Lars Juhl Jensen

Lars Juhl Jensen

Professor, Group Leader, Professor

Member of:


    1. 2016
    2. 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 journalJournal articlepeer-review

    3. Published

      Seqenv: linking sequences to environments through text mining

      Sinclair, L., Ijaz, U. Z., Jensen, Lars Juhl, Coolen, M. J. L., Gubry-Rangin, C., Chroňáková, A., Oulas, A., Pavloudi, C., Schnetzer, J., Weimann, A., Ijaz, A., Eiler, A., Quince, C. & Pafilis, E., 20 Dec 2016, In: PeerJ. 4, p. 1-17 17 p., e2690.

      Research output: Contribution to journalJournal articlepeer-review

    4. 2017
    5. 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 journalJournal articlepeer-review

    6. Published

      Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification

      Mullari, M., Lyon, D., Jensen, Lars Juhl & Nielsen, Michael Lund, 2017, In: Journal of Proteome Research. 16, 8, p. 2762-2772 11 p.

      Research output: Contribution to journalJournal articlepeer-review

    7. Published

      Structure-based discovery of novel US28 small molecule ligands with different modes of action

      Lückmann, Michael, Amarandi, R., Papargyri, N., Jakobsen, M. H., Ulven, Elisabeth Rexen, Jensen, Lars Juhl, Pui, A., Schwartz, Thue W., Rosenkilde, Mette & Frimurer, Thomas Michael, 2017, In: Chemical Biology & Drug Design. 89, 3, p. 289–296

      Research output: Contribution to journalJournal articlepeer-review

    8. Published

      Pharos: Collating protein information to shed light on the druggable genome

      Nguyen, D-T., Mathias, S., Bologa, C., Brunak, S., Fernandez, N., Gaulton, A., Hersey, A., Holmes, J., Jensen, L. J., Karlsson, A., Liu, G., Ma'ayan, A., Mandava, G., Mani, S., Mehta, S., Overington, J., Patel, J., Rouillard, A. D., Schürer, S., Sheils, T. & 10 others, Simeonov, A., Sklar, L. A., Southall, N., Ursu, O., Vidovic, D., Waller, A., Yang, J., Jadhav, A., Oprea, T. I. & Guha, R., Jan 2017, In: Nucleic Acids Research. 45, D1, p. D995–D1002

      Research output: Contribution to journalJournal articlepeer-review

    9. Published

      The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

      Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos Delgado, A., Doncheva, Nadezhda Tsankova, Roth, A., Bork, P., Jensen, Lars Juhl & von Mering, C., Jan 2017, In: Nucleic Acids Research. 45, D1, p. D362-D368

      Research output: Contribution to journalJournal articlepeer-review

    10. 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

    11. 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 journalJournal articlepeer-review

    12. 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

    13. Published

      Accurate quantification of site-specific acetylation stoichiometry reveals the impact of sirtuin deacetylase CobB on the E. coli acetylome

      Weinert, B. T., Satpathy, S., Hansen, B. K., Lyon, D., Jensen, Lars Juhl & Choudhary, Chunaram, May 2017, In: Molecular and Cellular Proteomics. 16, p. 759-769

      Research output: Contribution to journalJournal articlepeer-review

    14. 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

    15. 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

    16. 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 journalJournal articlepeer-review

    17. 2018
    18. 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

    19. Published

      A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

      Westergaard, David, Stærfeldt, H., Tønsberg, C., Jensen, Lars Juhl & Brunak, Søren, 2018, In: PLoS Computational Biology. 14, 2, 16 p., e1005962.

      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

      Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

      Sinha, S., Eisenhaber, B., Jensen, Lars Juhl, Kalbuaji, B. & Eisenhaber, F., 2018, In: Proteomics. 18, 21-22, p. 1-13 e1800093.

      Research output: Contribution to journalJournal articlepeer-review

    22. Published

      Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

      Pan, X., Wenzel, Anne, Jensen, Lars Juhl & Gorodkin, Jan, 2018, In: PLoS ONE. 13, 8, 15 p., e0202369.

      Research output: Contribution to journalJournal articlepeer-review

    23. Published

      Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting

      Mackie, Meaghan, Rüther, P. L., Samodova-Sommer, Diana, Di Gianvincenzo, Fabiana, Granzotto, C., Lyon, D., Peggie, D. A., Howard, H., Harrison, L., Jensen, Lars Juhl, Olsen, Jesper Velgaard & Cappellini, Enrico, 2018, In: Angewandte Chemie (International ed. in English). 57, 25, p. 7369-7374 6 p.

      Research output: Contribution to journalJournal articlepeer-review

    24. 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 journalJournal articlepeer-review

    25. 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

    26. Published
    27. Published

      TISSUES 2.0: an integrative web resource on mammalian tissue expression

      Palasca, Oana, Santos, A., Stolte, C., Gorodkin, Jan & Jensen, Lars Juhl, 2018, In: Database: The Journal of Biological Databases and Curation. 2018, 1, p. 1-12

      Research output: Contribution to journalJournal articlepeer-review

    28. Published

      Unexplored therapeutic opportunities in the human genome

      Oprea, T. I., Bologa, C. G., Brunak, S., Campbell, A., Gan, G. N., Gaulton, A., Gomez, S. M., Guha, R., Hersey, A., Holmes, J., Jadhav, A., Jensen, L. J., Johnson, G. L., Karlson, A., Leach, A. R., Ma'ayan, A., Malovannaya, A., Mani, S., Mathias, S. L., McManus, M. T. & 21 others, Meehan, T. F., von Mering, C., Muthas, D., Nguyen, D., Overington, J. P., Papadatos, G., Qin, J., Reich, C., Roth, B. L., Schürer, S. C., Simeonov, A., Sklar, L. A., Southall, N., Tomita, S., Tudose, I., Ursu, O., Vidovic, D., Waller, A., Westergaard, David, Yang, J. J. & Zahoránszky-Köhalmi, G., 2018, In: Nature Reviews. Drug Discovery. 17, 5, p. 317-332 16 p.

      Research output: Contribution to journalReviewpeer-review

    29. 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

    30. Published

      miRandola 2017: a curated knowledge base of non-invasive biomarkers

      Russo, F., Di Bella, S., Vannini, F., Berti, G., Scoyni, F., Cook, H. V., Santos, A., Nigita, G., Bonnici, V., Laganà, A., Geraci, F., Pulvirenti, A., Giugno, R., De Masi, F., Belling, K., Jensen, Lars Juhl, Brunak, Søren, Pellegrini, M. & Ferro, A., 1 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D354-D359 6 p.

      Research output: Contribution to journalJournal articlepeer-review

    31. Published

      WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

      Pan, X., Xiong, K., Anthon, Christian, Hyttel, P., Freude, Kristine, Jensen, Lars Juhl & Gorodkin, Jan, 6 Nov 2018, In: Genes. 9, 11, 11 p., 536.

      Research output: Contribution to journalJournal articlepeer-review

    32. 2019
    33. 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

    34. 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

    35. 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 journalJournal articlepeer-review

    36. 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

    37. Published

      Design, implementation, and operation of a rapid, robust named entity recognition web service

      Pletscher-Frankild, S. & Jensen, Lars Juhl, 2019, In: Journal of Cheminformatics. 11, 6 p., 19.

      Research output: Contribution to journalJournal articlepeer-review

    38. 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

    39. 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 journalJournal articlepeer-review

    40. Published

      Inferring disease-associated long non-coding RNAs using genome - wide tissue expression profiles

      Pan, X., Jensen, Lars Juhl & Gorodkin, Jan, 2019, In: Bioinformatics. 35, 9, p. 1494-1502 9 p.

      Research output: Contribution to journalJournal articlepeer-review

    41. 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 journalJournal articlepeer-review

    42. 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 journalJournal articlepeer-review

    43. Published

      ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins

      Tagore, S., Gorohovski, A., Jensen, Lars Juhl & Frenkel-Morgenstern, M., 2019, In: PLOS Computational Biology. 15, 8, 16 p., e1007239.

      Research output: Contribution to journalJournal articlepeer-review

    44. Published

      STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

      Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, Nadezhda Tsankova, Morris, J. H., Bork, P., Jensen, Lars Juhl & von Mering, C., 2019, In: Nucleic Acids Research. 47, D1, p. D607-D613 7 p.

      Research output: Contribution to journalJournal articlepeer-review

    45. 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

    46. 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 journalLetterpeer-review

    47. Published

      Transcriptome landscape of protein-coding genes and long noncoding RNAs in the colon and blood of DSS-induced mouse model of Acute ulcerative colitis

      Yarani, R., Palasca, Oana, Doncheva, Nadezhda Tsankova, Anthon, Christian, Pilecki, B., Litman, Thomas, Holmskov, U., Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2019, In: Journal of Crohn's and Colitis. 13, p. S129-S130

      Research output: Contribution to journalConference abstract in journalpeer-review

    48. 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

    49. 2020
    50. 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

    51. 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 journalJournal articlepeer-review

    52. 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 journalJournal articlepeer-review

    53. 2021
    54. Published

      Homology-directed repair protects the replicating genome from metabolic assaults

      Somyajit, K., Spies, J., Coscia, F., Kirik, U., Rask, M., Lee, J., Neelsen, K. J., Mund, Andreas, Jensen, Lars Juhl, Paull, T. T., Mann, Matthias & Lukas, Jiri, 2021, In: Developmental Cell. 56, 4, p. 461-477.e7

      Research output: Contribution to journalJournal articlepeer-review

    55. 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

    56. Published

      Improved metagenome binning and assembly using deep variational autoencoders

      Nissen, J. N., Johansen, Joachim, Allesoe, R. L., Sonderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Jensen, Lars Juhl, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2021, In: Nature Biotechnology. 39, p. 555-560

      Research output: Contribution to journalJournal articlepeer-review

    ID: 9931112