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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. Erratum in: Database (Oxford). 2017 Jan 1;2017(1):.


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.


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.


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.


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.


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.

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