Publications

Submitted manuscripts

None available as preprints.

Research articles

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 T, Guha R (2017). Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research.
Abstract

Belstrøm D, Jersie-Christensen​ RR, Lyon D, Damgaard C, Jensen LJ, Holmstrup P and Olsen JV (2016). Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls. PeerJ, 4:2433.
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Wang Q, Abdul SS, 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 and Arighi CN (2016). Overview of the interactive task in BioCreative V. Database, 2016:baw119.
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Lückmann M, Amarandi RM, Papargyri N, Jakobsen MH, Christiansen E, Jensen LJ, Pui A, Schwartz TW, Rosenkilde MM and Frimurer TM (2016). Structure-based discovery of novel US28 small molecule ligands with different modes of action. Chemical Biology and Drug Design.
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Larsen SC, Sylvestersen KB, Mund A, Lyon D, Mullari M, Madsen MV, Daniel JA, Jensen LJ and Nielsen ML (2016). Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells. Science Signaling, 9:rs9.
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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 C-M, 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, Erik Sonnhammer E and Dessimoz C (2016). Standardized benchmarking in the quest for orthologs. Nature Methods, 13:425-430.
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Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C and Jensen LJ (2016). EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database, 2016:baw005.
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Franceschini A, Lin J, von Mering C and Jensen LJ (2016). SVD-Phy: Improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics, 32:1085-1087.
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Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P and Kuhn M (2016). STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research, 44:D380-D384.
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Huerta-Cepas J, Szklarczyk D, Forslund K, H. Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C and Bork P (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research, D1:D286-D293.
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Kuhn M, Letunic I, Jensen LJ and Bork P (2016). The SIDER database of drugs and side effects. Nucleic Acids Research, D1:D1075-D1079.
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Pedersen CC, Refsgaard JC, Østergaard O, Jensen LJ, Heegaard NHH, Borregaard N and Cowland JB (2015). Impact of microRNA-130a on the neutrophil proteome. BMC Immunology, 16:70.
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Schölz C, Lyon D, Refsgaard JC, Jensen LJ, Choudhary C and Weinert BT (2015). Avoiding abundance bias in the functional annotation of posttranslationally modified proteins. Nature Methods, 12:1003-1004.
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Deshmukh AS, Cox J, Jensen LJ, Meissner F and Mann M (2015). Secretome analysis of lipid induced insulin resistance in skeletal muscle cells by a combined experimental and bioinformatics workflow. Journal of Proteome Research, 14:4885-4895.
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Pallejà A and Jensen LJ (2015). HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. PeerJ, 3:e1057.
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Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O’Donoghue SI and Jensen LJ (2015). Comprehensive comparison of large-scale tissue expression datasets. PeerJ, 3:e1054.
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Warrer P, Jensen PB, Aagaard L, Jensen LJ, Brunak S, Krag MH, Rossing P, Almdal T, Andersen HU and Hansen EH (2015). Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines. Journal of Research in Pharmacy Practice, 4:64-72.
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Emdal KB, Pedersen A-K, Bekker-Jensen DB, Tsafou KP, Horn H, Lindner S, Schulte JH, Eggert A, Jensen LJ, Francavilla C and Olsen JV (2015). Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. Science Signaling, 8:ra40.
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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 and Choudhary C (2015). Acetylation site specificities of lysine deacetylase inhibitors in human cells. Nature Biotechnology, 33:415-423, 2015.
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Pafilis E, Pletscher-Frankild S, Schnetzer J, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou V, Leary P, Hammock J, Schulz K, Parr CS, Arvanitidis C and Jensen LJ (2015). ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics, 31:1872-1874.
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Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ and Mann M (2015). Mass spectrometry of HLA-I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Molecular and Cellular Proteomics, 14:658-673.
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Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX and Jensen LJ (2015). DISEASES: Text mining and data integration of disease–gene associations. Methods, 74:83-89.
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Santos A, Wernersson R and Jensen LJ (2015). Cyclebase 3.0: A multi-organism database on cell-cycle regulation and phenotypes. Nucleic Acids Research, 43:D1140-D1144.
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Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P*, Jensen LJ* and von Mering C* (2015). STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43:D447-D452.
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Eriksson R, Aagaard L, Jensen LJ, Borisova L, Hørlück D, Brunak S and Hansen EH (2014). 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.
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Jensen AB, Moseley PL, Oprea T, Ellesøe SG, Eriksson R, Schmock H, Jensen PB, Jensen LJ* and Brunak S* (2014). Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients. Nature Communications, 5:4022.
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Rudolf AF, Skovgaard T, Jensen* LJ and Berthelsen* J (2014). A comparison of protein kinases inhibitor screening methods using both enzymatic activity and binding affinity determination. PLOS ONE, 9:e98800.
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Horn H*, Schoof EM*, Kim J*, Robin X, Miller ML, Diella F, Palma A, Cesareni G, Jensen LJ* and Linding R* (2014). KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods, 11:603-604.
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Bøgebo R, Horn H, Olsen JV, Gammeltoft S, Jensen LJ, Hansen JL and Christensen GL (2014). Predicting kinase activity in Angiotensin receptor phosphoproteomes based on sequence-motifs and interactions. PLOS ONE, 9:e94672.
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Horn H, Haslam N and Jensen LJ (2014). DoReMi: context-based prioritization of linear motif matches. PeerJ, 2:e315.
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Sylvestersen KB, Horn H, Jungmichel S, Jensen LJ and Nielsen ML (2014). Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest. Molecular and Cellular Proteomics, 13:2072-2088.
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Eriksson R, Werge T, Jensen LJ and Brunak S (2014). Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population. Drug Safety, 37:237-247.
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Binder JX*, Pletscher-Frankild S*, Tsafou K, Stolte C, O’Donoghue SI, Schneider R and Jensen LJ (2014). COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database, 2014:bau012.
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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* and Bork P* (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42:D231-D239.
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Kuhn M*, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ* and Bork P* (2014). STITCH 4: integration of protein-chemical interactions with user data. Nucleic Acids Research, 42:D401-D407.
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Mørk S, Pletscher-Frankild S, Palleja A, Gorodkin J* and Jensen LJ* (2014). Protein-driven inference of miRNA-disease associations. Bioinformatics, 30:392-937.
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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, White KP and Rzhetsky A (2013). A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell, 155:70-80.
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Hekmat O, Munk S, Fogh L, Yadav R, Francavilla C, Horn H, Wurtz SO, Schrohl A-S, Damsgaard B, Romer MU, Belling K, Jensen NF, Gromova I, Bekker-Jensen DB, Moreira JM, Jensen LJ, Gupta R, Lademann U, Brunner N, Olsen JV and Stenvang J (2013). TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells. Journal of Proteome Research, 12:4136-4151.
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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, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup, CD Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J and Willerslev E (2013). Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature, 499:74-78.
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Lundby A, Andersen MN, Steffensen AB, Horn H, Kelstrup CD, Francavilla C, Jensen LJ, Schmitt N, Thomsen MB and Olsen JV (2013). In vivo phosphoproteomics analysis reveals the cardiac targets of β-adrenergic receptor signaling. Science Signalling, 6:rs11.
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Pafilis E, Pletscher-Frankild S, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, Arvanitidis C and Jensen LJ (2013). The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text. PLOS ONE, 8:e65390.
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Eriksson R, Jensen PB, Pletscher-Frankild S, Jensen LJ and Brunak S (2013). Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. Journal of the American Medical Informatics Association, 20:947-953.
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Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin A-C and Bork P (2013). Systematic identification of proteins that elicit drug side effects. Molecular Systems Biology, 9:663.
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Franceschini A, Szklarczyk D, Pletscher-Frankild S*, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P*, von Mering C* and Jensen LJ* (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research, 41:D808-D815.
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Croft LJ, Szklarczyk D, Jensen LJ and Gorodkin J (2012). Multiple independent analyses reveal transcription factors are the only enriched functional class associated with microRNAs. BMC Systems Biology, 6:90.
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Poulsen JW, Madsen CT, Young C, Kelstrup CD, Grell HC, Henriksen P, Jensen LJ and Nielsen ML (2012). Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. Journal of Proteomics, 75:3886-3897.
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Frenkel-Morgenstern M, Danon T, Christian T, Igarashi T, Cohen L, Hou Y-M and Jensen LJ (2012). Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Molecular Systems Biology, 8:572.
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Bergholdt R, Brorsson C, Palleja A, Berchtold LA, Fløyel T, Bang-Berthelsen CH, Frederiksen KS, Jensen LJ, Størling J and Pociot F (2012). Identification of Novel Type 1 Diabetes Candidate Genes by Integrating Genome-Wide Association Data, Protein-Protein Interactions, and Human Pancreatic Islet Gene Expression. Diabetes, 61:954-962.
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Romanel A, Jensen LJ, Cardelli L and Csikász-Nagy A (2012). Transcriptional regulation is a major controller of cell cycle transition dynamics. PLoS One, 7:e29716.
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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* and Bork P* (2012). eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research, 40:D284-D289.
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Kuhn M*, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ and Bork P* (2012). STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research, 40:D876-D880.
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Pallejà A, Horn H, Eliasson S and Jensen LJ (2012). DistiLD Database: diseases and traits in linkage disequilibrium blocks. Nucleic Acids Research, 40:D1036-D1040.
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Warrer P, Hansen EH, Jensen LJ and Aagaard L (2011). Using text-mining techniques in electronic patient records to identify ADRs from medicine use. British Journal of Clinical Pharmacology, 73:674-684.
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Cappellini E, Jensen LJ, Szklarczyk D, Ginolhac A, da Fonseca RA, Stafford TW, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MT and Olsen JV (2011). Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins. Journal of Proteome Research, 11:917-926.
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Parnell LD, Lindenbaum P, Shameer K, Dall’Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, Albert I (2011). BioStar: An Online Question & Answer Resource for the Bioinformatics Community. PLoS Computational Biology, 7:e1002216.
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Waters MR, Stafford Jr. TW, McDonald HG, Gustafson C, Rasmussen M, Cappellini E, Olsen JV, Szklarczyk D, Jensen LJ, Gilbert MTP, Willerslev E (2011). Pre-Clovis Mastodon Hunting 13,800 Years Ago at the Manis Site, Washington. Science, 334:351-353.
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Roque FS*, Jensen PB*, Schmock H, Dalgaard M, Andreatta M, Hansen T, Søeby K, Bredkjær S, Juul A, Werge T, Jensen LJ and Brunak S (2011). Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. PLoS Computational Biology, 7:e1002141.
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Weinert BT, Wagner SA, Horn H, Henriksen P, Liu WR, Olsen JV, Jensen LJ and Choudhary C (2011). Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Science Signaling, 4:ra48.
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Raes J, Letunic I, Yamada T, Jensen LJ and Bork P (2011). Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology, 7:473.
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Fedorov O, Huber K, Eisenreich A, Filippakopoulos P, King O, Bullock AN, Szklarczyk D, Jensen LJ, Fabbro D, Trappe J, Rauch U, Bracher F and Knapp S (2011). Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing. Chemistry and Biology, 18:67-76.
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Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ*, Mailand N* and Nielsen ML* (2011). Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Molecular and Cellular Proteomics, 10:M110.003590.
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Dinkel H, Chica C, Via A, Gould C, Jensen LJ, Gibson T and Diella F (2011). Phospho.ELM: a database of phosphorylation sites – update 2011. Nucleic Acids Research, 39:D261-D267.
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Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ and von Mering C (2011). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research, 39:D561-D568.
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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, Kaksonen M, Russell RB and Gavin A-C (2010). A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae. Molecular Systems Biology, 6:430.
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Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V and Bork P (2010). Drug-induced regulation of target expression. PLoS Computational Biology, 6:e1000925.
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O’Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R and Jensen LJ (2010). Reflect: a practical approach to web semantics. Journal of Web Semantics, 8:182-189.
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Larsen MW, Zielinska DF, Martinelle M, Hidalgo A, Jensen LJ, Bornscheuer UT and Hult K (2010). Suppression of water as a nucleophile in Candida antarctica Lipase B catalysis. ChemBioChem, 11:796-801.
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Granovskaia MV*, Jensen LJ*, Ritchie ME*, Toedling J, Ning Y, Bork P, Huber W and Steinmetz LM (2010). High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biology, 11:R24.
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Trachana K, Jensen LJ and Bork P (2010). Evolution and regulation of cellular periodic processes: a role for paralogues. EMBO Reports, 11:233-238.
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Kuhn M, Campillos M, Letunic I, Jensen LJ and Bork P (2010). A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology, 6:343.
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Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S and Mann M (2010). A systems view of the cell cycle by quantitative phosphoproteomics reveals widespread stoichiometric phosphorylation events in mitosis. Science Signaling, 3:ra3.
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Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ and Bork P (2010). eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced Non-supervised Orthologous Groups, species and functional annotations. Nucleic Acids Research, 38:D190-D195.
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Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A and Bork P (2010). STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research, 38:D552-D566.
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Gauthier N, Jensen LJ, Wernersson R, Brunak S and Jensen TS (2010). Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Research, 38:D699-D702.
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Soldatos T, O’Donoghue SI, Satagopam V, Jensen LJ, Brown N, Barbosa da Silva A and Schneider R (2010). Martini: using literature keywords to compare gene sets. Nucleic Acids Research, 38:26-38.
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Pafilis E, O’Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP and Schneider R (2009). Reflect: augmented browsing for the life scientist. Nature Biotechnology, 27:508-510.
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Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P and Gerstein MB (2009).Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences, 106:1374-1379.
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Csikász-Nagy A, Kapuy O, Tóth A, Pál C, Jensen LJ, Uhlmann F, Tyson JJ and Novák B (2009). Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Molecular Systems Biology, 5:236.
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Jensen LJ*, Kuhn M*, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P and von Mering C (2009). STRING 8 – a global view on proteins and their functional interactions in 630 model organisms. Nucleic Acids Research, 37:D412-D416.
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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, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R (2008). Linear motif atlas for phosphorylation-dependent signaling. Science Signaling, 1:ra2.
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Campillos M*, Kuhn M*, Gavin A-C, Jensen LJ and Bork P (2008). Drug target identification using side-effect similarity. Science, 321:263-266.
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Jensen LJ*, de Lichtenberg U*, Jensen TS, Brunak S and Bork P (2008). Circular reasoning rather than cyclic expression. Genome Biology, 9:403.
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Kuhn M, von Mering C, Campillos M, Jensen LJ and Bork P (2008). STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research, 36:D684-D688.
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Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MP and Pawson T (2008). NetworKIN: a resource for exploring cellular phosphorylation network. Nucleic Acids Research, 36:D695-D699.
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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 and Preissner R (2008). SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research, 36:D919-D922.
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Jensen LJ*, Julien P*, Kuhn M, von Mering C, Muller J, Doerks T and Bork P (2008). eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research, 36:D250-D254.
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Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ and Brunak S (2008). Cyclebase.org – a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Research, 36, D854-D859.
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Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P and Sowdhamini R (2008). Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Gene, 407:199-215.
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Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J and Bork P (2007). Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences, 104:13913-13918.
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Linding R*, Jensen LJ*, Ostheimer GJ*, van Vugt MATM, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB and Pawson T (2007). Systematic discovery of in vivo phosphorylation networks. Cell, 129:1415-1426.
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von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N and Bork P (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315:1126-1130.
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Hooper SD*, Boue S*, Krause R*, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE and Bork P (2007). Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Molecular Systems Biology, 3:72.
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von Mering C*, Jensen LJ*, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B and Bork P (2007). STRING 7 – recent developments in the integration and prediction of protein interactions. Nucleic Acids Research, 35:D358-D362.
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Perocchi F, Jensen LJ, Gagneur J, Athing U, von Mering C, Bork P, Prokisch H and Steinmetz LM (2006). Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genetics, 2:1612-1624.
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Jensen LJ*, Jensen TS*, de Lichtenberg U*, Brunak S and Bork P (2006). Co-evolution of transcriptional and posttranslational cell cycle regulation. Nature, 433:594-597.
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Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P and Furlong EE (2006). A temporal map of transcription factor activity: Mef2 directly regulates target genes at all stages of muscle development. Developmental Cell, 10:797-807.
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Marguerat S*, Jensen TS*, de Lichtenberg U, Wilhelm BT, Jensen LJ and Bähler J (2006). The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast, 23:261-277.
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Campillos M, von Mering C, Jensen LJ and Bork P (2006). Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Research, 16:374-382.
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Gavin A-C*, 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, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB and Superti-Furga G (2006). Proteome survey reveals modularity of the yeast cell machinery. Nature, 440:631-636.
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Worning P*, Jensen LJ*, Hallin PF, Stærfeldt HH and Ussery DW (2006). Origin of replication in circular prokaryotic chromosomes. Environmental Microbiology, 8:353-361.
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Saric J*, Jensen LJ*, Ouzounova R, Rojas R and Bork P (2006). Extraction of regulatory gene/protein networks from Medline. Bioinformatics, 22:645-650.
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Taxis C, Kavagiou Z, Keller P, Jensen LJ, Colombelli J, Bork P, Stelzer EHK and Knop M. Spore number control and breeding in Saccharomyces cerevisiae a key role for a self-organizing system. Journal of Cell Biology, 171:627-640.
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Shah PK, Jensen LJ, Boue S and Bork P (2005). Extraction of transcript diversity from scientific literature. PLoS Computational Biology, 1:e10.
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Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, S. Kaczanowski, S.D. Hooper, M.A. Andrade, and P. Bork (2005). Systematic association of genes to phenotypes by genome and literature mining. PLoS Biology, 5:e134.
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Jensen LJ and Steinmetz LM (2005). Re-analysis of data and its integration. FEBS Letters, 579:1802-1807.
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de Lichtenberg U*, Jensen LJ*, Brunak S and Bork P (2005). Dynamic complex formation during the yeast cell cycle. Science, 307:724-727.
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de Lichtenberg U*, Jensen LJ*, Fausbøll A, Jensen TS, Bork P and Brunak S (2005). Comparison of computational methods for the identification of cell cycle regulated genes. Bioinformatics, 21:1164-1171.
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von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA and Bork P (2005). STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research, 33:D433-D437.
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Saric J, Jensen LJ, and Rojas I (2004). Large-scale extraction of gene regulation for model organisms in an ontological context. In Silico Biology, 5:0004.
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Korbel JO, Jensen LJ, von Mering C and Bork P (2004). Analysis of genomic context: Prediction of functional associations from bidirectionally transcribed gene pairs. Nature Biotechnology, 22:911-917.
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Jensen LJ, Lagarde J, von Mering C and Bork P (2004). ArrayProspector: A web resource of functional associations inferred from microarray expression data. Nucleic Acids Research, 32:W445-W448.
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Bork P*, Jensen LJ*, von Mering C*, Ramani AK*, Lee I* and Marcotte EM* (2004). Protein interaction networks from yeast to human. Current Opinions in Structural Biology, 14:292-299.
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Bendtsen JD, Jensen LJ, Blom N, von Heijne G and Brunak S (2004). Feature based prediction of non-classical and leaderless protein secretion. Protein Engineering Design and Selection, 17:349-356.
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Linding R*, Jensen LJ*, Diella F, Bork P, Gibson TJ and Russell RB (2003). Protein disorder prediction: implications for structural proteomics. Structure, 11:1453-1459.
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Jensen LJ, Ussery DW, and Brunak S (2003). Functionality of system components: Conservation of protein function in protein feature space. Genome Research, 13:2444-2449.
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de Lichtenberg U, Jensen TS, Jensen LJ, and Brunak S (2003). Protein feature based identification of cell cycle regulated proteins in yeast. Journal of Molecular Biology, 329:663-674.
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Jensen LJ, Skovgaard M, Sicheritz-Pontén T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N and Ussery DW (2003). Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome. BMC Genomics, 4:12.
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Jensen LJ, Gupta R, Stærfeldt HH and Brunak S (2003). Prediction of human protein function according to Gene Ontology categories. Bioinformatics, 19:635-642.
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Jensen LJ, Skovgaard M, and Brunak S (2002). Prediction of novel archaeal enzymes from sequence-derived features. Protein Science, 11:2894-2898.
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Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Saxild HH, Nielsen C, Brunak S, and Knudsen S (2002). A new non-linear normalization method to reduce variability in DNA microarray experiments. Genome Biology, 3:0048.1-0048.16.
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Jensen LJ*, Gupta R*, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Stærfeldt HH, Rapacki K, Workman C, Andersen CAF, Knudsen S, Krogh A, Valencia A and Brunak S (2002). Prediction of human protein function from post-translational modifications and localization features. Journal of Molecular Biology, 319:1257-1265.
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Skovgaard M, Jensen LJ, Brunak S, Ussery DW and Krogh A (2001). On the total number of genes and their length distribution in complete microbial genomes. Trends in Genetics, 17:425-428.
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Worning P, Jensen LJ, Nelson KE, Brunak S and Ussery DW (2000). Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Research, 28:706-709.
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Friis C, Jensen LJ and Ussery DW (2000). Visualization of pathogenicity regions in bacteria. Genetica, 108:47-51.
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Jensen LJ and Knudsen S (2000). Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics, 16:326-333.
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Pedersen AG*, Jensen LJ*, Stærfeldt HH, Brunak S and Ussery DW (2000). A DNA structural atlas of E. coli. Journal of Molecular Biology, 299:907-930.
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Jensen LJ, Friis C and Ussery DW (1999). Three views of microbial genomes. Research in Microbiology, 150:773-777.
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Jensen LJ, Andersen KV, Svendsen A and Kretzschmar T (1998). Scoring functions for computational algorithms applicable to the design of spiked oligonucleotides. Nucleic Acids Research, 26:697-702.
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Conference proceedings

Cook H, Pafilis E and Jensen LJ (2016). A dictionary- and rule-based system for identification of bacteria and habitats in text. Proceedings of the 4th BioNLP Shared Task Workshop, 50-55.
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Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C and Jensen LJ (2015). EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Proceedings of BioCreative V, 384-395.
WWW

Wang Q, Abdul SS, Almeida L, Ananiadou S, Balderas-Martnez YI, Batista-Navarro R, Campos D, Chilton L, Chou H-J, Contreras G, Cooper L, Dai H-J, Fluck J, Gama S, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue T, Keseler I, Madan S, Matos S, McQuilton P, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Salgado D, Singh O, Stefancsik R, Su C-H, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-aryamontri A, Laulederkind S, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Hirschman L and Arighi C (2015). Overview of the Interactive Task in BioCreative V. Proceedings of BioCreative V, 364-383.

Pyysalo S, Campos J, Cejuela JM, Ginter F, Hakala K, Li C, Stenetorp S and Jensen LJ (2015). Sharing annotations better: RESTful Open Annotation. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics, 91-96.
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Goldberg T, Vinchurkar S, Cejuela JM, Jensen LJ* and B. Rost B* (2015). Linked annotations: a middle ground for manual curation of biomedical databases and text corpora. BMC Proceedings, 9(Suppl 5):A4.
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Saric J, Jensen LJ, Ouzounova R, Rojas I and Bork P (2004). Extracting Regulatory Gene Expression Networks from PubMed. Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics, 192-199.
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Reviews

Jensen PB, Jensen LJ and Brunak S (2013). Reply to ‘Mining electronic health records: an additional perspective’. Nature Reviews Genetics, 14:75.
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Jensen PB, Jensen LJ and Brunak S (2012). Mining electronic health records: towards better research applications and clinical care. Nature Reviews Genetics, 13:395-405.
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Jensen LJ and Bork P (2010). Ontologies in quantitative biology: A basis for comparison, integration and discovery. PLoS Biology, 8:e1000374.
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Blicher T, Gupta R, Wesolowska A, Jensen LJ and Brunak S (2010). Protein Annotation in the Era of Personal Genomics. Current Opinion in Structural Biology, 20:335-341.
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Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R and Brunak S (2009). Sequence-based feature prediction and annotation of proteins. Genome Biology, 10:206.
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Kuhn M*, Campillos M*, Gonzales P*, Jensen LJ* and Bork P* (2008). Large-scale prediction of drug-target relationships. FEBS Letters, 582:1283-1290.
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Harrington E, Jensen LJ and Bork P (2008). Predicting biological networks from genomic data. FEBS Letters, 582:1251-1258.
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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, Rebholz-Schuhmann D, Shatkay H and Valencia A (2008). Text mining for biology – the way forward: opinions from leading scientists. Genome Biology, 9:S7.
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de Lichtenberg U*, Jensen TS*, Brunak S, Bork P and Jensen LJ (2007). Evolution of Cell Cycle Control – Same Molecular Machines, Different Regulation. Cell Cycle, 6:1819-1825.
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Jensen LJ, Saric J and Bork P (2006). Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews Genetics, 7:119-129.
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Jensen LJ and Bork P (2004). Quality analysis and integration of large-scale molecular data sets. Drug Discovery Today: TARGETS, 3:51-56.
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Editorials

Have CT and Jensen LJ (2013). Are graph databases ready for bioinformatics? Bioinformatics, 29:3107-3108.
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Jensen LJ and Bateman A (2011). The rise and fall of supervised machine learning techniques. Bioinformatics, 27:3331–3332, 2011.
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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 and Laayouni H (2011). Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology, 7:e1002202.
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Saunders N, Beltrão P, Jensen LJ, Jurczak D, Krause R, Kuhn M and Wu S (2009). Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Computational Biology, 5:e1000263.
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Jensen LJ and Bork P (2008). Not comparable, but complementary. Science, 322:56-57.
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Ussery DW, de Lichtenberg U and Jensen LJ (2005). Systems biology: in the broadest sense of the word. Environmental Microbiology, 7:482-483.
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Book chapters

Refsgaard JC, Munk S and Jensen LJ (2016). Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics. Methods in Molecular Biology, 1355:323-339.
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Munk S, Refsgaard JC, Olsen JV and Jensen LJ. From Phosphosites to Kinases. Methods in Molecular Biology, 1355:307-321.
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Tsafou K and Jensen LJ (2016). Integrative systems biology. Encyclopedia of Cell Biology, 4:245-251.

Szklarczyk D and Jensen LJ (2015). Protein-protein interaction databases. Methods Molecular Biology, 1278:39-56.
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Frishman D, Albert M, Blankenburg H, Bork P, Harrington ED, Hermjakob H, Jensen LJ, Juan DA, Lengauer T, Pagel P, Schachter V and Valencia A (2009). Protein–protein interactions: analysis and prediction. Modern Genome Annotation: The BioSapiens Network, 353-410.

Veuthey AL, Boeckmann B, Jensen LJ, Valencia A, Rausell A and Bork P (2009). Homologous and non-homologous sequence methods for assigning protein function. Modern Genome Annotation: The BioSapiens Network, 213-238.

Jensen LJ, Skovgaard M, Sicheritz-Pontén T, Hansen NT, Johanson H, Jørgensen MK, Kiil K and Ussery DW (2004). Comparative genomics of four Pseudomonas species. The Pseudomonads, 1:139-164.
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Skovgaard M, Jensen LJ, Friis C, Stærfeldt HH, Worning P, Brunak S and Ussery DW (2002). The atlas visualisation of genome-wide information. Methods in Microbiology, 33:49-63.

Gupta R, Jensen LJ and Brunak S (2002). Orphan protein function and its relation to glycosylation. Ernst Schering Research Foundation Proceedings, 38, 275-294.
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* Joint first and/or joint corresponding authors.