Lars Juhl Jensen - Publications

Affiliations: 
Center for Protein Research University of Copenhagen, København, Denmark 
Website:
http://www.cpr.ku.dk/organisation/staff/CV_LJJensen/

151 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Cuesta-Astroz Y, Santos A, Oliveira G, Jensen LJ. Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. Frontiers in Immunology. 10: 212. PMID 30815000 DOI: 10.3389/fimmu.2019.00212  0.4
2018 Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research. PMID 30476243 DOI: 10.1093/nar/gky1131  1
2018 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. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research. PMID 30418610 DOI: 10.1093/nar/gky1085  1
2017 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, et al. miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Research. PMID 29036351 DOI: 10.1093/nar/gkx854  0.4
2017 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. Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer. Cell Reports. 18: 3242-3256. PMID 28355574 DOI: 10.1016/j.celrep.2017.03.015  0.8
2016 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. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Research. PMID 27924014 DOI: 10.1093/nar/gkw937  1
2016 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, ... ... Jensen LJ, et al. Overview of the interactive task in BioCreative V. Database : the Journal of Biological Databases and Curation. 2016. PMID 27589961 DOI: 10.1093/database/baw119  0.36
2016 Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ, Nielsen ML. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells. Science Signaling. 9: rs9. PMID 27577262 DOI: 10.1126/scisignal.aaf7329  1
2016 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, ... ... Jensen LJ, et al. Standardized benchmarking in the quest for orthologs. Nature Methods. PMID 27043882 DOI: 10.1038/nmeth.3830  1
2016 Refsgaard JC, Munk S, Jensen LJ. Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics. Methods in Molecular Biology (Clifton, N.J.). 1355: 323-39. PMID 26584936 DOI: 10.1007/978-1-4939-3049-4_22  1
2016 Munk S, Refsgaard JC, Olsen JV, Jensen LJ. From Phosphosites to Kinases. Methods in Molecular Biology (Clifton, N.J.). 1355: 307-21. PMID 26584935 DOI: 10.1007/978-1-4939-3049-4_21  1
2015 Franceschini A, Lin J, von Mering C, Jensen LJ. SVD-Phy: Improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics (Oxford, England). PMID 26614125 DOI: 10.1093/bioinformatics/btv696  1
2015 Pedersen CC, Refsgaard JC, Østergaard O, Jensen LJ, Heegaard NH, Borregaard N, Cowland JB. Impact of microRNA-130a on the neutrophil proteome. Bmc Immunology. 16: 70. PMID 26608132 DOI: 10.1186/s12865-015-0134-8  1
2015 Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research. PMID 26590256 DOI: 10.1093/nar/gkv1277  1
2015 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. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research. PMID 26582926 DOI: 10.1093/nar/gkv1248  1
2015 Schölz C, Lyon D, Refsgaard JC, Jensen LJ, Choudhary C, Weinert BT. Avoiding abundance bias in the functional annotation of posttranslationally modified proteins. Nature Methods. 12: 1003-4. PMID 26513550 DOI: 10.1038/nmeth.3621  1
2015 Kuhn M, Letunic I, Jensen LJ, Bork P. The SIDER database of drugs and side effects. Nucleic Acids Research. PMID 26481350 DOI: 10.1093/nar/gkv1075  1
2015 Deshmukh AS, Cox J, Jensen LJ, Meissner F, Mann M. Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow. Journal of Proteome Research. 14: 4885-95. PMID 26457550 DOI: 10.1021/acs.jproteome.5b00720  1
2015 Palleja A, Jensen LJ. HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. Peerj. 3: e1057. PMID 26157625 DOI: 10.7717/peerj.1057  1
2015 Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ. Comprehensive comparison of large-scale tissue expression datasets. Peerj. 3: e1054. PMID 26157623 DOI: 10.7717/peerj.1054  1
2015 Warrer P, Jensen PB, Aagaard L, Jensen LJ, Brunak S, Krag MH, Rossing P, Almdal T, Andersen HU, Hansen EH. Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines. Journal of Research in Pharmacy Practice. 4: 64-72. PMID 25984543 DOI: 10.4103/2279-042X.155753  0.8
2015 Emdal KB, Pedersen AK, Bekker-Jensen DB, Tsafou KP, Horn H, Lindner S, Schulte JH, Eggert A, Jensen LJ, Francavilla C, Olsen JV. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. Science Signaling. 8: ra40. PMID 25921289 DOI: 10.1126/scisignal.2005769  1
2015 Szklarczyk D, Jensen LJ. Protein-protein interaction databases. Methods in Molecular Biology (Clifton, N.J.). 1278: 39-56. PMID 25859942 DOI: 10.1007/978-1-4939-2425-7_3  1
2015 Schölz C, Weinert BT, Wagner SA, Beli P, Miyake Y, Qi J, Jensen LJ, Streicher W, McCarthy AR, Westwood NJ, Lain S, Cox J, Matthias P, Mann M, Bradner JE, et al. Acetylation site specificities of lysine deacetylase inhibitors in human cells. Nature Biotechnology. 33: 415-23. PMID 25751058 DOI: 10.1038/nbt.3130  1
2015 Pafilis E, Frankild SP, Schnetzer J, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou K, Leary P, Hammock J, Schulz K, Parr CS, Arvanitidis C, Jensen LJ. ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics (Oxford, England). 31: 1872-4. PMID 25619994 DOI: 10.1093/bioinformatics/btv045  1
2015 Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Molecular & Cellular Proteomics : McP. 14: 658-73. PMID 25576301 DOI: 10.1074/mcp.M114.042812  1
2015 Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ. DISEASES: text mining and data integration of disease-gene associations. Methods (San Diego, Calif.). 74: 83-9. PMID 25484339 DOI: 10.1016/j.ymeth.2014.11.020  1
2015 Santos A, Wernersson R, Jensen LJ. Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. Nucleic Acids Research. 43: D1140-4. PMID 25378319 DOI: 10.1093/nar/gku1092  1
2015 Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research. 43: D447-52. PMID 25352553 DOI: 10.1093/nar/gku1003  1
2015 Pyysalo S, Campos J, Cejuela JM, Ginter F, Hakala K, Li C, Stenetorp P, Jensen LJ. Sharing annotations better: RESTful open annotation Acl-Ijcnlp 2015 - 53rd Annual Meeting of the Association For Computational Linguistics and the 7th International Joint Conference On Natural Language Processing, Proceedings of System Demonstrations. 91-96.  1
2014 Eriksson R, Aagaard L, Jensen LJ, Borisova L, Hørlück D, Brunak S, Hansen EH. Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA. Pharmacology Research & Perspectives. 2: e00038. PMID 25505588 DOI: 10.1002/prp2.38  0.8
2014 Jensen AB, Moseley PL, Oprea TI, Ellesøe SG, Eriksson R, Schmock H, Jensen PB, Jensen LJ, Brunak S. Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients. Nature Communications. 5: 4022. PMID 24959948 DOI: 10.1038/ncomms5022  1
2014 Rudolf AF, Skovgaard T, Knapp S, Jensen LJ, Berthelsen J. A comparison of protein kinases inhibitor screening methods using both enzymatic activity and binding affinity determination. Plos One. 9: e98800. PMID 24915177 DOI: 10.1371/journal.pone.0098800  1
2014 Horn H, Schoof EM, Kim J, Robin X, Miller ML, Diella F, Palma A, Cesareni G, Jensen LJ, Linding R. KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods. 11: 603-4. PMID 24874572 DOI: 10.1038/nmeth.2968  1
2014 Bøgebo R, Horn H, Olsen JV, Gammeltoft S, Jensen LJ, Hansen JL, Christensen GL. Predicting kinase activity in angiotensin receptor phosphoproteomes based on sequence-motifs and interactions. Plos One. 9: e94672. PMID 24722691 DOI: 10.1371/journal.pone.0094672  1
2014 Horn H, Haslam N, Jensen LJ. DoReMi: context-based prioritization of linear motif matches. Peerj. 2: e315. PMID 24711967 DOI: 10.7717/peerj.315  1
2014 Eriksson R, Werge T, Jensen LJ, Brunak S. Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population. Drug Safety. 37: 237-47. PMID 24634163 DOI: 10.1007/s40264-014-0145-z  1
2014 Boonen HC, Moesgaard SG, Birck MM, Christoffersen BO, Cirera S, Heegaard PM, Højbøge TR, Jensen LJ, Mortensen A, Olsen LH, Sheykhzade M, Tang J, Lykkesfeldt J. Functional network analysis of obese and lean Göttingen minipigs elucidates changes in oxidative and inflammatory networks in obese pigs. PflüGers Archiv : European Journal of Physiology. 466: 2167-76. PMID 24590510 DOI: 10.1007/s00424-014-1486-2  1
2014 Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database : the Journal of Biological Databases and Curation. 2014: bau012. PMID 24573882 DOI: 10.1093/database/bau012  1
2014 Sylvestersen KB, Horn H, Jungmichel S, Jensen LJ, Nielsen ML. Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest. Molecular & Cellular Proteomics : McP. 13: 2072-88. PMID 24563534 DOI: 10.1074/mcp.O113.032748  1
2014 Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research. 42: D231-9. PMID 24297252 DOI: 10.1093/nar/gkt1253  1
2014 Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P. STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Research. 42: D401-7. PMID 24293645 DOI: 10.1093/nar/gkt1207  1
2014 Mørk S, Pletscher-Frankild S, Palleja Caro A, Gorodkin J, Jensen LJ. Protein-driven inference of miRNA-disease associations. Bioinformatics (Oxford, England). 30: 392-7. PMID 24273243 DOI: 10.1093/bioinformatics/btt677  1
2013 Have CT, Jensen LJ. Are graph databases ready for bioinformatics? Bioinformatics (Oxford, England). 29: 3107-8. PMID 24135261 DOI: 10.1093/bioinformatics/btt549  1
2013 Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, et al. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell. 155: 70-80. PMID 24074861 DOI: 10.1016/j.cell.2013.08.030  1
2013 Hekmat O, Munk S, Fogh L, Yadav R, Francavilla C, Horn H, Würtz SØ, Schrohl AS, Damsgaard B, Rømer MU, Belling KC, Jensen NF, Gromova I, Bekker-Jensen DB, Moreira JM, ... Jensen LJ, et al. TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells. Journal of Proteome Research. 12: 4136-51. PMID 23909892 DOI: 10.1021/pr400457u  1
2013 Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, Arvanitidis C, Jensen LJ. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. Plos One. 8: e65390. PMID 23823062 DOI: 10.1371/journal.pone.0065390  1
2013 Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, ... ... Jensen LJ, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 499: 74-8. PMID 23803765 DOI: 10.1038/nature12323  1
2013 Lundby A, Andersen MN, Steffensen AB, Horn H, Kelstrup CD, Francavilla C, Jensen LJ, Schmitt N, Thomsen MB, Olsen JV. In vivo phosphoproteomics analysis reveals the cardiac targets of β-adrenergic receptor signaling. Science Signaling. 6: rs11. PMID 23737553 DOI: 10.1126/scisignal.2003506  1
2013 Eriksson R, Jensen PB, Frankild S, Jensen LJ, Brunak S. Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. Journal of the American Medical Informatics Association : Jamia. 20: 947-53. PMID 23703825 DOI: 10.1136/amiajnl-2013-001708  1
2013 Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P. Systematic identification of proteins that elicit drug side effects. Molecular Systems Biology. 9: 663. PMID 23632385 DOI: 10.1038/msb.2013.10  1
2013 Jensen PB, Jensen LJ, Brunak S. Reply to 'Mining electronic health records: an additional perspective'. Nature Reviews. Genetics. 14: 75. PMID 23247438 DOI: 10.1038/nrg3208-c2  1
2013 Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research. 41: D808-15. PMID 23203871 DOI: 10.1093/nar/gks1094  1
2013 Pafilis E, Pavlopoulos GA, Satagopam VP, Papanikolaou N, Horn H, Arvanitidis C, Jensen LJ, Schneider R, Iliopoulos I. OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction 13th Ieee International Conference On Bioinformatics and Bioengineering, Ieee Bibe 2013. DOI: 10.1109/BIBE.2013.6701679  1
2012 Croft L, Szklarczyk D, Jensen LJ, Gorodkin J. Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. Bmc Systems Biology. 6: 90. PMID 22824421 DOI: 10.1186/1752-0509-6-90  1
2012 Jensen PB, Jensen LJ, Brunak S. Mining electronic health records: towards better research applications and clinical care. Nature Reviews. Genetics. 13: 395-405. PMID 22549152 DOI: 10.1038/nrg3208  1
2012 Frenkel-Morgenstern M, Danon T, Christian T, Igarashi T, Cohen L, Hou YM, Jensen LJ. Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Molecular Systems Biology. 8: 572. PMID 22373820 DOI: 10.1038/msb.2012.3  1
2012 Bergholdt R, Brorsson C, Palleja A, Berchtold LA, Fløyel T, Bang-Berthelsen CH, Frederiksen KS, Jensen LJ, Størling J, Pociot F. Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression. Diabetes. 61: 954-62. PMID 22344559 DOI: 10.2337/db11-1263  1
2012 Romanel A, Jensen LJ, Cardelli L, Csikász-Nagy A. Transcriptional regulation is a major controller of cell cycle transition dynamics. Plos One. 7: e29716. PMID 22238641 DOI: 10.1371/journal.pone.0029716  1
2012 Cappellini E, Jensen LJ, Szklarczyk D, Ginolhac A, da Fonseca RA, Stafford TW, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MT, Olsen JV. Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins. Journal of Proteome Research. 11: 917-26. PMID 22103443 DOI: 10.1021/pr200721u  1
2012 Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. 40: D284-9. PMID 22096231 DOI: 10.1093/nar/gkr1060  1
2012 Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research. 40: D876-80. PMID 22075997 DOI: 10.1093/nar/gkr1011  1
2012 Pallejà A, Horn H, Eliasson S, Jensen LJ. DistiLD Database: diseases and traits in linkage disequilibrium blocks. Nucleic Acids Research. 40: D1036-40. PMID 22058129 DOI: 10.1093/nar/gkr899  1
2011 Jensen LJ, Bateman A. The rise and fall of supervised machine learning techniques. Bioinformatics (Oxford, England). 27: 3331-2. PMID 22101152 DOI: 10.1093/bioinformatics/btr585  1
2011 Parnell LD, Lindenbaum P, Shameer K, Dall'Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, Albert I. BioStar: an online question & answer resource for the bioinformatics community. Plos Computational Biology. 7: e1002216. PMID 22046109 DOI: 10.1371/journal.pcbi.1002216  1
2011 Waters MR, Stafford TW, McDonald HG, Gustafson C, Rasmussen M, Cappellini E, Olsen JV, Szklarczyk D, Jensen LJ, Gilbert MT, Willerslev E. Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington. Science (New York, N.Y.). 334: 351-3. PMID 22021854 DOI: 10.1126/science.1207663  1
2011 Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H. Ten simple rules for getting help from online scientific communities. Plos Computational Biology. 7: e1002202. PMID 21980280 DOI: 10.1371/journal.pcbi.1002202  1
2011 Roque FS, Jensen PB, Schmock H, Dalgaard M, Andreatta M, Hansen T, Søeby K, Bredkjær S, Juul A, Werge T, Jensen LJ, Brunak S. Using electronic patient records to discover disease correlations and stratify patient cohorts. Plos Computational Biology. 7: e1002141. PMID 21901084 DOI: 10.1371/journal.pcbi.1002141  1
2011 Weinert BT, Wagner SA, Horn H, Henriksen P, Liu WR, Olsen JV, Jensen LJ, Choudhary C. Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Science Signaling. 4: ra48. PMID 21791702 DOI: 10.1126/scisignal.2001902  1
2011 Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology. 7: 473. PMID 21407210 DOI: 10.1038/msb.2011.6  1
2011 Fedorov O, Huber K, Eisenreich A, Filippakopoulos P, King O, Bullock AN, Szklarczyk D, Jensen LJ, Fabbro D, Trappe J, Rauch U, Bracher F, Knapp S. Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing. Chemistry & Biology. 18: 67-76. PMID 21276940 DOI: 10.1016/j.chembiol.2010.11.009  1
2011 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Molecular & Cellular Proteomics : McP. 10: M110.003590. PMID 21139048 DOI: 10.1074/mcp.M110.003590  1
2011 Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Research. 39: D261-7. PMID 21062810 DOI: 10.1093/nar/gkq1104  1
2011 Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research. 39: D561-8. PMID 21045058 DOI: 10.1093/nar/gkq973  1
2010 Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, et al. A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Molecular Systems Biology. 6: 430. PMID 21119626 DOI: 10.1038/msb.2010.87  1
2010 Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P. Drug-induced regulation of target expression. Plos Computational Biology. 6. PMID 20838579 DOI: 10.1371/journal.pcbi.1000925  1
2010 Jensen LJ, Bork P. Ontologies in quantitative biology: a basis for comparison, integration, and discovery. Plos Biology. 8: e1000374. PMID 20520843 DOI: 10.1371/journal.pbio.1000374  1
2010 Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S. Protein annotation in the era of personal genomics. Current Opinion in Structural Biology. 20: 335-41. PMID 20403684 DOI: 10.1016/j.sbi.2010.03.008  1
2010 Larsen MW, Zielinska DF, Martinelle M, Hidalgo A, Jensen LJ, Bornscheuer UT, Hult K. Suppression of water as a nucleophile in Candida antarctica lipase B catalysis. Chembiochem : a European Journal of Chemical Biology. 11: 796-801. PMID 20235107 DOI: 10.1002/cbic.200900743  1
2010 Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biology. 11: R24. PMID 20193063 DOI: 10.1186/gb-2010-11-3-r24  1
2010 Trachana K, Jensen LJ, Bork P. Evolution and regulation of cellular periodic processes: a role for paralogues. Embo Reports. 11: 233-8. PMID 20168326 DOI: 10.1038/embor.2010.9  1
2010 Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology. 6: 343. PMID 20087340 DOI: 10.1038/msb.2009.98  1
2010 Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Science Signaling. 3: ra3. PMID 20068231 DOI: 10.1126/scisignal.2000475  1
2010 Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS. Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Research. 38: D699-702. PMID 19934261 DOI: 10.1093/nar/gkp1044  1
2010 Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research. 38: D190-5. PMID 19900971 DOI: 10.1093/nar/gkp951  1
2010 Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research. 38: D552-6. PMID 19897548 DOI: 10.1093/nar/gkp937  1
2010 Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider R. Martini: using literature keywords to compare gene sets. Nucleic Acids Research. 38: 26-38. PMID 19858102 DOI: 10.1093/nar/gkp876  1
2010 O'Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJ. Reflect: A practical approach to web semantics Journal of Web Semantics. 8: 182-189. DOI: 10.1016/j.websem.2010.03.003  1
2009 Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Reflect: augmented browsing for the life scientist. Nature Biotechnology. 27: 508-10. PMID 19513049 DOI: 10.1038/nbt0609-508  1
2009 Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/gb-2009-10-2-206  1
2009 Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, Kuhn M, Wu S. Microblogging the ISMB: a new approach to conference reporting. Plos Computational Biology. 5: e1000263. PMID 19180175 DOI: 10.1371/journal.pcbi.1000263  1
2009 Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/pnas.0808022106  1
2009 Csikász-Nagy A, Kapuy O, Tóth A, Pál C, Jensen LJ, Uhlmann F, Tyson JJ, Novák B. Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Molecular Systems Biology. 5: 236. PMID 19156128 DOI: 10.1038/msb.2008.73  1
2009 Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research. 37: D412-6. PMID 18940858 DOI: 10.1093/nar/gkn760  1
2008 Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, et al. Text mining for biology--the way forward: opinions from leading scientists. Genome Biology. 9: S7. PMID 18834498 DOI: 10.1186/gb-2008-9-s2-s7  1
2008 Jensen LJ, Bork P. Biochemistry. Not comparable, but complementary. Science (New York, N.Y.). 322: 56-7. PMID 18832636 DOI: 10.1126/science.1164801  1
2008 Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, et al. Linear motif atlas for phosphorylation-dependent signaling. Science Signaling. 1: ra2. PMID 18765831 DOI: 10.1126/scisignal.1159433  1
2008 Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science (New York, N.Y.). 321: 263-6. PMID 18621671 DOI: 10.1126/science.1158140  1
2008 Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P. Circular reasoning rather than cyclic expression. Genome Biology. 9: 403. PMID 18598377 DOI: 10.1186/gb-2008-9-6-403  1
2008 Harrington ED, Jensen LJ, Bork P. Predicting biological networks from genomic data. Febs Letters. 582: 1251-8. PMID 18294967 DOI: 10.1016/j.febslet.2008.02.033  1
2008 Kuhn M, Campillos M, González P, Jensen LJ, Bork P. Large-scale prediction of drug-target relationships. Febs Letters. 582: 1283-90. PMID 18291108 DOI: 10.1016/j.febslet.2008.02.024  1
2008 Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research. 36: D684-8. PMID 18084021 DOI: 10.1093/nar/gkm795  1
2008 Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Gene. 407: 199-215. PMID 17996400 DOI: 10.1016/j.gene.2007.10.012  1
2008 Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T. NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Research. 36: D695-9. PMID 17981841 DOI: 10.1093/nar/gkm902  1
2008 Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, et al. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research. 36: D919-22. PMID 17942422 DOI: 10.1093/nar/gkm862  1
2008 Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research. 36: D250-4. PMID 17942413 DOI: 10.1093/nar/gkm796  1
2008 Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS. Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Research. 36: D854-9. PMID 17940094 DOI: 10.1093/nar/gkm729  1
2008 Yeats C, Orengo C, Veuthey AL, Boeckmann B, Jensen LJ, Valencia A, Rausell A, Bork P. Modern genome annotation: The BioSapiens network Modern Genome Annotation: the Biosapiens Network. 213-238. DOI: 10.1007/978-3-211-75123-7_11  1
2007 Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences of the United States of America. 104: 13913-8. PMID 17717083 DOI: 10.1073/pnas.0702636104  1
2007 de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ. Evolution of cell cycle control: same molecular machines, different regulation. Cell Cycle (Georgetown, Tex.). 6: 1819-25. PMID 17671420  1
2007 Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, et al. Systematic discovery of in vivo phosphorylation networks. Cell. 129: 1415-26. PMID 17570479 DOI: 10.1016/j.cell.2007.05.052  1
2007 von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science (New York, N.Y.). 315: 1126-30. PMID 17272687 DOI: 10.1126/science.1133420  1
2007 Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Molecular Systems Biology. 3: 72. PMID 17224916 DOI: 10.1038/msb4100112  1
2007 von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research. 35: D358-62. PMID 17098935 DOI: 10.1093/nar/gkl825  1
2006 Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM. Assessing systems properties of yeast mitochondria through an interaction map of the organelle. Plos Genetics. 2: e170. PMID 17054397 DOI: 10.1371/journal.pgen.0020170  1
2006 Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature. 443: 594-7. PMID 17006448 DOI: 10.1038/nature05186  1
2006 Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE. A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development. Developmental Cell. 10: 797-807. PMID 16740481 DOI: 10.1016/j.devcel.2006.04.009  1
2006 Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bähler J. The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast (Chichester, England). 23: 261-77. PMID 16544289 DOI: 10.1002/yea.1351  1
2006 Campillos M, von Mering C, Jensen LJ, Bork P. Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Research. 16: 374-82. PMID 16449501 DOI: 10.1101/gr.4336406  1
2006 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, et al. Proteome survey reveals modularity of the yeast cell machinery. Nature. 440: 631-6. PMID 16429126 DOI: 10.1038/nature04532  1
2006 Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW. Origin of replication in circular prokaryotic chromosomes. Environmental Microbiology. 8: 353-61. PMID 16423021 DOI: 10.1111/j.1462-2920.2005.00917.x  0.56
2006 Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews. Genetics. 7: 119-29. PMID 16418747 DOI: 10.1038/nrg1768  1
2006 Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P. Extraction of regulatory gene/protein networks from Medline. Bioinformatics (Oxford, England). 22: 645-50. PMID 16046493 DOI: 10.1093/bioinformatics/bti597  1
2005 Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M. Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system. The Journal of Cell Biology. 171: 627-40. PMID 16286509 DOI: 10.1083/jcb.200507168  1
2005 Shah PK, Jensen LJ, Boué S, Bork P. Extraction of transcript diversity from scientific literature. Plos Computational Biology. 1: e10. PMID 16103899 DOI: 10.1371/journal.pcbi.0010010  1
2005 Saric J, Jensen LJ, Rojas I. Large-scale extraction of gene regulation for model organisms in an ontological context. In Silico Biology. 5: 21-32. PMID 15972005  0.64
2005 Ussery DW, de Lichtenberg U, Jensen LJ. Crystal ball. Systems biology: in the broadest sense of the word. Environmental Microbiology. 7: 482-3. PMID 15816924 DOI: 10.1111/j.1462-2920.2005.803_12.x  0.8
2005 Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P. Systematic association of genes to phenotypes by genome and literature mining. Plos Biology. 3: e134. PMID 15799710 DOI: 10.1371/journal.pbio.0030134  1
2005 Jensen LJ, Steinmetz LM. Re-analysis of data and its integration. Febs Letters. 579: 1802-7. PMID 15763555 DOI: 10.1016/j.febslet.2005.02.006  1
2005 de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science (New York, N.Y.). 307: 724-7. PMID 15692050 DOI: 10.1126/science.1105103  1
2005 von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research. 33: D433-7. PMID 15608232 DOI: 10.1093/nar/gki005  1
2005 de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (Oxford, England). 21: 1164-71. PMID 15513999 DOI: 10.1093/bioinformatics/bti093  1
2004 Korbel JO, Jensen LJ, von Mering C, Bork P. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nature Biotechnology. 22: 911-7. PMID 15229555 DOI: 10.1038/nbt988  1
2004 Jensen LJ, Lagarde J, von Mering C, Bork P. ArrayProspector: a web resource of functional associations inferred from microarray expression data. Nucleic Acids Research. 32: W445-8. PMID 15215427 DOI: 10.1093/nar/gkh407  1
2004 Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. Protein interaction networks from yeast to human. Current Opinion in Structural Biology. 14: 292-9. PMID 15193308 DOI: 10.1016/j.sbi.2004.05.003  1
2004 Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S. Feature-based prediction of non-classical and leaderless protein secretion. Protein Engineering, Design & Selection : Peds. 17: 349-56. PMID 15115854 DOI: 10.1093/protein/gzh037  1
2003 Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure (London, England : 1993). 11: 1453-9. PMID 14604535 DOI: 10.1016/j.str.2003.10.002  1
2003 Jensen LJ, Ussery DW, Brunak S. Functionality of system components: conservation of protein function in protein feature space. Genome Research. 13: 2444-9. PMID 14559779 DOI: 10.1101/gr.1190803  1
2003 de Lichtenberg U, Jensen TS, Jensen LJ, Brunak S. Protein feature based identification of cell cycle regulated proteins in yeast. Journal of Molecular Biology. 329: 663-74. PMID 12787668 DOI: 10.1016/S0022-2836(03)00490-X  1
2003 Jensen LJ, Skovgaard M, Sicheritz-Pontén T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D. Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome. Bmc Genomics. 4: 12. PMID 12697059  0.48
2003 Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. Prediction of human protein function according to Gene Ontology categories. Bioinformatics (Oxford, England). 19: 635-42. PMID 12651722 DOI: 10.1093/bioinformatics/btg036  1
2002 Jensen LJ, Skovgaard M, Brunak S. Prediction of novel archaeal enzymes from sequence-derived features. Protein Science : a Publication of the Protein Society. 11: 2894-8. PMID 12441387 DOI: 10.1110/ps.0225102  1
2002 Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB, Saxild HH, Nielsen C, Brunak S, Knudsen S. A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biology. 3: research0048. PMID 12225587  1
2002 Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki K, Workman C, Andersen CA, Knudsen S, Krogh A, Valencia A, Brunak S. Prediction of human protein function from post-translational modifications and localization features. Journal of Molecular Biology. 319: 1257-65. PMID 12079362 DOI: 10.1016/S0022-2836(02)00379-0  1
2002 Gupta R, Jensen LJ, Brunak S. Orphan protein function and its relation to glycosylation. Ernst Schering Research Foundation Workshop. 276-94. PMID 12061006  1
2001 Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A. On the total number of genes and their length distribution in complete microbial genomes. Trends in Genetics : Tig. 17: 425-8. PMID 11485798 DOI: 10.1016/S0168-9525(01)02372-1  1
2000 Friis C, Jensen LJ, Ussery DW. Visualization of pathogenicity regions in bacteria. Genetica. 108: 47-51. PMID 11145420  0.56
2000 Jensen LJ, Knudsen S. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics (Oxford, England). 16: 326-33. PMID 10869030  0.36
2000 Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escherichia coli. Journal of Molecular Biology. 299: 907-30. PMID 10843847 DOI: 10.1006/jmbi.2000.3787  1
2000 Worning P, Jensen LJ, Nelson KE, Brunak S, Ussery DW. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Research. 28: 706-9. PMID 10637321  1
1999 Jensen LJ, Friis C, Ussery DW. Three views of microbial genomes. Research in Microbiology. 150: 773-7. PMID 10673014  0.56
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