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

      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

    2. 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

    3. 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

    4. 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

    5. 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

    6. 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

    7. 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

    8. 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

    9. 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

    10. 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

    11. 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

    12. 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

    13. 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

    14. 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

    15. 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

    16. 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

    17. 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

    18. 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

    19. 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

    20. 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

    21. 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

    22. Published

      STITCH 3: zooming in on protein-chemical interactions

      Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, Lars Juhl & Bork, P., 2012, In: Nucleic Acids Research. 40, Database issue, p. D876-80

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

    23. Published

      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

    24. 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

    25. 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

    26. 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

    27. 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

    28. 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

    29. 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

    30. 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

    31. 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

    32. 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

    33. 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

    34. 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

    35. 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

    36. 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

    37. 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

    38. 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

    39. 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

    40. 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

    41. 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

    42. 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

    43. 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

    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. 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

    46. 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

    47. 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

    48. 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

    49. 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

    50. 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

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