Lars Juhl Jensen
Lars Juhl Jensen

professor, group leader


  1. 2019
  2. 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

  3. Published

    Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism

    Cuesta-Astroz, Y., Santos Delgado, Alberto, Oliveira, G. & Jensen, Lars Juhl, 2019, In : Frontiers in Immunology. 10, 17 p., 212.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 2018
  19. Published

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

    Pan, X., Xiong, Kai, 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

  20. 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 Delgado, Alberto, 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. Published

    TISSUES 2.0: an integrative web resource on mammalian tissue expression

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

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. 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

  32. 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

  33. 2017
  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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, Alberto, 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

  43. Published

    RAIN: RNA-protein Association and Interaction Networks

    Junge, A., Refsgaard, J. C., Garde, C., Pan, X., Santos Delgado, Alberto, Alkan, Ferhat, 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

  44. 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

  45. 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

  46. 2016
  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. Published

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

    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 journalJournal articleResearchpeer-review

  55. 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 journalConference articleResearchpeer-review

  56. 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., Contreras, G., Cooper, L., Dai, H., Ferrell, B., Fluck, J., Gama-Castro, S., George, N., Gkoutos, G., Irin, A. K., Jensen, Lars Juhl, Jimenez, S., 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. 2016, 18 p., baw119.

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

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

    Szklarczyk, D., Santos Delgado, Alberto, 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 journalJournal articleResearchpeer-review

  58. 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 journalJournal articleResearchpeer-review

  59. 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 proceedingBook chapterResearchpeer-review

  60. 2015
  61. Published

    Impact of microRNA-130a on the neutrophil proteome

    Pedersen, C. C., Refsgaard, J. C., Østergaard, Ole, Jensen, Lars Juhl, Heegaard, N. H. H., Borregaard, N. & Cowland, J. B., 25 Nov 2015, In : B M C Immunology. 16, 10 p., 70.

    Research output: Contribution to journalJournal articleResearchpeer-review

  62. 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 journalJournal articleResearchpeer-review

  63. Published

    Avoiding abundance bias in the functional annotation of posttranslationally modified proteins

    Schölz, C., Lyon, D., Refsgaard, J. C., Jensen, Lars Juhl, Choudhary, Chuna Ram & Weinert, B. T., Nov 2015, In : Nature Methods. 12, p. 1003-4 2 p.

    Research output: Contribution to journalComment/debateResearchpeer-review

  64. Published

    Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines

    Warrer, P., Jensen, P. B., Aagaard, L., Jensen, Lars Juhl, Brunak, S., Krag, M. H., Rossing, P., Almdal, T., Andersen, H. U. & Hansen, Ebba Holme, 20 May 2015, In : Journal of Research in Pharmacy Practice. 4, 2, p. 64-72 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. Published

    DISEASES: Text mining and data integration of disease-gene associations

    Pletscher-Frankild, S., Pallejà, A., Tsafou, K., Binder, J. X. & Jensen, Lars Juhl, Mar 2015, In : Methods. 74, p. 83-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. 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 journalJournal articleResearchpeer-review

  67. 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, Alberto, 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 journalJournal articleResearchpeer-review

  68. Published

    Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

    Santos Delgado, Alberto, Wernersson, R. & Jensen, Lars Juhl, Jan 2015, In : Nucleic Acids Research. 43, D1, p. D1140-4 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    Acetylation site specificities of lysine deacetylase inhibitors in human cells

    Schölz, C., Weinert, B. T., Wagner, S. A., Beli, P., Miyake, Y., Qi, J., Jensen, Lars Juhl, Streicher, W., McCarthy, A. R., Westwood, N. J., Lain, S., Cox, J., Matthias, P., Mann, M., Bradner, J. E. & Choudhary, Chuna Ram, 2015, In : Nature Biotechnology. 33, p. 415–423

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. Published

    Comprehensive comparison of large-scale tissue expression datasets

    Santos Delgado, Alberto, Tsafou, K., Stolte, C., Pletscher-Frankild, S., O'Donoghue, S. I. & Jensen, Lars Juhl, 2015, In : PeerJ. 3, p. e1054

    Research output: Contribution to journalJournal articleResearchpeer-review

  71. Published

    ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

    Pafilis, E., Pletscher-Frankild, S., Schnetzer, J., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, K., Leary, P., Hammock, J., Schulz, K., Parr, C. S., Arvanitidis, C. & Jensen, Lars Juhl, 2015, In : Bioinformatics. 31, 11, p. 1872-1874

    Research output: Contribution to journalJournal articleResearchpeer-review

  72. Published

    HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases

    Palleja, A. & Jensen, Lars Juhl, 2015, In : PeerJ. 3, p. 1-10 10 p., e1057.

    Research output: Contribution to journalJournal articleResearchpeer-review

  73. 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 proceedingBook chapterResearchpeer-review

  74. Published

    Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation

    Emdal, Kristina Bennet, Pedersen, Anna-Kathrine, Bekker-Jensen, D. B., Tsafou, K. P., Horn, H., Lindner, S., Schulte, J. H., Eggert, A., Jensen, Lars Juhl, Francavilla, C. & Olsen, Jesper Velgaard, 2015, In : Science signaling. 8, 374, ra40.

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. 2014
  76. Published

    Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

    Jensen, A. B., Moseley, Pope Lloyd, Oprea, T. I., Ellesøe, S. G., Eriksson, Robert, Schmock, H., Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 24 Jun 2014, In : Nature Communications. 5, 10 p., 4022.

    Research output: Contribution to journalJournal articleResearchpeer-review

  77. Published

    KinomeXplorer: an integrated platform for kinome biology studies

    Horn, H., Schoof, E. M., Kim, J., Robin, X., Miller, M. L., Diella, F., Palma, A., Cesareni, G., Jensen, Lars Juhl & Linding, R., 29 May 2014, In : Nature Methods. 11, 6, p. 603-4 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  78. Published

    Erratum to: Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population

    Eriksson, Robert, Werge, T., Jensen, Lars Juhl & Brunak, Søren, May 2014, In : Drug Safety. 37, 5, p. 379

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. Published

    Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population

    Eriksson, Robert, Werge, T., Jensen, Lars Juhl & Brunak, Søren, Apr 2014, In : Drug Safety. 37, 4, p. 237-47 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  80. Published

    DoReMi: context-based prioritization of linear motif matches

    Horn, H., Haslam, N. & Jensen, Lars Juhl, 20 Mar 2014, In : PeerJ. 2, 10 p., e315.

    Research output: Contribution to journalJournal articleResearchpeer-review

  81. 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 journalJournal articleResearchpeer-review

  82. Published

    A comparison of protein kinases inhibitor screening methods using both enzymatic activity and binding affinity determination

    Rudolf, A. F., Skovgaard, T., Knapp, S., Jensen, Lars Juhl & Berthelsen, J., 2014, In : PloS one. 9, 6, p. 1-5 6 p., e98800.

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    COMPARTMENTS: unification and visualization of protein subcellular localization evidence

    Binder, J. X., Pletscher-Frankild, S., Tsafou, K., Stolte, C., O'Donoghue, S. I., Schneider, R. & Jensen, Lars Juhl, 2014, In : Database. 2014, 9 p., bau012.

    Research output: Contribution to journalJournal articleResearchpeer-review

  84. Published

    Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA

    Eriksson, Robert, Aagaard, L., Jensen, Lars Juhl, Borisova, L., Hørlück, D., Brunak, Søren & Hansen, Ebba Holme, 2014, In : Pharmacology Research & Perspectives. 2, 3, p. 1-10 e00038.

    Research output: Contribution to journalJournal articleResearchpeer-review

  85. 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 journalJournal articleResearchpeer-review

  86. Published

    Protein-driven inference of miRNA-disease associations

    Mørk, Søren, 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 journalJournal articleResearchpeer-review

  87. 2013
  88. Published

    eggNOG v4.0: nested orthology inference across 3686 organisms

    Powell, S., Forslund, K., Szklarczyk, D. M., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, Lars Juhl, von Mering, C. & Bork, P., 1 Dec 2013, In : Nucleic Acids Research. 42, D1, p. D231-D239 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  89. 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 journalJournal articleResearchpeer-review

  90. Published

    Are graph databases ready for bioinformatics?

    Have, C. T. & Jensen, Lars Juhl, 21 Oct 2013, In : Bioinformatics (Online). 2 p.

    Research output: Contribution to journalEditorialResearch

  91. Published

    A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk

    Blair, D. R., Lyttle, C. S., Mortensen, J. M., Bearden, C. F., Jensen, A. B., Khiabanian, H., Melamed, R., Rabadan, R., Bernstam, E. V., Brunak, Søren, Jensen, Lars Juhl, Nicolae, D., Shah, N. H., Grossman, R. L., Cox, N. J., White, K. P. & Rzhetsky, A., 26 Sep 2013, In : Cell. 155, 1, p. 70-80 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  92. 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., Damsgaard, B., Romer, M. U., Belling, Kirstine G, Jensen, N. F., Gromova, I., Bekker-Jensen, D. B., Moreira, José, Jensen, Lars Juhl, Gupta, R., Lademann, U. A., Brünner, Nils, Olsen, Jesper Velgaard & Stenvang, Jan, 5 Aug 2013, In : Journal of Proteome Research. 12, 9, p. 4136-4151 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  93. Published

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

    Orlando, Ludovic Antoine Alexandre, Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, Anders, Stiller, M., Schubert, M., Cappellini, Enrico, Petersen, Bent, Moltke, Ida, Johnson, P. L. F., Fumagalli, M., Mouatt, J. T. V., Raghavan, M., Korneliussen, Thorfinn Sand, Malaspinas, A. S., Vogt, J., Szklarczyk, D. M., Kelstrup, C., Vinther, J., Dolocan, A., Stenderup, J., 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, Jun & Willerslev, Eske, 4 Jul 2013, In : Nature. 499, 7456, p. 74-78 5 p.

    Research output: Contribution to journalLetterResearchpeer-review

  94. Published

    The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

    Pafilis, E., Pletscher-Frankild, S., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, A., Arvanitidis, C. & Jensen, Lars Juhl, 18 Jun 2013, In : PloS one. 8, 6, p. e65390

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of β-Adrenergic Receptor Signaling

    Lundby, Alicia, Andersen, M. N., Steffensen, Annette Buur, Horn, H., Kelstrup, C. D., Francavilla, C., Jensen, Lars Juhl, Schmitt, Nicole, Thomsen, Morten Bækgaard & Olsen, Jesper Velgaard, 4 Jun 2013, In : Science Signaling. 6, 278, p. rs11 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text

    Eriksson, R., Jensen, P. B., Pletscher-Frankild, S., Jensen, Lars Juhl & Brunak, Søren, 23 May 2013, In : JAMIA - Journal of the American Medical Informatics Association. 20, 5, p. 947-953 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. 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 journalJournal articleResearchpeer-review

  98. 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 journalComment/debateResearchpeer-review

  99. 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 journalJournal articleResearchpeer-review

  100. 2012
  101. Published

    Using text-mining techniques in electronic patient records to identify ADRs from medicine use

    Warrer, P., Hansen, Ebba Holme, Jensen, Lars Juhl & Aagaard, L., May 2012, In : British Journal of Clinical Pharmacology. 73, 5, p. 674-684 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  102. Published

    Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes

    Poulsen, J. W., Madsen, C. T., Young, C., Kelstrup, C. D., Grell, H. C., Henriksen, P., Jensen, Lars Juhl & Nielsen, Michael Lund, 2012, In : Journal of Proteomics. 75, 13, p. 3886-97 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  103. Published

    DistiLD Database: diseases and traits in linkage disequilibrium blocks

    Palleja, A., Horn, H., Eliasson, S. & Jensen, Lars Juhl, 2012, In : Nucleic Acids Research. 40, Database issue, p. D1036-40

    Research output: Contribution to journalJournal articleResearchpeer-review

  104. Published

    Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

    Frenkel-Morgenstern, M., Danon, T., Christian, T., Igarashi, T., Cohen, L., Hou, Y. & Jensen, Lars Juhl, 2012, In : Molecular Systems Biology. 8, p. 572

    Research output: Contribution to journalJournal articleResearchpeer-review

  105. Published

    Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression

    Bergholdt, R., Brorsson, C., Palleja, A., Berchtold, L. A., Fløyel, T., Bang-Berthelsen, C. H., Frederiksen, K. S., Jensen, Lars Juhl, Størling, J. & Pociot, F., 2012, In : Diabetes. 61, 4, p. 954-62 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  106. 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 journalJournal articleResearchpeer-review

  107. 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 journalJournal articleResearchpeer-review

  108. 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, Ludovic Antoine Alexandre, 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 journalJournal articleResearchpeer-review

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