Lars Juhl Jensen
Professor, Group Leader, Professor
Jensen Group
Blegdamsvej 3, 2200 København N., 06 Bygning 6, Building: 06-2-26
Member of:
- Published
S1000: a better taxonomic name corpus for biomedical information extraction
Luoma, J., Nastou, Katerina, Ohta, T., Toivonen, H., Pafilis, E., Jensen, Lars Juhl & Pyysalo, S., 2023, In: Bioinformatics. 39, 6, 8 p., btad369.Research output: Contribution to journal › Journal article › Research › peer-review
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In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of β-Adrenergic Receptor Signaling
Lundby, Alicia, Andersen, M. N., Steffensen, Annette Buur, Horn, H., Kelstrup, C. D., Francavilla, C., Jensen, Lars Juhl, Schmitt, Nicole, Thomsen, Morten Bækgaard & Olsen, Jesper Velgaard, 4 Jun 2013, In: Science Signaling. 6, 278, p. rs11 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites
Lundby, Alicia, Franciosa, Giulia, Emdal, Kristina Bennet, Refsgaard, J. C., Gnosa, S. P., Bekker-Jensen, D. B., Secher, A., Maurya, S. R., Paul, I., Mendez, B. L., Kelstrup, C. D., Francavilla, C., Kveiborg, Marie, Montoya, Guillermo, Jensen, Lars Juhl & Olsen, Jesper Velgaard, 2019, In: Cell. 179, 2, p. 543-560Research output: Contribution to journal › Journal article › Research › peer-review
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Comparing 22 Popular Phosphoproteomics Pipelines for Peptide Identification and Site Localization
Locard-Paulet, Marie, Bouyssié, D., Froment, C., Burlet-Schiltz, O. & Jensen, Lars Juhl, 2020, In: Journal of Proteome Research. 19, 3, p. 1338-1345 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies
Locard-Paulet, Marie, Palasca, Oana & Jensen, Lars Juhl, 2022, In: PLOS Computational Biology. 18, 10, 20 p., e1010604.Research output: Contribution to journal › Journal article › Research › peer-review
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Quantitative proteome comparison of human hearts with those of model organisms
Linscheid, N., Santos, A., Poulsen, P. C., Mills, Robert William, Callø, Kirstine, Leurs, U., Ye, J. Z., Stolte, C., Thomsen, Morten Bækgaard, Bentzen, Bo Hjorth, Lundegaard, Pia Rengtved, Olesen, Morten Steen Salling, Jensen, Lars Juhl, Olsen, Jesper Velgaard & Lundby, Alicia, 2021, In: PLOS Biology. 19, 4, 22 p., e3001144.Research output: Contribution to journal › Journal article › Research › peer-review
Protein disorder prediction: implications for structural proteomics
Linding, R., Jensen, Lars Juhl, Diella, F., Bork, P., Gibson, T. J. & Russell, R. B., 2003, In: Structure. 11, 11, p. 1453-9 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
Systematic discovery of in vivo phosphorylation networks
Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A. T. M., Jørgensen, C., Miron, I. M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J. G., Samson, L. D., Woodgett, J. R., Russell, R. B., Bork, P., Yaffe, M. B. & 1 others, , 2007, In: Cell. 129, 7, p. 1415-26 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
NetworKIN: a resource for exploring cellular phosphorylation networks
Linding, R., Jensen, Lars Juhl, Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., Yaffe, M. B. & Pawson, T., 2008, In: Nucleic Acids Research. 36, Database issue, p. D695-9Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Drug target ontology to classify and integrate drug discovery data
Lin, Y., Mehta, S., Küçük-McGinty, H., Turner, J. P., Vidovic, D., Forlin, M., Koleti, A., Nguyen, D-T., Jensen, L. J., Guha, R., Mathias, S. L., Ursu, O., Stathias, V., Duan, J., Nabizadeh, N., Chung, C., Mader, C., Visser, U., Yang, J. J., Bologa, C. G. & 2 others, , 9 Nov 2017, In: Journal of Biomedical Semantics. 8, 1, 16 p., 50.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Visualize omics data on networks with Omics Visualizer, a Cytoscape App
Legeay, M., Doncheva, Nadezhda Tsankova, Morris, J. H. & Jensen, Lars Juhl, 2020, In: F1000Research. 9, 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Systems-wide Analysis of Serine ADP-Ribosylation Reveals Widespread Occurrence and Site-Specific Overlap with Phosphorylation
Buch-Larsen, Sara Charlotte, Hendriks, Ivo Alexander, Lyon, D., Jensen, Lars Juhl & Nielsen, Michael Lund, 2018, In: Cell Reports. 24, 9, p. 2493-2505Research output: Contribution to journal › Journal article › Research › peer-review
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Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells
Buch-Larsen, Sara Charlotte, Sylvestersen, K. B., Mund, Andreas, Lyon, D., Mullari, M., Madsen, M. V., Daniel, J. A., Jensen, Lars Juhl & Nielsen, Michael Lund, 30 Aug 2016, In: Science Signaling. 9, 443, 14 p., rs9.Research output: Contribution to journal › Journal article › Research › peer-review
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Suppression of water as a nucleophile in Candida antarctica lipase B catalysis
Larsen, M. W., Zielinska, D. F., Martinelle, M., Hidalgo, A., Jensen, Lars Juhl, Bornscheuer, U. T. & Hult, K., 12 Apr 2010, In: ChemBioChem. 11, 6, p. 796-801 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Large-scale prediction of drug-target relationships
Kuhn, M., Campillos, M., González, P., Jensen, Lars Juhl & Bork, P., 2008, In: F E B S Letters. 582, 8, p. 1283-90 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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STITCH 2: an interaction network database for small molecules and proteins
Kuhn, M., Szklarczyk, D., Franceschini, A., Campillos, M., von Mering, C., Jensen, Lars Juhl, Beyer, A. & Bork, P., 2010, In: Nucleic Acids Research. 38, Database issue, p. D552-6Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A side effect resource to capture phenotypic effects of drugs
Kuhn, M., Campillos, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 1 Jan 2010, In: Molecular Systems Biology. 6, p. 343Research output: Contribution to journal › Journal article › Research › peer-review
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STITCH 4: integration of protein-chemical interactions with user data
Kuhn, M., Szklarczyk, D. M., Pletscher-Frankild, S., Blicher, T. H., von Mering, C., Jensen, Lars Juhl & Bork, P., 28 Nov 2013, In: Nucleic Acids Research. 42, D1, p. D401-D407 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Systematic identification of proteins that elicit drug side effects
Kuhn, M., Al Banchaabouchi, M., Campillos, M., Jensen, Lars Juhl, Gross, C., Gavin, A. & Bork, P., 30 Apr 2013, In: Molecular Systems Biology. 9, p. 663 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
STITCH: interaction networks of chemicals and proteins
Kuhn, M., von Mering, C., Campillos, M., Jensen, Lars Juhl & Bork, P., 2008, In: Nucleic Acids Research. 36, Database issue, p. D684-8Research output: Contribution to journal › Journal article › Research › peer-review
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The SIDER database of drugs and side effects
Kuhn, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 4 Jan 2016, In: Nucleic Acids Research. 44, p. D1075-9Research output: Contribution to journal › Journal article › Research › peer-review
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STITCH 3: zooming in on protein-chemical interactions
Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, Lars Juhl & Bork, P., 2012, In: Nucleic Acids Research. 40, Database issue, p. D876-80Research output: Contribution to journal › Journal article › Research › peer-review
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miRNAs in Human Subcutaneous Adipose Tissue: Effects of Weight Loss Induced by Hypocaloric Diet and Exercise
Kristensen, M. M., Davidsen, P. K., Vigelso, A., Hansen, C. N., Jensen, Lars Juhl, Jessen, N., Bruun, J. M., Dela, Flemming & Helge, Jørn Wulff, Mar 2017, In: Obesity. 25, 3, p. 572-580 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
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U-CIE [/juː ‘siː/]: Color encoding of high-dimensional data
Koutrouli, Mikaela, Morris, J. H. & Jensen, Lars Juhl, 2022, In: Protein Science. 31, 9, 8 p., e4388.Research output: Contribution to journal › Journal article › Research › peer-review
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FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data
Koutrouli, Mikaela, Nastou, Katerina, Piera Líndez, Pau, Bouwmeester, R., Rasmussen, Simon, Martens, L. & Jensen, Lars Juhl, 2024, In: Bioinformatics. 40, 2, 11 p., btae010.Research output: Contribution to journal › Journal article › Research › peer-review
Systematic association of genes to phenotypes by genome and literature mining
Korbel, J. O., Doerks, T., Jensen, Lars Juhl, Perez-Iratxeta, C., Kaczanowski, S., Hooper, S. D., Andrade, M. A. & Bork, P., 2005, In: P L o S Biology (Online). 3, 5, p. e134Research output: Contribution to journal › Journal article › Research › peer-review
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs
Korbel, J. O., Jensen, Lars Juhl, von Mering, C. & Bork, P., 2004, In: Nature Biotechnology. 22, 7, p. 911-7 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration
Kokoli, M., Karatzas, E., Baltoumas, F. A., Schneider, R., Pafilis, E., Paragkamian, S., Doncheva, Nadezhda Tsankova, Jensen, Lars Juhl & Pavlopoulos, G. A., 2023, In: NAR Genomics and Bioinformatics. 5, 2, 8 p., lqad053.Research output: Contribution to journal › Journal article › Research › peer-review
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Differential Expression of the β3 Subunit of Voltage-Gated Ca2+ Channel in Mesial Temporal Lobe Epilepsy
Kjær, C., Palasca, Oana, Barzaghi, G., Bak, Lasse Kristoffer, Durhuus, R. K. J., Jakobsen, Emil, Pedersen, Louise, Bartels, Emil Daniel, Woldbye, David Paul Drucker, Pinborg, Lars Hageman & Jensen, Lars Juhl, 2023, In: Molecular Neurobiology. 60, p. 5755–5769Research output: Contribution to journal › Journal article › Research › peer-review
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Transcriptome analysis in patients with temporal lobe epilepsy
Kjær, C., Barzaghi, G., Bak, Lasse Kristoffer, Goetze, Jens P. , Yde, C. W., Woldbye, David Paul Drucker, Pinborg, Lars Hageman & Jensen, Lars Juhl, 2019, In: Brain. 142, 10, p. 49-64 16 p., e55.Research output: Contribution to journal › Letter › Research › peer-review
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Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining
Kirk, I. K., Simon, C., Banasik, K., Holm, P. C., Haue, A. D., Jensen, P. B., Jensen, L. J., Rodriguez, C. L., Pedersen, M. K., Eriksson, R., Andersen, H. U., Almdal, T., Bork-Jensen, J., Grarup, N., Borch-Johnsen, K., Pedersen, O., Pociot, F., Hansen, T., Bergholdt, R., Rossing, P. & 1 others, , 2019, In: eLife. 8, 19 p., e44941.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Improving Peptide-Spectrum Matching by Fragmentation Prediction Using Hidden Markov Models
Kirik, U., Refsgaard, J. C. & Jensen, Lars Juhl, 2019, In: Journal of Proteome Research. 18, 6, p. 2385-2396Research output: Contribution to journal › Journal article › Research › peer-review
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Pharos 2023: an integrated resource for the understudied human proteome
Kelleher, K. J., Sheils, T. K., Mathias, S. L., Yang, J. J., Metzger, V. T., Siramshetty, V. B., Nguyen, D., Jensen, Lars Juhl, Vidovic, D., Schurer, S. C., Holmes, J., Sharma, K. R., Pillai, A., Bologa, C. G., Edwards, J. S., Mathe, E. A. & Oprea, T., 2023, In: Nucleic Acids Research. 51, D1, p. D1405-D1416 12 p., gkac1033.Research output: Contribution to journal › Journal article › Research › peer-review
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CoCoScore: Context-aware co-occurrence scoring for text mining applications using distant supervision
Junge, A. & Jensen, Lars Juhl, 2019, In: Bioinformatics. 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
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RAIN: RNA-protein Association and Interaction Networks
Junge, A., Refsgaard, J. C., Garde, C., Pan, X., Santos, A., Alkan, F., Anthon, Christian, von Mering, C., Workman, C. T., Jensen, Lars Juhl & Gorodkin, Jan, 2017, In: Database: The Journal of Biological Databases and Curation. 2017, 9 p., baw167.Research output: Contribution to journal › Journal article › Research › peer-review
Sequence-based feature prediction and annotation of proteins
Juncker, A., Jensen, Lars Juhl, Pierleoni, A., Bernsel, A., Tress, M. L., Bork, P., von Heijne, G., Valencia, A., Ouzounis, C. A., Casadio, R. & Brunak, S., 2009, In: Genome Biology (Online Edition). 10, 2, p. 206Research output: Contribution to journal › Journal article › Research › peer-review
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Quantitative metaproteomics of medieval dental calculus reveals individual oral health status
Jersie-Christensen, R. R., Lanigan, Liam Thomas, Lyon, D., Mackie, Meaghan, Midjord-Belstrøm, Daniel, Kelstrup, C. D., Fotaki, Anna Katerina, Willerslev, Eske, Lynnerup, Niels, Jensen, Lars Juhl, Cappellini, Enrico & Olsen, Jesper Velgaard, 2018, In: Nature Communications. 9, p. 1-12 4744.Research output: Contribution to journal › Journal article › Research › peer-review
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Reply to 'Mining electronic health records: An additional perspective'
Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 1 Jan 2013, In: Nature Reviews. Genetics. 14, 1 p.Research output: Contribution to journal › Comment/debate › Research › peer-review
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Mining electronic health records: towards better research applications and clinical care
Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 2012, In: Nature Reviews. Genetics. 13, 6, p. 395-405 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures
Jensen, P. S. H., Johansen, M., Bak, Lasse Kristoffer, Jensen, Lars Juhl & Kjær, C., 2021, In: Neurochemical Research. 46, p. 447-454Research output: Contribution to journal › Journal article › Research › peer-review
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Biochemistry. Not comparable, but complementary
Jensen, Lars Juhl & Bork, P., 3 Oct 2008, In: Science (New York, N.Y.). 322, 5898, p. 56-7 2 p.Research output: Contribution to journal › Comment/debate › Research › peer-review
Co-evolution of transcriptional and post-translational cell-cycle regulation
Jensen, Lars Juhl, Jensen, T. S., de Lichtenberg, U., Brunak, S. & Bork, P., 2006, In: Nature Study. 443, 7111, p. 594-7 4 p.Research output: Contribution to journal › Journal article › Research › peer-review
Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
Jensen, Lars Juhl, Skovgaard, M., Sicheritz-Pontén, T., Jørgensen, M. K., Lundegaard, C., Pedersen, C. C., Petersen, N. & Ussery, D., 2003, In: B M C Genomics. 4, 1, p. 12Research output: Contribution to journal › Journal article › Research › peer-review
Re-analysis of data and its integration
Jensen, Lars Juhl & Steinmetz, L. M., 2005, In: F E B S Letters. 579, 8, p. 1802-7 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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Circular reasoning rather than cyclic expression
Jensen, Lars Juhl, de Lichtenberg, U., Jensen, T. S., Brunak, Søren & Bork, P., 2008, In: Genome Biology. 9, 6, p. 403Research output: Contribution to journal › Journal article › Research › peer-review
Comparative genomics of four Pseudomonas species
Jensen, Lars Juhl, Skovgaard, M., Sicheritz-Ponten, T., Hansen, N. T., Johansen, H., Jørgensen, M. K., Kiil, K. & Ussery, D. W., 2004, The Phedomonads. p. 139-164Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Communication
Functionality of system components: conservation of protein function in protein feature space
Jensen, Lars Juhl, Ussery, D. & Brunak, S., 2003, In: Genome Research. 13, 11, p. 2444-9 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
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The rise and fall of supervised machine learning techniques
Jensen, Lars Juhl & Bateman, A., 2011, In: Bioinformatics (Online). 27, 24, p. 3331-2 2 p.Research output: Contribution to journal › Journal article › Research › peer-review
Literature mining for the biologist: from information retrieval to biological discovery
Jensen, Lars Juhl, Saric, J. & Bork, P., 2006, In: Nature Reviews. Genetics. 7, 2, p. 119-29 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
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One tagger, many uses: Illustrating the power of ontologies in dictionary-based named entity recognition
Jensen, Lars Juhl, 2016, In: CEUR Workshop Proceedings. 1747, 2 p.Research output: Contribution to journal › Conference article › Research › peer-review
ID: 9931112
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TISSUES 2.0: an integrative web resource on mammalian tissue expression
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
514
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STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
Research output: Contribution to journal › Journal article › Research › peer-review
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473
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Drug target ontology to classify and integrate drug discovery data
Research output: Contribution to journal › Journal article › Research › peer-review
Published