Preprints

Batth TS, Locard-Paulet M, Doncheva NT, Mendez BL, Jensen LJ, Olsen JV (2024). Streamlined proteome-wide identification of drug targets indicates organ-specific engagement. bioRxiv.
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Nastou K, Koutrouli M, Pyysalo S and Jensen LJ (2023). Improving dictionary-based named entity recognition with deep learning. bioRxiv.
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Mehryary F*, Nastou K*, Ohta T, Jensen LJ* and Pyysalo S* (2023). STRING-ing together protein complexes: extracting physical protein interactions from the literature. bioRxiv.
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Webel H, Niu L, Nielsen AB, Locard-Paulet M, Mann M, Jensen LJ and Rasmussen S (2023). Mass spectrometry-based proteomics imputation using self supervised deep learning. bioRxiv.
Preprint

Research articles

2024

Rebak AS, Hendriks IA, Elsborg JD, Buch-Larsen SC, Nielsen CH, Terslev L, Kirsch R, Damgaard D, Doncheva NT, Lennartsson C, Rykaer M, Jensen LJ, Christophorou MA, Nielsen ML (2024). A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nature Structural & Molecular Biology.
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Koutrouli M, Nastou K, Lindez PP, Bouwmeester R, Rasmussen S, Martens L and Jensen LJ (2024). FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data. Bioinformatics, 2024:btae010.
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2023

Hjaltelin JX, Novitski SI, Jørgensen IF, Siggaard T, Vulpius SA, Westergaard D, Johansen JS, Chen IM, Jensen LJ and Brunak S (2023). Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records. eLife, 12:e84919.
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Rieneck K, Rasmussen KK, Schoof EM, Clausen FB, Holze H, Bergholt T, Jørgensen MH, Christensen VB, Almaas R, Jordal PL, Locard-Paulet M, Runager K, Nielsen LK, Schlotmann BC, Weischenfeldt JL, Jensen LJ and Dziegiel MH (2023). Hunting for the elusive target antigen in gestational alloimmune liver disease (GALD). PLOS One, 18:e0286432.
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Tantoso E, Eisenhaber B, Sinha S, Jensen LJ and Eisenhaber F (2023). Did the early full genome sequencing of yeast boost gene function discovery? Biology Direct, 18:46.
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Guzman UH, Aksnes H, Ree R, Krogh N, Jakobsson ME, Jensen LJ, Arnesen, T and Olsen JV (2023). Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae. Nature Communications, 4:4517.
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Israelsen M, Alvarez-Silva C, Madsen BS, Hansen CD, Torp NC, Johansen S, Hansen JK, Lindvig KP, Insonere J, Riviere V, Juel HB, Brejnrod A, Jensen LJ, Thiele M, Lelouvier B, Hansen T, Arumugam M, Krag A, MicrobLiver consortium and GALAXY consortium (2023). Impact of acute alcohol consumption on circulating microbiome in asymptomatic alcohol-related liver disease. Gut.
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Kjær C, Palasca O, Barzaghi G, Bak LK, Durhuus RKJ, Jakobsen E, Pedersen L, Bartels ED, Woldbye DPD, Pinborg LH and Jensen LJ (2023). Differential Expression of the β3 Subunit of Voltage-Gated Ca2+ Channel in Mesial Temporal Lobe Epilepsy. Molecular Neurobiology.
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Luoma M*, Nastou K*, Ohta T, Toivonen H, Pafilis E, Jensen LJ* and Pyysalo S* (2023). S1000: A better taxonomic name corpus for biomedical information extraction. Bioinformatics, 39:btad369.
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Diaz-delCastillo M, Palasca O, Nemler TT, Thygesen DM, Chávez-Saldaña NA, Vázquez-Mora JA, Ponce Gomez LY, Jensen LJ, Evans H, Andrews RE, Mandal A, Neves D, Mehlen P, Caruso JP, Dougherty PM, Price TJ, Chantry A, Lawson MA, Andersen TL, Jimenez-Andrade JM and Heegaard AM (2023). Metastatic infiltration of nervous tissue and periosteal nerve sprouting in multiple myeloma induced bone pain in mice and human. Journal of Neuroscience, 43:5414-5430.
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Kokoli M, Karatzas E, Baltoumas FA, Schneider R, Pafilis E, Paragkamian S, Doncheva NT, Jensen LJ and Pavlopoulos GA (2023). Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. Nucleic Acids Research Genomics and Bioinformatics, 5:lqad053.
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Tantoso E, Eisenhaber B, Sinha S, Jensen LJ and Eisenhaber F (2023). About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature. Biology Direct, 18:7.
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Doncheva NT, Morris JH, Holze H, Kirsch R, Nastou KC, Cuesta-Astroz Y, Rattei T, Szklarczyk D, von Mering C and Jensen LJ (2023). Cytoscape stringApp 2.0: Analysis and visualization of heterogeneous biological networks. Journal of Proteome Research, 22:637-646.
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Yarani R*, Palasca O*, Doncheva NT, Anthon C, Pilecki B, Svane CAS, Mirza AH, Litman T, Holmskov U, Bang-Berthelsen CH, Vilien M, Jensen LJ, Gorodkin J and Pociot F (2023). Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis. Frontiers in Molecular Biosciences, 9:1081176.
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Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger VT, Siramshetty VB, Nguyen D-T, Jensen LJ, Vidović D, Schürer SC, Holmes J, Sharma KR, Pillai A, Bologa CG, Edwards JS, Mathé EA and Oprea TI (2023). Pharos 2023: an integrated resource for the understudied human proteome. Nucleic Acids Research, 51:D1405-D1416.
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Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C and Jaime Huerta-Cepas J (2023). eggNOG 6.0: enabling comparative genomics across 12535 organisms. Nucleic Acids Research, 51:D389-D394.
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Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P*, Jensen LJ* and Christian von Mering C* (2023). The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51:D638-D646.
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2022

Locard-Paulet M, Palasca O and Jensen LJ (2022). Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies. PLOS Computational Biology, 18:e1010604.
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Koutrouli M, Morris JH, and Jensen LJ (2022). U-CIE [/juː 'siː/]: Color encoding of high-dimensional data. Protein Science, 31:e4388.
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Geissler A, Poulsen LD, Doncheva NT, Anthon C, Seemann SE, González-Tortuero E, Breüner A, Jensen LJ, Hjort C, Vinther J and Gorodkin J (2022). The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production. Frontiers in Microbiology, 13:909493.
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Versace E, Sgadò P, George J, Loveland JL, Ward J, Thorpe P, Jensen LJ, Spencer KA, Paracchini S and Vallortigara G (2022). Light-induced asymmetries in embryonic retinal gene expression are mediated by the vascular system and extracellular matrix. Scientific Reports, 12:12086.
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Bernard C*, Locard-Paulet M*, Noël C*, Duchateau M, Gianetto QG, Moumen B, Rattei T, Hechard Y, Jensen LJ, Matondo M and Samba-Louaka A (2022). A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nature Communications, 13:4104.
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Pfeiffer A, Franciosa G, Locard-Paulet M, Piga I, Reckzeh K, Vemulapalli V, Blacklow SC, Theilgaard-Mönch K, Jensen LJ and Olsen JV (2022). Phosphorylation of SHP2 at Tyr62 enables acquired resistance to SHP2 allosteric inhibitors in FLT3-ITD-driven AML. Cancer Research, 82:2141-2155.
PubMed Full text

Grissa D, Junge A, Oprea TI and Jensen LJ (2022). DISEASES 2.0: a weekly updated database of disease–gene associations from text mining and data integration. Database, 2022:baac019.
PubMed Full text Preprint WWW

Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ and Oprea TI (2022). A workflow of integrated resources to catalyze network pharmacology driven COVID-19 research. Journal of Chemical Information and Modeling, 62:718-729.
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Santos A, Colaço AR, Nielsen AB, Niu L, Strauss M, Geyer PE, Coscia F, Albrechtsen NJW, Mundt F, Jensen LJ and Mann M (2022). Clinical knowledge graph integrates proteomics data into clinical decision-making. Nature Biotechnology, 40:692-702.
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2021

Baltoumas FA, Zafeiropoulou S, Karatzas E, Paragkamian S, Thanati F, Iliopoulos I, Eliopoulos AG, Schneider R, Jensen LJ, Pafilis E and Pavlopoulos GA (2021). OnTheFly 2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. Nucleic Acids Research Genomics and Bioinformatics, 3:lqab090.
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Yang JJ, Grissa D, Lambert CG, Bologa CG, Mathias SL, Waller A, Wild DJ, Jensen LJ and Oprea TI (2021). TIGA: Target illumination GWAS analytics. Bioinformatics, 21:3865-3873.
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Linscheid N, Santos A, Poulsen PC, Mills RW, Calloe K, Leurs U, Ye JZ, Stolte C, Thomsen MB, Bentzen BH, Lundegaard PR, Olesen MS, Jensen LJ, Olsen JV and Lundby A (2021). Quantitative proteome comparison of human hearts with those of model organisms. PLOS Biology, 19:e3001144.
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Somyajit K, Spies J, Coscia F, Kirik U, Rask M-B, Lee J-H, Neelsen KJ, Mund A, Jensen LJ, Paull TT, Mann M, and Lukas J (2021). Homology-directed repair protects the replicating genome from metabolic assaults. Developmental Cell, 56:461-477.
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Doncheva NT, Palasca O, Yarani R, Litman T, Anthon C, Groenen M, Stadler PF, Pociot F, Jensen LJ*, and Gorodkin J* (2021). Human pathways in animal models: possibilities and limitations. Nucleic Acids Research, 49:1859-1871.
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Nissen JN, Johansen J, Allesøe RL, Sønderby CK, Armenteros JJA, Grønbech CH, Jensen LJ, Nielsen HB, Petersen TN, Winther O and Rasmussen S (2021). Improved metagenome binning and assembly using deep variational autoencoders. Nature Biotechnology, 39:555-560.
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Jensen PSH, Johansen M, Bak LK, Jensen LJ and Kjær C (2021). Yield and integrity of RNA from brain samples are largely unaffected by pre-analytical procedures. Neurochemical Research, 46:447-454.
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Szklarczyk D*, Gable AL*, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P*, Jensen LJ* and von Mering C* (2021). The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research, 49:D605–D612.
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Sheils T, Mathias S, Kelleher K, Siramshetty V, Nguyen D-T, Bologa C, Jensen LJ, Vidovic D, Koleti A, Schürer S, Waller A, Yang J, Holmes J, Bocci G, Southall N, Dharkar P, Mathé E, Simeonov A and Oprea TI (2021). TCRD and Pharos 2020: Mining the human proteome for disease biology. Nucleic Acids Research, 49:D1334-D1346.
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2020

Ashwood C, Bittremieux W, Deutsch EW, Doncheva NT, Dorfer V, Gabriels R, Gorshkov V, Gupta S, Jones AR, Käll L, Kopczynski D, Lane L, Lautenbacher L, Legeay M, Locard-Paulet M, Mesuere B, Perez-Riverol Y, Netz E, Pfeuffer J, Sachsenberg T, Salz R, Samaras P, Schiebenhoefer H, Schmidt T, Schwämmle V, Soggiu A, Uszkoreit J, Van Den Bossche T, Van Puyvelde B, Van Strien J, Verschaffelt P, Webel H, Willems S (2020). Proceedings of the EuBIC-MS 2020 Developers’ Meeting. EuPA Open Proteomics, 24:1-6.
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Grissa D, Rasmussen DN, Krag A, Brunak S and Jensen LJ (2020). Alcoholic liver disease: A registry view on comorbidities and disease prediction. PLOS Computational Biology, 16:e1008244.
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Legeay M, Doncheva NT, Morris JH and Jensen LJ (2020). Visualize omics data on networks with Omics Visualizer, a Cytoscape App. F1000Research, 9:157.
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Locard-Paulet M, Bouyssié D, Froment C, Burlet-Schiltz O and Jensen LJ (2020). Comparing 22 Popular Phosphoproteomics Pipelines for Peptide Identification and Site Localization. Journal of Proteome Research, 19:1338-1345.
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2019

Kirk IK, Simon C, Banasik K, Holm PC, Haue AD, Jensen PB, Jensen LJ, Rodríguez CL, Pedersen MK, Eriksson R, Andersen HU, Almdal T, Bork-Jensen J, Grarup N, Borch-Johnsen K, Pedersen O, Pociot F, Hansen T, Bergholdt R, Rossing P and Brunak S (2019). Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining. eLife, 8:e44941.
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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 and Olsen JV (2019). Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites. Cell, 179:543-560.
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Kjær C, Barzaghi G, Bak LK, Goetze JP, Yde CW, Woldbye D, Pinborg LH and Jensen LJ (2019). Transcriptome analysis in patients with temporal lobe epilepsy. Brain, 141:e55.
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Tagore S, Gorohovski A, Jensen LJ and Frenkel-Morgenstern M (2019). ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins. PLOS Computational Biology, 15:e1007239.
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Hjaltelin JX, Izarzugaza JMG, Jensen LJ, Russo F, Westergaard D and Brunak S (2019). Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types. NPG Systems Biology and Applications, 5:27.
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Junge A and Jensen LJ (2019). CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision. Bioinformatics, 36:264-271.
Abstract Full text Preprint Source code

Kirik U, Refsgaard JC and Jensen LJ (2019). Improving peptide-spectrum matching by fragmentation prediction using Hidden Markov Models. Journal of Proteome Research, 18:2385-2396.
Abstract Full text Preprint Source code

Pan X, Jensen LJ* and Gorodkin J* (2019). Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. Bioinformatics, 35:1494-1502.
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Pletscher-Frankild S and Jensen LJ (2019). Design, implementation, and operation of a rapid, robust named entity recognition web service. Journal of Cheminformatics, 11:19.
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Cuesta-Astroz Y*, Santos A*, Oliveira G and Jensen LJ (2019). An integrative method to unravel the host-parasite interactome: An orthology-based approach. Frontiers in Immunology, 10:212.
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Doncheva NT, Morris JH, Gorodkin J and Jensen LJ (2019). Cytoscape stringApp: Network analysis and visualization of proteomics data. Journal of Proteome Research, 18:623-632.
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Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P*, Jensen LJ* and von Mering C* (2019). STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47:D607-D613.
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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 and Bork P (2019). eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47:D309-D314.
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2018

Jersie-Christensen RR, Lanigan LT, Lyon D, Mackie M, Belstrøm D, Kelstrup C, Fotakis AK, Willerslev E, Lynnerup N, Jensen LJ, Cappellini E and Olsen JV (2018). Quantitative metaproteomics of medieval dental calculus reveals individual oral health status. Nature Communications, 9:4744.
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Pan X, Xiong K, Anthon C, Hyttel P, Freude KK, Jensen LJ* and Gorodkin J* (2018). WebCircRNA: Classifying the circular RNA potential of coding and noncoding RNA. Genes, 9:E536.
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Sinha S, Eisenhaber B, Jensen LJ, Kalbuaji B and Eisenhaber F (2018). 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. Proteomics, 18:e1800093.
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Cook HV, Doncheva NT, Szklarczyk D, von Mering C and Jensen LJ (2018). Viruses.STRING: A virus–host protein–protein interaction database. Viruses, 10:E519.
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Larsen SC, Hendriks IA, Lyon D, Jensen LJ and Nielsen ML (2018). Systems-wide analysis of serine ADP-ribosylation reveals widespread occurrence and site-specific overlap with phosphorylation. Cell Reports, 24:2493-2505.
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Pan X, Wenzel A, Jensen LJ*, Gorodkin J* (2018). Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates. PLOS ONE, 13:e0202369.
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Hendriks IA, Lyon D, Su D, Skotte NH, Daniel JA, Jensen LJ and Nielsen ML (2018). Site-specific characterization of endogenous SUMOylation across species and organs. Nature Communications, 9:2456.
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Mackie M, Rüther P, Samodova D, Di Gianvincenzo F, Granzotto C, Lyon D, Peggie DA, Howard H, Harrison L, Jensen LJ, Olsen JV and Cappellini E (2018). Palaeoproteomic profiling of conservation layers on a 14th century Italian wall painting. Angewandte Chemie International Edition, 57:7369-7374.
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Westergaard D, Stærfeldt H-H, Tønsberg C, Jensen LJ* and Brunak S* (2018). Text mining of 15 million full-text scientific articles. PLOS Computational Biology, 14:e1005962.
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Palasca O, Santos A, Stolte C, Gorodkin J* and Jensen LJ* (2018). TISSUES 2.0: an integrative web resource on mammalian tissue expression. Database, 2018:bay003.
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Cejuela JM, Vinchurkar S, Goldberg T, Shankar MSP, Baghudana A, Bojchevski A, Uhlig C, Ofner A, Raharja-Liu P, Jensen LJ* and Rost B* (2018). LocText: relation extraction of protein localizations to assist database curation. BMC Bioinformatics, 19:15.
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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 and Ferro A (2018). miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Research, 46:D354-D359.
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2017

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 and Schürer SC (2017). Drug target ontology to classify and integrate drug discovery data. Journal of Biomedical Semantics, 8:50.
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Mullari M, Lyon D, Jensen LJ and Nielsen ML (2017). Specifying RNA-binding regions in proteins by peptide Cross-Linking and Affinity Purification. Journal of Proteome Research, 16:2762-2772.
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Cannon DC, Yang JJ, Mathias SL, Ursu O, Mani S, Waller A, Schürer SC, Jensen LJ, Sklar LA, Bologa CG and Oprea TI (2017). TIN-X: Target Importance and Novelty Explorer. Bioinformatics, 33:2601-2603.
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Huerta-Cepas J, Forslund K, Szklarczyk D, Jensen LJ, von Mering C and Bork P (2017). Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Molecular Biology and Evolution, 34:2115-2122.
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Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U and Olsen JV (2017). Phosphoproteomics of primary cells reveals druggable kinase signatures in ovarian cancer. Cell Reports, 18:3242-3256.
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Weinert BT, Satpathy S, Hansen BK, Lyon D, Jensen LJ and Choudhary C (2017). Accurate quantification of site-specific acetylation stoichiometry reveals the impact of sirtuin deacetylase CobB on the E. coli acetylome. Molecular and Cellular Proteomics, 16:759-769.
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Kristensen MM, Davidsen PK, Vigelsø A, Hansen CN, Jensen LJ, Jessen N, Bruun JM, Dela F and Helge JW (2017). miRNAs in human subcutaneous adipose tissue: Effects of weight loss induced by hypocaloric diet and exercise. Obesity, 25:572-580.
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Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC and Nielsen ML (2017). Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nature Structural & Molecular Biology, 24:325-335.
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Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ* and Gorodkin J* (2017). RAIN: RNA–protein Association and Interaction Networks. Database, 2017:baw167.
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Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P*, Jensen LJ* and von Mering C* (2017). The STRING database in 2017: quality-controlled protein-protein association. Nucleic Acids Research, 45:D362-D368.
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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 and Guha R (2017). Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research, 45:D995-D1002.
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2016

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 and Pafilis E (2016). Seqenv: linking sequences to environments through text mining. PeerJ, 4:e2690.
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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:e2433.
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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, 44: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, 44:D1075-D1079.
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2015

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.
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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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2014

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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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, 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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2012

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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2011

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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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, 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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2009

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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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, 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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2007

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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2006

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 (2006). 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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2005

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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2004

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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2003

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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2002

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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2001

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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2000

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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1999

Jensen LJ, Friis C and Ussery DW (1999). Three views of microbial genomes. Research in Microbiology, 150:773-777.
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1998

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

Pafilis E, Bērziņš R and Jensen LJ (2017). EXTRACT 2.0: text-mining-assisted interactive annotation of biomedical named entities and ontology terms. Proceedings of Bio-Ontologies 2017.
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Jensen LJ (2017). Tagger: BeCalm API for rapid named entity recognition. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 122-129
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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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Jensen LJ (2016). One tagger, many uses: Illustrating the power of ontologies in dictionary-based named entity recognition. Proceedings of the Joint International Conference on Biological Ontology and BioCreative.
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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.
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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 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

Oprea TI, Bologa C, Holmes J, Mathias S, Metzger VT, Waller A, Yang JJ, Leach AR, Jensen LJ, Kelleher KJ, Sheils TK, Mathé E, Avram SA and Edwards JS (2024). Overview of the Knowledge Management Center for Illuminating the Druggable Genome. Drug Discovery Today, 29:103882.
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Franciosa G, Locard-Paulet M, Jensen LJ and Olsen JV (2023). Recent advances in kinase signaling network profiling by mass spectrometry. Current Opinion in Chemical Biology, 73:102260.
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Yarani R, Shojaeian A, Palasca O, Nadezhda T Doncheva NT, Jensen LJ, Gorodkin J and Pociot F (2022). Differentially Expressed miRNAs in Ulcerative Colitis and Crohn's Disease. Frontiers in Immunology, 13:865777.
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Burgess A, Vuong J, Marzec KA, de Lichtenberg U, O’Donoghue SI and Jensen LJ (2019). SnapShot: S-Phase Entry and Exit. Cell, 179:802.
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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 J1, 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 and Zahoránszky-Köhalmi G (2018). Unexplored therapeutic opportunities in the human genome. Nature Reviews Drug Discovery, 17:317-332.
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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

Cook HV and Jensen LJ (2019). A guide to dictionary-based text mining. Methods in Molecular Biology, 1939:73-89.
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Cook HV and Jensen LJ (2018). An integrative approach to virus–host protein–protein interactions. Methods in Molecular Biology, 1819:175-196.
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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 (2016). 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.