Lars Juhl Jensen

Lars Juhl Jensen

Professor, Group Leader, Professor

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    ORCID: 0000-0001-7885-715X

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    1. 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

    2. Published

      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

    3. Published

      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. 543-560

      Research output: Contribution to journal › Journal article › Research › peer-review

    4. Published

      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

    5. Published

      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

    6. Published

      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

    7. 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

    8. 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, Pawson, T., 2007, In: Cell. 129, 7, p. 1415-26 12 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    9. 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. D695-9

      Research output: Contribution to journal › Journal article › Research › peer-review

    10. 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, Oprea, T. I. & Schürer, S. C., 9 Nov 2017, In: Journal of Biomedical Semantics. 8, 1, 16 p., 50.

      Research output: Contribution to journal › Journal article › Research › peer-review

    11. 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

    12. Published

      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. 2493-2505

      Research output: Contribution to journal › Journal article › Research › peer-review

    13. Published

      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

    14. Published

      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

    15. Published

      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

    16. Published

      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. D552-6

      Research output: Contribution to journal › Journal article › Research › peer-review

    17. 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. 343

      Research output: Contribution to journal › Journal article › Research › peer-review

    18. Published

      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

    19. Published

      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

    20. 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. D684-8

      Research output: Contribution to journal › Journal article › Research › peer-review

    21. Published

      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. D1075-9

      Research output: Contribution to journal › Journal article › Research › peer-review

    22. Published

      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. D876-80

      Research output: Contribution to journal › Journal article › Research › peer-review

    23. Published

      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

    24. Published

      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

    25. Published

      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

    26. 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. e134

      Research output: Contribution to journal › Journal article › Research › peer-review

    27. 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

    28. Published

      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

    29. Published

      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. 5755–5769

      Research output: Contribution to journal › Journal article › Research › peer-review

    30. Published

      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

    31. Published

      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, Brunak, Søren, 2019, In: eLife. 8, 19 p., e44941.

      Research output: Contribution to journal › Journal article › Research › peer-review

    32. 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. 2385-2396

      Research output: Contribution to journal › Journal article › Research › peer-review

    33. Published

      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

    34. Published

      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

    35. Published

      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

    36. 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. 206

      Research output: Contribution to journal › Journal article › Research › peer-review

    37. Published

      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

    38. Published

      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

    39. Published

      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

    40. Published

      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. 447-454

      Research output: Contribution to journal › Journal article › Research › peer-review

    41. Published

      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

    42. ArrayProspector: a web resource of functional associations inferred from microarray expression data

      Jensen, Lars Juhl, Lagarde, J., von Mering, C. & Bork, P., 2004, In: Nucleic Acids Research. 32, Web Server issue, p. W445-8

      Research output: Contribution to journal › Journal article › Research › peer-review

    43. Published

      STRING 8--a global view on proteins and their functional interactions in 630 organisms

      Jensen, Lars Juhl, Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P. & von Mering, C., 2008, In: Nucleic Acids Research. 37, suppl 1, p. D412-D416 5 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    44. eggNOG: automated construction and annotation of orthologous groups of genes

      Jensen, Lars Juhl, Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. & Bork, P., 2008, In: Nucleic Acids Research. 36, Database issue, p. D250-4

      Research output: Contribution to journal › Journal article › Research › peer-review

    45. Prediction of novel archaeal enzymes from sequence-derived features

      Jensen, Lars Juhl, Skovgaard, M. & Brunak, S., 2002, In: Protein Science. 11, 12, p. 2894-8 5 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    46. 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

    47. 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. 12

      Research output: Contribution to journal › Journal article › Research › peer-review

    48. 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

    49. Published

      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. 403

      Research output: Contribution to journal › Journal article › Research › peer-review

    50. 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. 139-164

      Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Communication

    51. 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

    52. Published

      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

    53. 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

    54. Published

      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

    55. Published

      Ontologies in quantitative biology: a basis for comparison, integration, and discovery

      Jensen, Lars Juhl & Bork, P., 1 May 2010, In: PLoS Biology. 8, 5, p. e1000374

      Research output: Contribution to journal › Journal article › Research › peer-review

    56. Prediction of human protein function from post-translational modifications and localization features

      Jensen, Lars Juhl, Gupta, R., Blom, N., Devos, D., Tamames, J., Kesmir, C., Nielsen, H., Staerfeldt, H. H., Rapacki, K., Workman, C., Andersen, C. A. F., Knudsen, S., Krogh, A., Valencia, A. & Brunak, S., 2002, In: Journal of Molecular Biology. 319, 5, p. 1257-65 9 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    57. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation

      Jensen, Lars Juhl & Knudsen, S., 2000, In: Bioinformatics. 16, 4, p. 326-33 8 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    58. Visualization of pathogenicity regions in bacteria

      Jensen, Lars Juhl, Friis, C. & Ussery, D., 2000, In: Genetica. 108, 1, p. 47-51 5 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    59. Three views of microbial genomes

      Jensen, Lars Juhl, Friis, C. & Ussery, D., 2012, In: Research in Microbiology. 150, 9-10, p. 773-7 5 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    60. Scoring functions for computational algorithms applicable to the design of spiked oligonucleotides

      Jensen, Lars Juhl, Andersen, K. V., Svendsen, A. & Kretzschmar, T., 1998, In: Nucleic Acids Research. 26, 3, p. 697-702 6 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    61. Prediction of human protein function according to Gene Ontology categories

      Jensen, Lars Juhl, Gupta, R., Staerfeldt, H. & Brunak, S., 2003, In: Bioinformatics. 19, 5, p. 635-42 8 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    62. Published

      Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

      Jensen, A. B., Moseley, P. L., Oprea, T. I., Ellesøe, S. G., Eriksson, R., Schmock, H., Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 24 Jun 2014, In: Nature Communications. 5, 10 p., 4022.

      Research output: Contribution to journal › Journal article › Research › peer-review

    63. E-pub ahead of print

      Impact of acute alcohol consumption on circulating microbiome in asymptomatic alcohol-related liver disease

      Israelsen, M., Alvarez Silva, Maria Camila, Madsen, B. S., Hansen, C. D., Torp, N. C., Johansen, S., Hansen, J. K., Prier Lindvig, K., Insonere, J., Riviere, V., Juel, H. B., Brejnrod, A., Jensen, Lars Juhl, Thiele, M., Lelouvier, B., Hansen, Torben, Arumugam, Mani & Krag, A., 2023, (E-pub ahead of print) In: Gut. gutjnl-2023-330360.

      Research output: Contribution to journal › Letter › Research › peer-review

    64. Published

      Drug-induced regulation of target expression

      Iskar, M., Campillos, M., Kuhn, M., Jensen, Lars Juhl, van Noort, V. & Bork, P., 1 Jan 2010, In: PLoS Computational Biology. 6, 9

      Research output: Contribution to journal › Journal article › Research › peer-review

    65. Published

      eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

      Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., Jensen, Lars Juhl, von Mering, C. & Bork, P., 4 Jan 2016, In: Nucleic Acids Research. 44, D1, p. D286-93

      Research output: Contribution to journal › Journal article › Research › peer-review

    66. Published

      Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

      Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, Lars Juhl, von Mering, C. & Bork, P., 1 Aug 2017, In: Molecular Biology and Evolution. 34, 8, p. 2115-2122 8 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    67. Published

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

      Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunic, I., Rattei, T., Jensen, Lars Juhl, von Mering, C. & Bork, P., 2019, In: Nucleic Acids Research. 47, D1, p. D309-D314 6 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    68. Published

      KinomeXplorer: an integrated platform for kinome biology studies

      Horn, H., Schoof, E. M., Kim, J., Robin, X., Miller, M. L., Diella, F., Palma, A., Cesareni, G., Jensen, Lars Juhl & Linding, R., 29 May 2014, In: Nature Methods. 11, 6, p. 603-4 2 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    69. Published

      DoReMi: context-based prioritization of linear motif matches

      Horn, H., Haslam, N. & Jensen, Lars Juhl, 20 Mar 2014, In: PeerJ. 2, 10 p., e315.

      Research output: Contribution to journal › Journal article › Research › peer-review

    70. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

      Hooper, S. D., Boué, S., Krause, R., Jensen, Lars Juhl, Mason, C. E., Ghanim, M., White, K. P., Furlong, E. E. M. & Bork, P., 2007, In: Molecular Systems Biology. 3, p. 72

      Research output: Contribution to journal › Journal article › Research › peer-review

    71. Published

      Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records

      Hjaltelin, Jessica Xin, Novitski, Sif Ingibergsdóttir, Jørgensen, Isabella Friis, Siggaard, T., Vulpius, S. A., Westergaard, David, Johansen, Julia Sidenius, Chen, I. M., Jensen, Lars Juhl & Brunak, Søren, 2023, In: eLife. 12, 15 p., e84919.

      Research output: Contribution to journal › Journal article › Research › peer-review

    72. Published

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

      Hjaltelin, Jessica Xin, Izarzugaza, J. M. G., Jensen, Lars Juhl, Russo, F., Westergaard, David & Brunak, Søren, 2019, In: npj Systems Biology and Applications. 5, 10 p., 27.

      Research output: Contribution to journal › Journal article › Research › peer-review

    73. Published

      eggNOG 6.0: enabling comparative genomics across 12 535 organisms

      Hernández-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C. P., Giner-Lamia, J., Mende, D. R., Kirsch, Rebecca, Rattei, T., Letunic, I., Jensen, Lars Juhl, Bork, P., von Mering, C. & Huerta-Cepas, J., 2023, In: Nucleic Acids Research. 51, D1, p. D389-D394 6 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    74. Published

      Site-specific characterization of endogenous SUMOylation across species and organs

      Hendriks, Ivo Alexander, Lyon, D., Su, D., Skotte, Niels Henning, Daniel, J. A., Jensen, Lars Juhl & Nielsen, Michael Lund, 2018, In: Nature Communications. 9, p. 1-17 2456.

      Research output: Contribution to journal › Journal article › Research › peer-review

    75. Published

      Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

      Hendriks, Ivo Alexander, Lyon, D., Young, C., Jensen, Lars Juhl, Vertegaal, A. C. O. & Nielsen, Michael Lund, Mar 2017, In: Nature Structural and Molecular Biology. 24, 3, p. 325-336 12 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    76. Published

      TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells

      Hekmat, O., Munk, S., Fogh, L., Yadav, R., Francavilla, C., Horn, H., Würtz, S. Ø., Schrohl, A-S., Damsgaard, B., Romer, M. U., Belling, K., Jensen, N. F., Gromova, I., Bekker-Jensen, D. B., Moreira, J., Jensen, L. J., Gupta, R., Lademann, U. A., Brünner, N., Olsen, J. V. & 1 others, Stenvang, Jan, 5 Aug 2013, In: Journal of Proteome Research. 12, 9, p. 4136-4151 16 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    77. Published

      Are graph databases ready for bioinformatics?

      Have, C. T. & Jensen, Lars Juhl, 21 Oct 2013, In: Bioinformatics (Online). 2 p.

      Research output: Contribution to journal › Editorial › Research

    78. Published

      Predicting biological networks from genomic data

      Harrington, E. D., Jensen, Lars Juhl & Bork, P., 2008, In: F E B S Letters. 582, 8, p. 1251-8 8 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    79. Quantitative assessment of protein function prediction from metagenomics shotgun sequences

      Harrington, E. D., Singh, A., Doerks, T., Letunic, I., von Mering, C., Jensen, Lars Juhl, Raes, J. & Bork, P., 2007, In: Proceedings of the National Academy of Sciences of the United States of America. 104, 35, p. 13913-8 6 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    80. SuperTarget and Matador: resources for exploring drug-target relationships

      Günther, S., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., Ahmed, J., Urdiales, E. G., Gewiess, A., Jensen, Lars Juhl, Schneider, R., Skoblo, R., Russell, R. B., Bourne, P. E., Bork, P. & Preissner, R., 2008, In: Nucleic Acids Research. 36, Database issue, p. D919-22

      Research output: Contribution to journal › Journal article › Research › peer-review

    81. Published

      Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae

      Hernández Guzmán, Ulises, Aksnes, H., Ree, R., Krogh, Nicolai, Jakobsson, M. E., Jensen, Lars Juhl, Arnesen, T. & Olsen, Jesper Velgaard, 2023, In: Nature Communications. 14, 4517.

      Research output: Contribution to journal › Journal article › Research › peer-review

    82. Orphan protein function and its relation to glycosylation

      Gupta, R., Jensen, Lars Juhl & Brunak, S., 2002, In: Ernst Schering Foundation Symposium Proceedings. 38, p. 276-94 19 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    83. Published

      Alcoholic liver disease: A registry view on comorbidities and disease prediction

      Grissa, Dhouha, Nytoft Rasmussen, D., Krag, A., Brunak, Søren & Jensen, Lars Juhl, 2020, In: P L o S One. 16, 9, 19 p., 1008244.

      Research output: Contribution to journal › Journal article › Research › peer-review

    84. Published

      Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration

      Grissa, Dhouha, Junge, A., Oprea, T. I. & Jensen, Lars Juhl, 2022, In: Database : the journal of biological databases and curation. 2022, 2022, 8 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    85. Published

      High-resolution transcription atlas of the mitotic cell cycle in budding yeast

      Granovskaia, M. V., Jensen, Lars Juhl, Ritchie, M. E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L. M., 1 Jan 2010, In: Genome Biology (Online Edition). 11, 3, p. R24

      Research output: Contribution to journal › Journal article › Research › peer-review

    86. Published

      Quantifying environmental adaptation of metabolic pathways in metagenomics

      Gianoulis, T. A., Raes, J., Patel, P. V., Bjornson, R., Korbel, J. O., Letunic, I., Yamada, T., Paccanaro, A., Snyder, M., Bork, P., Gerstein, M. B. & Jensen, Lars Juhl, 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 5, p. 1374-9 5 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    87. Published

      The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production

      Geissler, Adrian Sven, Poulsen, L. D., Doncheva, Nadezhda Tsankova, Anthon, Christian, Seemann, Ernst Stefan, González-Tortuero, E., Breüner, A., Jensen, Lars Juhl, Hjort, C., Vinther, Jeppe & Gorodkin, Jan, 2022, In: Frontiers in Microbiology. 13, 17 p., 909493.

      Research output: Contribution to journal › Journal article › Research › peer-review

    88. Proteome survey reveals modularity of the yeast cell machinery

      Gavin, A-C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M-A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A-M., Schelder, M., Schirle, M., Remor, M. & 12 others, Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B. & Superti-Furga, G., 2006, In: Nature Study. 440, 7084, p. 631-6 6 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    89. Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments

      Gauthier, N. P., Larsen, M. E., Wernersson, R., de Lichtenberg, U., Jensen, Lars Juhl, Brunak, S. & Jensen, T. S., 2008, In: Nucleic Acids Research. 36, Database issue, p. D854-9

      Research output: Contribution to journal › Journal article › Research › peer-review

    90. Published

      Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

      Gauthier, N. P., Jensen, Lars Juhl, Wernersson, R., Brunak, Søren & Jensen, T. S., 2010, In: Nucleic Acids Research. 38, Database issue, p. D699-702

      Research output: Contribution to journal › Journal article › Research › peer-review

    91. A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae

      Gallego, O., Betts, M. J., Gvozdenovic-Jeremic, J., Maeda, K., Matetzki, C., Aguilar-Gurrieri, C., Beltran-Alvarez, P., Bonn, S., Fernández-Tornero, C., Jensen, Lars Juhl, Kuhn, M., Trott, J., Rybin, V., Müller, C. W., Bork, P., Kaksonen, M., Russell, R. B. & Gavin, A., 2010, In: Molecular Systems Biology. 6, p. 430

      Research output: Contribution to journal › Journal article › Research › peer-review

    92. Published

      Protein-protein interactions: analysis and prediction

      Frishman, D., Albert, M., Blankenburg, H., Bork, P., Harrington, E. D., Hermjakob, H., Jensen, Lars Juhl, Juan, D. A., Pagel, P., Schachter, V. & Valencia, A., 2009, Modern Genome Annotation: The BioSapien Network. Springer Publishing Company, p. 353-410 (Modern Genome Annotation: The BioSapiens network).

      Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research

    93. Published

      Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

      Frenkel-Morgenstern, M., Danon, T., Christian, T., Igarashi, T., Cohen, L., Hou, Y. & Jensen, Lars Juhl, 2012, In: Molecular Systems Biology. 8, p. 572

      Research output: Contribution to journal › Journal article › Research › peer-review

    94. Published

      Recent advances in kinase signaling network profiling by mass spectrometry

      Franciosa, Giulia, Locard-Paulet, Marie, Jensen, Lars Juhl & Olsen, Jesper Velgaard, 2023, In: Current Opinion in Chemical Biology. 73, 11 p., 102260.

      Research output: Contribution to journal › Review › Research › peer-review

    95. Published

      SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles

      Franceschini, A., Lin, J., von Mering, C. & Jensen, Lars Juhl, 2016, In: Bioinformatics. 32, 7, p. 1085-7 3 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    96. Published

      STRING v9.1: Protein-protein interaction networks, with increased coverage and integration

      Franceschini, A., Simonovic, M., Roth, A., Von Mering, C., Szklarczyk, D., Pletscher-Frankild, S., Jensen, Lars Juhl, Kuhn, M. M., Lin, J., Minguez, P. & Bork, P., 1 Jan 2013, In: Nucleic Acids Research. 41, D1, p. D808-D815 8 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    97. Published

      Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer

      Francavilla, C., Lupia, M., Tsafou, K., Villa, A., Kowalczyk, K., Rakownikow Jersie-Christensen, R., Bertalot, G., Confalonieri, S., Brunak, Søren, Jensen, Lars Juhl, Cavallaro, U. & Olsen, Jesper Velgaard, 28 Mar 2017, In: Cell Reports. 18, 13, p. 3242-3256 15 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    98. Published

      Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing

      Fedorov, O., Huber, K., Eisenreich, A., Filippakopoulos, P., King, O., Bullock, A. N., Szklarczyk, D., Jensen, Lars Juhl, Fabbro, D., Trappe, J., Rauch, U., Bracher, F. & Knapp, S., 2011, In: Chemistry & Biology. 18, 1, p. 67-76 10 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    99. Published

      Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text

      Eriksson, R., Jensen, P. B., Pletscher-Frankild, S., Jensen, Lars Juhl & Brunak, Søren, 23 May 2013, In: JAMIA - Journal of the American Medical Informatics Association. 20, 5, p. 947-953 7 p.

      Research output: Contribution to journal › Journal article › Research › peer-review

    100. Published

      Erratum to: Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population

      Eriksson, R., Werge, T., Jensen, Lars Juhl & Brunak, Søren, May 2014, In: Drug Safety. 37, 5, p. 379

      Research output: Contribution to journal › Journal article › Research › peer-review

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    ID: 9931112