Lars Juhl Jensen

Lars Juhl Jensen

professor, group leader


  1. 2020
  2. 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, 6 Mar 2020, In : Journal of Proteome Research. 19, 3, p. 1338-1345 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. 2019
  4. 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

  5. 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 articleResearchpeer-review

  6. 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 articleResearchpeer-review

  7. 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 articleResearchpeer-review

  8. 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 articleResearchpeer-review

  9. 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, Francesco, Westergaard, David & Brunak, Søren, 2019, In : npj Systems Biology and Applications. 5, 10 p., 27.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. 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 articleResearchpeer-review

  11. 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 articleResearchpeer-review

  12. Published

    Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining

    Kirk, I. K., Simon, C., Banasik, Karina, Holm, Peter Christoffer, Haue, Amalie Dahl, Jensen, P. B., Jensen, Lars Juhl, Leal Rodriguez, Cristina, Pedersen, M. K., Eriksson, Robert, Andersen, H. U., Almdal, Thomas Peter, Bork-Jensen, J., Grarup, Niels, Borch-Johnsen, K., Pedersen, Oluf Borbye, Pociot, Flemming, Hansen, Torben, Bergholdt, R., Rossing, Peter & Brunak, Søren, 2019, In : eLife. 8, 19 p., e44941.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites

    Lundby, Alicia, Franciosa, Giulia, Emdal, Kristina Bennet, Refsgaard, J. C., Gnosa, Sebastian Peter, 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 articleResearchpeer-review

  14. 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 articleResearchpeer-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 journalJournal articleResearchpeer-review

  16. 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/debateResearchpeer-review

  17. 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 journalLetterResearchpeer-review

  18. 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, O., 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 journalResearchpeer-review

  19. 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 articleResearchpeer-review

  20. 2018
  21. Published

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

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

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

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

    Russo, Francesco, 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, Kirstine G, Jensen, Lars Juhl, Brunak, Søren, Pellegrini, M. & Ferro, A., 4 Jan 2018, In : Nucleic Acids Research. 46, D1, p. D354-D359 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. 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 articleResearchpeer-review

  24. 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 articleResearchpeer-review

  25. 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

  26. 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 articleResearchpeer-review

  27. 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 articleResearchpeer-review

  28. Published

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

    Mackie, Meaghan, Rüther, Patrick, Samodova, 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 articleResearchpeer-review

  29. Published

    Quantitative metaproteomics of medieval dental calculus reveals individual oral health status

    Jersie-Christensen, R. R., Lanigan, Liam Thomas, Lyon, D., Mackie, Meaghan, 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 articleResearchpeer-review

  30. 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 articleResearchpeer-review

  31. 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 journalJournal articleResearchpeer-review

  32. Published

    TISSUES 2.0: an integrative web resource on mammalian tissue expression

    Palasca, O., Santos, A., Stolte, C., Gorodkin, Jan & Jensen, Lars Juhl, 2018, In : Database. 2018, 1, p. 1-12

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Unexplored therapeutic opportunities in the human genome

    Oprea, T. I., Bologa, C. G., Brunak, Søren, Campbell, A., Gan, G. N., Gaulton, A., Gomez, S. M., Guha, R., Hersey, A., Holmes, J., Jadhav, A., Jensen, Lars Juhl, Johnson, G. L., Karlson, A., Leach, A. R., Ma'ayan, A., Malovannaya, A., Mani, S., Mathias, S. L., McManus, M. T., 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 journalReviewResearchpeer-review

  34. 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 articleResearchpeer-review

  35. 2017
  36. 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., Jensen, Lars Juhl, 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., Oprea, T. I. & Schürer, S. C., 9 Nov 2017, In : Journal of Biomedical Semantics. 8, 1, 16 p., 50.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. 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 articleResearchpeer-review

  38. 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 articleResearchpeer-review

  39. 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, Chuna Ram, May 2017, In : Molecular and Cellular Proteomics. 16, p. 759-769

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. 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 articleResearchpeer-review

  41. 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 articleResearchpeer-review

  42. 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, Jens Meldgaard, Dela, Flemming & Helge, Jørn Wulff, Mar 2017, In : Obesity. 25, 3, p. 572-580 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

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

    Nguyen, D., Mathias, S., Bologa, C., Brunak, Søren, Fernandez, N., Gaulton, A., Hersey, A., Holmes, J., Jensen, Lars Juhl, Karlsson, A., Liu, G., Ma'ayan, A., Mandava, G., Mani, S., Mehta, S., Overington, J., Patel, J., Rouillard, A. D., Schürer, S., Sheils, T., 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 articleResearchpeer-review

  44. 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 articleResearchpeer-review

  45. 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. 2017, 9 p., baw167.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

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

    Mullari, Meeli, 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 articleResearchpeer-review

  47. 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 articleResearchpeer-review

  48. 2016
  49. 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 articleResearchpeer-review

  50. 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, Meeli, Vistrup-Parry, Maria, 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 articleResearchpeer-review

  51. 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., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjölander, K., Jensen, Lars Juhl, Martin, M. J., Muffato, M., Gabaldón, T., Lewis, S. E., Thomas, P. D., Sonnhammer, E., Dessimoz, C. & Quest for Orthologs consortium, Q. F. O. C., May 2016, In : Nature Methods. 13, p. 425-30 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    The SIDER database of drugs and side effects

    Kuhn, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 4 Jan 2016, In : Nucleic Acids Research. 44, p. D1075-9

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Published

    eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

    Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., Jensen, Lars Juhl, von Mering, C. & Bork, P., 4 Jan 2016, In : Nucleic Acids Research. 44, D1, p. D286-93

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. Published

    EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

    Pafilis, E., Buttigieg, P. L., Ferrell, B., Pereira, E., Schnetzer, J., Arvanitidis, C. & Jensen, Lars Juhl, 2016, In : Database. 2016, 7 p., baw005.

    Research output: Contribution to journalJournal articleResearchpeer-review

  55. Published

    From Phosphosites to Kinases

    Munk, S., Refsgaard, J. C., Olsen, Jesper Velgaard & Jensen, Lars Juhl, 2016, Phospho-Proteomics: Methods and Protocols. Stechow, L. V. (ed.). Springer, Vol. 1355. p. 307-21 15 p. (Methods in molecular biology (Clifton, N.J.)).

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

Previous 1 2 3 4 Next

ID: 9931112