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

      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

    2. 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

    3. 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

    4. Martini: using literature keywords to compare gene sets

      Soldatos, T. G., O'Donoghue, S. I., Satagopam, V. P., Jensen, Lars Juhl, Brown, N. P., Barbosa-Silva, A. & Schneider, R., 2010, In: Nucleic Acids Research. 38, 1, p. 26-38 13 p.

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

    5. 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 journal › Journal article › Research › peer-review

    6. 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 journal › Journal article › Research › peer-review

    7. Published

      Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls

      Midjord-Belstrøm, Daniel, Jersie-Christensen, R. R., Lyon, D., Damgaard, Christian, Jensen, Lars Juhl, Holmstrup, Palle & Olsen, Jesper Velgaard, 2016, In: PeerJ. 4, 17 p., e2433.

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

    8. 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 journal › Journal article › Research › peer-review

    9. Published

      Microblogging the ISMB: a new approach to conference reporting

      Saunders, N., Beltrão, P., Jurczak, D., Krause, R., Kuhn, M., Wu, S. & Jensen, Lars Juhl, 2009, In: PLoS Computational Biology. 5, 1, p. e1000263

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

    10. 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

    11. 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 journal › Journal article › Research › peer-review

    12. 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 journal › Conference abstract in journal › Research › peer-review

    13. 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

    14. Published

      On the total number of genes and their length distribution in complete microbial genomes

      Skovgaard, M., Jensen, Lars Juhl, Brunak, Søren, Ussery, D. & Krogh, Anders, 2001, In: Trends in Genetics. 17, 8, p. 425-8 4 p.

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

    15. 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 journal › Journal article › Research › peer-review

    16. 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

    17. 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

    18. 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

    19. Origin of replication in circular prokaryotic chromosomes

      Worning, P., Jensen, Lars Juhl, Hallin, P. F., Staerfeldt, H. & Ussery, D., 2006, In: Environmental Microbiology. 8, 2, p. 353-61 9 p.

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

    20. 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

    21. Published

      Overview of the Knowledge Management Center for Illuminating the Druggable Genome

      Oprea, T. I., Bologa, C., Holmes, J., Mathias, S., Metzger, V. T., Waller, A., Yang, J. J., Leach, A. R., Jensen, Lars Juhl, Kelleher, K. J., Sheils, T. K., Mathé, E., Avram, S. & Edwards, J. S., 2024, In: Drug Discovery Today. 29, 3, 8 p., 103882.

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

    22. Published

      Overview of the interactive task in BioCreative V

      Wang, Q., S Abdul, S., Almeida, L., Ananiadou, S., Balderas-Martínez, Y. I., Batista-Navarro, R., Campos, D., Chilton, L., Chou, H-J., Contreras, G., Cooper, L., Dai, H-J., Ferrell, B., Fluck, J., Gama-Castro, S., George, N., Gkoutos, G., Irin, A. K., Jensen, L. J., Jimenez, S. & 36 others, Jue, T. R., Keseler, I., Madan, S., Matos, S., McQuilton, P., Milacic, M., Mort, M., Natarajan, J., Pafilis, E., Pereira, E., Rao, S., Rinaldi, F., Rothfels, K., Salgado, D., Silva, R. M., Singh, O., Stefancsik, R., Su, C., Subramani, S., Tadepally, H. D., Tsaprouni, L., Vasilevsky, N., Wang, X., Chatr-Aryamontri, A., Laulederkind, S. J. F., Matis-Mitchell, S., McEntyre, J., Orchard, S., Pundir, S., Rodriguez-Esteban, R., Van Auken, K., Lu, Z., Schaeffer, M., Wu, C. H., Hirschman, L. & Arighi, C. N., 2016, In: Database: The Journal of Biological Databases and Curation. 2016, 18 p., baw119.

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

    23. Published

      PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

      Zafeiropoulos, H., Paragkamian, S., Ninidakis, S., Pavlopoulos, G. A., Jensen, Lars Juhl & Pafilis, E., 2022, In: Microorganisms. 10, 2, 22 p., 293.

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

    24. 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 journal › Journal article › Research › peer-review

    25. 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

    26. 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 journal › Journal article › Research › peer-review

    27. 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

    28. 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 journal › Journal article › Research › peer-review

    29. 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

    30. Published

      Phosphorylation of SHP2 at Tyr62 enables acquired resistance to SHP2 allosteric inhibitors in FLT3-ITD-driven AML

      Pfeiffer, A., Franciosa, Giulia, Locard-Paulet, Marie, Piga, I., Reckzeh, K., Vemulapalli, V., Blacklow, S. C., Theilgaard-Mønch, Kim, Jensen, Lars Juhl & Olsen, Jesper Velgaard, 2022, In: Cancer Research. 82, 11, p. 2141-2155 15 p.

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

    31. Published

      Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington

      Waters, M. R., Stafford jr., T., McDonald, H. G., Gustafson, C., Rasmussen, M., Cappellini, Enrico, Olsen, Jesper Velgaard, Szklarczyk, D. M., Jensen, Lars Juhl, Gilbert, M Thomas P & Willerslev, Eske, 2011, In: Science. 334, 6054, p. 351-353 3 p.

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

    32. 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 journal › Journal article › Research › peer-review

    33. 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

    34. 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

    35. 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

    36. 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

    37. 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 journal › Journal article › Research › peer-review

    38. 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 journal › Journal article › Research › peer-review

    39. 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

    40. Protein feature based identification of cell cycle regulated proteins in yeast

      de Lichtenberg, U., Jensen, T. S., Jensen, Lars Juhl & Brunak, S., 2003, In: Journal of Molecular Biology. 329, 4, p. 663-74 12 p.

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

    41. 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 journal › Journal article › Research › peer-review

    42. Published

      Protein-Protein Interaction Databases

      Szklarczyk, D. & Jensen, Lars Juhl, 2015, Protein-Protein Interactions: Methods and Applications. Meyerkord, C. L. & Fu, H. (eds.). 2 ed. New York: Springer Publishing Company, Vol. 1278. p. 39-56 18 p. (Methods in Molecular Biology, Vol. 1278).

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

    43. Published

      Protein-driven inference of miRNA-disease associations

      Mørk, S., Pletscher-Frankild, S., Palleja, A., Gorodkin, Jan & Jensen, Lars Juhl, 2014, In: Bioinformatics (Oxford, England). 30, 3, p. 392-397 6 p.

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

    44. 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

    45. 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

    46. 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

    47. Published

      Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation

      Weinert, B. T., Wagner, S. A., Horn, H., Henriksen, P., Liu, W. R., Olsen, Jesper Velgaard, Jensen, Lars Juhl & Choudhary, Chunaram, 2011, In: Science Signaling. 4, 183, p. ra48

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

    48. 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 journal › Journal article › Research › peer-review

    49. Published

      Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest

      Sylvestersen, K. B., Horn, H., Jungmichel, S., Jensen, Lars Juhl & Nielsen, Michael Lund, 21 Feb 2014, In: Molecular & Cellular Proteomics. 13, p. 2072-2088 17 p.

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

    50. 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

    51. 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

    52. 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

    53. Published

      Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

      Olsen, Jesper Velgaard, Vermeulen, M., Santamaria, A., Kumar, C., Miller, M. L., Jensen, Lars Juhl, Gnad, F., Cox, J., Jensen, T. S., Nigg, E. A., Brunak, Søren & Mann, Matthias, 2010, In: Science Signaling. 3, 104, p. ra3 15 p.

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

    54. Quantitative phylogenetic assessment of microbial communities in diverse environments

      von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, Lars Juhl, Ward, N. & Bork, P., 2007, In: Science (New York, N.Y.). 315, 5815, p. 1126-30 5 p.

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

    55. 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

    56. 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

    57. 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

    58. Published

      Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

      Orlando, L. A. A., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P. L. F., Fumagalli, M., Mouatt, J. T. V., Raghavan, M., Korneliussen, T. S., Malaspinas, A. S., Vogt, J., Szklarczyk, D. M., Kelstrup, C., Vinther, J. & 36 others, Dolocan, A., Stenderup, Jesper Tandberg, Velazquez, A. M. V., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G. D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J. F., Weinstock, J., Gregersen, K., Røed, K. H., Eisenmann, V., Rubin, C. J., Miller, D. C., Antczak, D. F., Bertelsen, M. F., Brunak, S., Al-Rasheid, K. A. S., Ryder, O., Andersson, L., Mundy, J., Krogh, Anders, Gilbert, M Thomas P, Kjær, Kurt H., Sicheritz-Pontén, T., Jensen, Lars Juhl, Olsen, Jesper Velgaard, Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J. & Willerslev, Eske, 4 Jul 2013, In: Nature. 499, 7456, p. 74-78 5 p.

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

    59. 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

    60. Published

      Reflect: a practical approach to web semantics

      O'Donoghue, S. I., Horn, H., Pafilisa, E., Haag, S., Kuhn, M., Satagopam, V. P., Schneider, R. & Jensen, Lars Juhl, Jul 2010, In: Journal of Web Semantics. 8, 2-3, p. 182-189

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

    61. Published

      Reflect: augmented browsing for the life scientist

      Pafilis, E., O'Donoghue, S. I., Jensen, Lars Juhl, Horn, H., Kuhn, M., Brown, N. P. & Schneider, R., 2009, In: Nature Biotechnology. 27, 6, p. 508-10 2 p.

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

    62. 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

    63. 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

    64. 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

    65. 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

    66. 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

    67. 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

    68. Published

      STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data

      Szklarczyk, D., Santos Delgado, A., von Mering, C., Jensen, Lars Juhl, Bork, P. & Kuhn, M., 2016, In: Nucleic Acids Research. 44, D1, p. D380-84 5 p.

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

    69. STRING: known and predicted protein-protein associations, integrated and transferred across organisms

      von Mering, C., Jensen, Lars Juhl, Snel, B., Hooper, S. D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M. A. & Bork, P., 2005, In: Nucleic Acids Research. 33, Database issue, p. D433-7

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

    70. STRING 7--recent developments in the integration and prediction of protein interactions

      von Mering, C., Jensen, Lars Juhl, Kuhn, M., Chaffron, S., Doerks, T., Krüger, B., Snel, B. & Bork, P., 2007, In: Nucleic Acids Research. 35, Database issue, p. D358-62

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

    71. 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

    72. Published

      STRING v10: protein-protein interaction networks, integrated over the tree of life

      Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos Delgado, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, Lars Juhl & von Mering, C., 28 Jan 2015, In: Nucleic Acids Research. 43, D1, p. D447-52 6 p.

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

    73. 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 journal › Journal article › Research › peer-review

    74. 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

    75. 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

    76. 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

    77. Published

      Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics

      Refsgaard, J. C., Munk, S. & Jensen, Lars Juhl, 2016, Phospho-Proteomics: Methods and Protocols. Stechow, L. V. (ed.). Springer Publishing Company, Vol. 1355. p. 323-39 17 p. (Methods in molecular biology (Clifton, N.J.)).

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

    78. 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 journal › Journal article › Research › peer-review

    79. 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 journal › Journal article › Research › peer-review

    80. 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

    81. 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

    82. 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

    83. 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 journal › Comment/debate › Research › peer-review

    84. 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

    85. 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 journal › Journal article › Research › peer-review

    86. Spore number control and breeding in saccharomyces cerevisiae a key role for a self-organixzing system

      Taxis, C., Kavagiou, Z., Keller, P., Jensen, Lars Juhl, Colombelli, J., Bork, P., Stelzer, E. H. K. & Knop, M., 2005, In: Journal of Cell Biology. 171, p. 627-640

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

    87. 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 journal › Journal article › Research › peer-review

    88. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

      Worning, P., Jensen, Lars Juhl, Nelson, K. E., Brunak, S. & Ussery, D., 2000, In: Nucleic Acids Research. 28, 3, p. 706-9 4 p.

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

    89. 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 journal › Journal article › Research › peer-review

    90. 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

    91. 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

    92. 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

    93. 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

    94. 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

    95. 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

    96. Published

      TCRD and Pharos 2021: mining the human proteome for disease biology

      Sheils, T. K., Mathias, S. L., Kelleher, K. J., Siramshetty, V. B., Nguyen, D. T., Bologa, C. G., Jensen, Lars Juhl, Vidović, D., Koleti, A., Schürer, S. C., Waller, A., Yang, J. J., Holmes, J., Bocci, G., Southall, N., Dharkar, P., Mathé, E., Simeonov, A. & Oprea, T. I., 2021, In: Nucleic Acids Research. 49, D1, p. D1334-D1346 13 p.

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

    97. Published

      TIGA: target illumination GWAS analytics

      Yang, J. J., Grissa, Dhouha, Lambert, C. G., Bologa, C. G., Mathias, S. L., Waller, A., Wild, D. J., Jensen, Lars Juhl & Oprea, T. I., 2021, In: Bioinformatics. 37, 21, p. 3865-3873

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

    98. 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

    99. 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 journal › Journal article › Research › peer-review

    100. 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 journal › Journal article › Research › peer-review

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