Lars Juhl Jensen

Lars Juhl Jensen

Professor, Group Leader, Professor

Member of:


    1. Published

      Standardized benchmarking in the quest for orthologs

      Altenhoff, A. M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D. A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L. P., Schreiber, F., da Silva, A. S., Szklarczyk, D., Train, C-M., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjölander, K., Jensen, L. J. & 8 others, Martin, M. J., Muffato, M., Gabaldón, T., Lewis, S. E., Thomas, P. D., Sonnhammer, E., Dessimoz, C. & Quest for Orthologs consortium, Q. F. O. C., May 2016, In: Nature Methods. 13, p. 425-30 6 p.

      Research output: Contribution to journalJournal articlepeer-review

    2. Published

      Text mining for biology--the way forward: opinions from leading scientists

      Altman, R. B., Bergman, C. M., Blake, J., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, Lars Juhl, Krallinger, M., Mons, B., O'Donoghue, S. I., Peitsch, M. C., Rebholz-Schuhmann, D., Shatkay, H. & Valencia, A., 2008, In: Genome Biology (Online Edition). 9 Suppl 2, p. S7

      Research output: Contribution to journalJournal articlepeer-review

    3. Published

      OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

      Baltoumas, F. A., Zafeiropoulou, S., Karatzas, E., Paragkamian, S., Thanati, F., Iliopoulos, I., Eliopoulos, A. G., Schneider, R., Jensen, Lars Juhl, Pafilis, E. & Pavlopoulos, G. A., 2021, In: NAR Genomics and Bioinformatics. 3, 4, 10 p., lqab090.

      Research output: Contribution to journalJournal articlepeer-review

    4. Published

      Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

      Bassani-Sternberg, M., Pletscher-Frankild, S., Jensen, Lars Juhl & Mann, Matthias, Mar 2015, In: Molecular and Cellular Proteomics. 14, 3, p. 658-73 16 p.

      Research output: Contribution to journalJournal articlepeer-review

    5. Published
    6. Feature-based prediction of non-classical and leaderless protein secretion

      Bendtsen, J. D., Jensen, Lars Juhl, Blom, N., Von Heijne, G. & Brunak, S., 2004, In: Protein Engineering Design and Selection (Print). 17, 4, p. 349-56 8 p.

      Research output: Contribution to journalJournal articlepeer-review

    7. Published

      Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression

      Bergholdt, R., Brorsson, C., Palleja, A., Berchtold, L. A., Fløyel, T., Bang-Berthelsen, C. H., Frederiksen, K. S., Jensen, Lars Juhl, Størling, J. & Pociot, F., 2012, In: Diabetes. 61, 4, p. 954-62 9 p.

      Research output: Contribution to journalJournal articlepeer-review

    8. Published

      A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment

      Bernard, C., Locard-Paulet, Marie, Noël, C., Duchateau, M., Giai Gianetto, Q., Moumen, B., Rattei, T., Hechard, Y., Jensen, Lars Juhl, Matondo, M. & Samba-Louaka, A., 2022, In: Nature Communications. 13, 1, 14 p., 4104.

      Research output: Contribution to journalJournal articlepeer-review

    9. Published

      COMPARTMENTS: unification and visualization of protein subcellular localization evidence

      Binder, J. X., Pletscher-Frankild, S., Tsafou, K., Stolte, C., O'Donoghue, S. I., Schneider, R. & Jensen, Lars Juhl, 2014, In: Database: The Journal of Biological Databases and Curation. 2014, 9 p., bau012.

      Research output: Contribution to journalJournal articlepeer-review

    10. Published

      A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk

      Blair, D. R., Lyttle, C. S., Mortensen, J. M., Bearden, C. F., Jensen, A. B., Khiabanian, H., Melamed, R., Rabadan, R., Bernstam, E. V., Brunak, Søren, Jensen, Lars Juhl, Nicolae, D., Shah, N. H., Grossman, R. L., Cox, N. J., White, K. P. & Rzhetsky, A., 26 Sep 2013, In: Cell. 155, 1, p. 70-80 11 p.

      Research output: Contribution to journalJournal articlepeer-review

    11. Published

      Protein annotation in the era of personal genomics

      Blicher, T., Gupta, R., Wesolowska, A., Jensen, Lars Juhl & Brunak, Søren, 1 Jun 2010, In: Current Opinion in Structural Biology. 20, 3, p. 335-41 7 p.

      Research output: Contribution to journalJournal articlepeer-review

    12. Protein interaction networks from yeast to human

      Bork, P., Jensen, Lars Juhl, von Mering, C., Ramani, A. K., Lee, I. & Marcotte, E. M., 2004, In: Current Opinion in Structural Biology. 14, 3, p. 292-9 8 p.

      Research output: Contribution to journalJournal articlepeer-review

    13. Published

      SnapShot: S-Phase Entry and Exit

      Burgess, A., Vuong, J., Marzec, K. A., de Lichtenberg, U. N., O'Donoghue, S. I. & Jensen, Lars Juhl, 2019, In: Cell. 179, 3, p. 802-802.e1 2 p.

      Research output: Contribution to journalComment/debatepeer-review

    14. Published

      Predicting Kinase Activity in Angiotensin Receptor Phosphoproteomes Based on Sequence-Motifs and Interactions

      Bøgebo, R., Horn, H., Olsen, Jesper Velgaard, Gammeltoft, S., Jensen, Lars Juhl, Hansen, J. L. & Christensen, G. L., 2014, In: PLOS ONE. 9, 4, p. 1-9 9 p., e94672.

      Research output: Contribution to journalJournal articlepeer-review

    15. Published

      Drug target identification using side-effect similarity

      Campillos, M., Kuhn, M., Gavin, A., Jensen, Lars Juhl & Bork, P., 2008, In: Science. 321, 5886, p. 263-6 3 p.

      Research output: Contribution to journalJournal articlepeer-review

    16. Identification and analysis of evolutionarily cohesive functional modules in protein networks

      Campillos, M., von Mering, C., Jensen, Lars Juhl & Bork, P., 2006, In: Genome Research. 16, 3, p. 374-82 9 p.

      Research output: Contribution to journalJournal articlepeer-review

    17. Published

      TIN-X: target importance and novelty explorer

      Cannon, D. C., Yang, J. J., Mathias, S. L., Ursu, O., Mani, S., Waller, A., Schürer, S. C., Jensen, Lars Juhl, Sklar, L. A., Bologa, C. G. & Oprea, T. I., 15 Aug 2017, In: Bioinformatics. 33, 16, p. 2601-2603 3 p.

      Research output: Contribution to journalJournal articlepeer-review

    18. Published

      Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins

      Cappellini, Enrico, Jensen, Lars Juhl, Szklarczyk, D. M., Ginolhac, A., Rodrigues da Fonseca, Rute Andreia, Stafford jr., T., Holen, S. R., Collins, M. J., Orlando, L. A. A., Willerslev, Eske, Gilbert, M Thomas P & Olsen, Jesper Velgaard, 2012, In: Journal of Proteome Research. 11, 2, p. 917-926 10 p.

      Research output: Contribution to journalJournal articlepeer-review

    19. Published

      LocText: relation extraction of protein localizations to assist database curation

      Cejuela, J. M., Vinchurkar, S., Goldberg, T., Prabhu Shankar, M. S., Baghudana, A., Bojchevski, A., Uhlig, C., Ofner, A., Raharja-Liu, P., Jensen, Lars Juhl & Rost, B., 2018, In: BMC Bioinformatics. 19, p. 1-11 15.

      Research output: Contribution to journalJournal articlepeer-review

    20. Published

      An Integrative Approach to Virus-Host Protein-Protein Interactions

      Cook, H. V. & Jensen, Lars Juhl, 2018, Computational Cell Biology. von Stechow, L. & Delgado, A. S. (eds.). Humana Press, p. 175-196 22 p. (Methods in Molecular Biology, Vol. 1819).

      Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

    21. Published

      A Guide to Dictionary-Based Text Mining

      Cook, H. V. & Jensen, Lars Juhl, 2019, Bioinformatics and Drug Discovery. Larson, R. S. & Oprea, T. I. (eds.). 3 ed. Humana Press, Vol. 1939. p. 73-89 17 p. (Methods in Molecular Biology).

      Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

    22. Published

      Viruses.STRING: A Virus-Host Protein-Protein Interaction Database

      Cook, H. V., Doncheva, Nadezhda Tsankova, Szklarczyk, D., von Mering, C. & Jensen, Lars Juhl, 2018, In: Viruses. 10, 10, p. 1-11 519.

      Research output: Contribution to journalJournal articlepeer-review

    23. Published

      Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

      Croft, L. J., Szklarczyk, D., Jensen, Lars Juhl & Gorodkin, Jan, 2012, In: B M C Systems Biology. 6, 1, p. 90

      Research output: Contribution to journalJournal articlepeer-review

    24. Published

      Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

      Csikász-Nagy, A., Kapuy, O., Tóth, A., Pál, C., Jensen, Lars Juhl, Uhlmann, F., Tyson, J. J. & Novák, B., 2009, In: Molecular Systems Biology. 5, p. 236

      Research output: Contribution to journalJournal articlepeer-review

    25. Published

      Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism

      Cuesta-Astroz, Y., Santos, A., Oliveira, G. & Jensen, Lars Juhl, 2019, In: Frontiers in Immunology. 10, 17 p., 212.

      Research output: Contribution to journalJournal articlepeer-review

    26. Published

      Ten simple rules for getting help from online scientific communities

      Dall'olio, G. M., Marino, J., Schubert, M., Keys, K. L., Stefan, M. I., Gillespie, C. S., Poulain, P., Shameer, K., Sugar, R., Invergo, B. M., Jensen, Lars Juhl, Bertranpetit, J. & Laayouni, H., 1 Sep 2011, In: P L o S Computational Biology. 7, 9, p. e1002202

      Research output: Contribution to journalJournal articlepeer-review

    27. Published

      Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level

      Danielsen, J. M. R., Sylvestersen, K. B., Bekker-Jensen, Simon Holst, Szklarczyk, D., Poulsen, J. W., Horn, H., Jensen, Lars Juhl, Mailand, Niels & Nielsen, Michael Lund, 1 Mar 2011, In: Molecular and Cellular Proteomics. 10, 3, p. M110.003590

      Research output: Contribution to journalJournal articlepeer-review

    28. Published

      Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

      Deshmukh, Atul Shahaji, Cox, J., Jensen, Lars Juhl, Meissner, F. & Mann, Matthias, 6 Nov 2015, In: Journal of Proteome Research. 14, 11, p. 4885-95 11 p.

      Research output: Contribution to journalJournal articlepeer-review

    29. Published

      Metastatic Infiltration of Nervous Tissue and Periosteal Nerve Sprouting in Multiple Myeloma-Induced Bone Pain in Mice and Human

      Diaz-delCastillo, M., Palasca, O., Nemler, T. T., Thygesen, D. M., Chávez-Saldaña, N. A., Vázquez-Mora, J. A., Ponce Gomez, L. Y., Jensen, L. J., Evans, H., Andrews, R. E., Mandal, A., Neves, D., Mehlen, P., Caruso, J. P., Dougherty, P. M., Price, T. J., Chantry, A., Lawson, M. A., Andersen, T. L., Jimenez-Andrade, J. M. & 1 others, Heegaard, Anne-Marie, 2023, In: The Journal of Neuroscience. 43, 29, p. 5414-5430

      Research output: Contribution to journalJournal articlepeer-review

    30. Published

      Myeloma-induced bone pain: lessons learnt from a localized, immunocompetent mouse model

      Diaz-delCastillo, M., Nemler, T., Thygesen, D. M., Chavez-Saldana, N. A., Vazquez-Mora, J. A., Palasca, Oana, Jensen, Lars Juhl, Evans, H., Andrews, R. E., Mandal, A., Chantry, A. D., Lawson, M. A., Andersen, T., Jimenez-Andrade, J. M. & Heegaard, Anne-Marie, 2022, In: Clinical Lymphoma, Myeloma & Leukemia. 22, Suppl., p. S108-S108 P-133.

      Research output: Contribution to journalConference abstract in journalpeer-review

    31. Published

      Phospho.ELM: a database of phosphorylation sites--update 2011

      Dinkel, H., Chica, C., Via, A., Gould, C. M., Jensen, Lars Juhl, Gibson, T. J. & Diella, F., 1 Jan 2011, In: Nucleic Acids Symposium Series. 39, Database issue, p. D261-7

      Research output: Contribution to journalJournal articlepeer-review

    32. Published

      Cytoscape stringApp: Network analysis and visualization of proteomics data

      Doncheva, Nadezhda Tsankova, Morris, J., Gorodkin, Jan & Jensen, Lars Juhl, 2019, In: Journal of Proteome Research. 18, 2, p. 623-632

      Research output: Contribution to journalJournal articlepeer-review

    33. Published

      Human pathways in animal models: possibilities and limitations

      Doncheva, Nadezhda Tsankova, Palasca, Oana, Yarani, R., Litman, Thomas, Anthon, Christian, Groenen, M. A. M., Stadler, P. F., Pociot, Flemming, Jensen, Lars Juhl & Gorodkin, Jan, 2021, In: Nucleic Acids Research. 49, 4, p. 1859-1871 13 p.

      Research output: Contribution to journalJournal articlepeer-review

    34. Published

      Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks

      Doncheva, Nadezhda Tsankova, Morris, J. H., Holze, H., Kirsch, Rebecca, Nastou, Katerina, Cuesta-Astroz, Y., Rattei, T., Szklarczyk, D., Von Mering, C. & Jensen, Lars Juhl, 2022, In: Journal of Proteome Research. 22, 2, p. 637-646

      Research output: Contribution to journalJournal articlepeer-review

    35. Published

      Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation

      Emdal, Kristina Bennet, Pedersen, Anna-Kathrine, Bekker-Jensen, D. B., Tsafou, K. P., Horn, H., Lindner, S., Schulte, J. H., Eggert, A., Jensen, Lars Juhl, Francavilla, C. & Olsen, Jesper Velgaard, 2015, In: Science Signaling. 8, 374, ra40.

      Research output: Contribution to journalJournal articlepeer-review

    36. 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 journalJournal articlepeer-review

    37. Published

      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, Apr 2014, In: Drug Safety. 37, 4, p. 237-47 11 p.

      Research output: Contribution to journalJournal articlepeer-review

    38. Published

      Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA

      Eriksson, R., Aagaard, L., Jensen, Lars Juhl, Borisova, L., Hørlück, D., Brunak, Søren & Hansen, E. H., 2014, In: Pharmacology Research & Perspectives. 2, 3, p. 1-10 e00038.

      Research output: Contribution to journalJournal articlepeer-review

    39. 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 journalJournal articlepeer-review

    40. 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 journalJournal articlepeer-review

    41. 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 journalJournal articlepeer-review

    42. 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 journalJournal articlepeer-review

    43. 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 journalJournal articlepeer-review

    44. 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 journalReviewpeer-review

    45. 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 journalJournal articlepeer-review

    46. 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 proceedingBook chapterResearch

    47. 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 journalJournal articlepeer-review

    48. 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 journalJournal articlepeer-review

    49. 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 journalJournal articlepeer-review

    50. 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 journalJournal articlepeer-review

    51. 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 journalJournal articlepeer-review

    52. 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 journalJournal articlepeer-review

    53. 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 journalJournal articlepeer-review

    54. 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 journalJournal articlepeer-review

    55. 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 journalJournal articlepeer-review

    56. 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 journalJournal articlepeer-review

    57. 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 journalJournal articlepeer-review

    58. 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 journalJournal articlepeer-review

    59. 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 journalJournal articlepeer-review

    60. 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 journalJournal articlepeer-review

    61. 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 journalEditorial

    62. 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 journalJournal articlepeer-review

    63. 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 journalJournal articlepeer-review

    64. 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 journalJournal articlepeer-review

    65. 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 journalJournal articlepeer-review

    66. Published
    67. 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 journalJournal articlepeer-review

    68. 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 journalJournal articlepeer-review

    69. 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 journalJournal articlepeer-review

    70. 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 journalJournal articlepeer-review

    71. 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 journalJournal articlepeer-review

    72. 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 journalJournal articlepeer-review

    73. 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 journalJournal articlepeer-review

    74. 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 journalJournal articlepeer-review

    75. 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 journalLetterpeer-review

    76. 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 journalJournal articlepeer-review

    77. 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 journalJournal articlepeer-review

    78. 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 journalJournal articlepeer-review

    79. 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 journalJournal articlepeer-review

    80. 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 journalJournal articlepeer-review

    81. 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 journalJournal articlepeer-review

    82. 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 journalJournal articlepeer-review

    83. 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 journalJournal articlepeer-review

    84. 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 journalComment/debatepeer-review

    85. 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 journalJournal articlepeer-review

    86. 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 journalJournal articlepeer-review

    87. 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 journalJournal articlepeer-review

    88. 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 journalJournal articlepeer-review

    89. 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 journalJournal articlepeer-review

    90. 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 journalJournal articlepeer-review

    91. 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 journalJournal articlepeer-review

    92. 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 journalJournal articlepeer-review

    93. 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 proceedingBook chapterCommunication

    94. 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 journalJournal articlepeer-review

    95. 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 journalJournal articlepeer-review

    96. 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 journalJournal articlepeer-review

    97. 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 journalConference articlepeer-review

    98. 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 journalJournal articlepeer-review

    99. 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 journalJournal articlepeer-review

    100. 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 journalComment/debatepeer-review

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