Lars Juhl Jensen

Lars Juhl Jensen

Professor, Group Leader, Professor

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    ORCID: 0000-0001-7885-715X

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    1. 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

    2. 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

    3. 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

    4. 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

    5. 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

    6. 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

    7. 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

    8. 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

    9. 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

    10. 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

    11. 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

    12. 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

    13. 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

    14. 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

    15. 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

    16. 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

    17. 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

    18. 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

    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. 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

    21. 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

    22. 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

    23. 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

    24. 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

    25. 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

    26. 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

    27. 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

    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 journal › Journal article › Research › peer-review

    29. 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

    30. 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

    31. 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

    32. 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

    33. 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

    34. 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

    35. 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

    36. 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

    37. 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

    38. 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

    39. 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

    40. 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

    41. 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

    42. 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

    43. 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

    44. 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

    45. 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

    46. 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

    47. 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

    48. 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

    49. 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

    50. 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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