Lars Juhl Jensen

Lars Juhl Jensen

professor, group leader

ORCID: 0000-0001-7885-715X

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  1. Published

    Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration

    Grissa, Dhouha, Junge, A., Oprea, T. I. & Jensen, Lars Juhl, 2022, In: Database : the journal of biological databases and curation. 2022, 2022, 8 p.

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

  2. 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 journal › Journal article › peer-review

  3. 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 journal › Journal article › peer-review

  4. Published

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

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

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

  5. Published

    Drug target identification using side-effect similarity

    Campillos, M., Kuhn, M., Gavin, A., Jensen, Lars Juhl & Bork, P., 2008, In: Science. 321, 5886, p. 263-6 3 p.

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

  6. 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 journal › Journal article › peer-review

  7. Published

    Drug-induced regulation of target expression

    Iskar, M., Campillos, M., Kuhn, M., Jensen, Lars Juhl, van Noort, V. & Bork, P., 1 Jan 2010, In: PLoS Computational Biology. 6, 9

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

  8. Dynamic complex formation during the yeast cell cycle

    de Lichtenberg, U., Jensen, Lars Juhl, Brunak, S. & Bork, P., 2005, In: Science (New York, N.Y.). 307, 5710, p. 724-7 4 p.

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

  9. 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 journal › Journal article › peer-review

  10. 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: The Journal of Biological Databases and Curation. 2016, 7 p., baw005.

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

  11. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families

    Shah, P. K., Tripathi, L. P., Jensen, Lars Juhl, Gahnim, M., Mason, C., Furlong, E. E., Rodrigues, V., White, K. P., Bork, P. & Sowdhamini, R., 2008, In: Gene. 407, 1-2, p. 199-215 17 p.

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

  12. Published

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

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

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

  13. Published

    Evolution and regulation of cellular periodic processes: a role for paralogues

    Trachana, K., Jensen, Lars Juhl & Bork, P., 1 Mar 2010, In: E M B O Reports. 11, 3, p. 233-8 6 p.

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

  14. Evolution of cell cycle control: same molecular machines, different regulation

    de Lichtenberg, U., Jensen, T. S., Brunak, S., Bork, P. & Jensen, Lars Juhl, 2007, In: Cell Cycle. 6, 15, p. 1819-25 7 p.

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

  15. Extraction of regulatory gene/protein networks from Medline

    Saric, J., Jensen, Lars Juhl, Ouzounova, R., Rojas, I. & Bork, P., 2006, In: Bioinformatics. 22, 6, p. 645-50 6 p.

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

  16. Extraction of transcript diversity from scientific literature

    Shah, P. K., Jensen, Lars Juhl, Boué, S. & Bork, P., 2005, In: P L o S Computational Biology. 1, 1, p. e10

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

  17. 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 journal › Journal article › peer-review

  18. Feature-based prediction of non-classical and leaderless protein secretion

    Bendtsen, J. D., Jensen, Lars Juhl, Blom, N., Von Heijne, G. & Brunak, S., 2004, In: Protein Engineering Design and Selection (Print). 17, 4, p. 349-56 8 p.

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

  19. 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 proceeding › Book chapter › Research › peer-review

  20. Functionality of system components: conservation of protein function in protein feature space

    Jensen, Lars Juhl, Ussery, D. & Brunak, S., 2003, In: Genome Research. 13, 11, p. 2444-9 6 p.

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

  21. 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 journal › Journal article › peer-review

  22. Published

    Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

    Pan, X., Wenzel, A., Jensen, Lars Juhl & Gorodkin, Jan, 2018, In: PLoS ONE. 13, 8, 15 p., e0202369.

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

  23. 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 journal › Journal article › peer-review

  24. Published

    High-resolution transcription atlas of the mitotic cell cycle in budding yeast

    Granovskaia, M. V., Jensen, Lars Juhl, Ritchie, M. E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L. M., 1 Jan 2010, In: Genome Biology (Online Edition). 11, 3, p. R24

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

  25. Published

    Homologous and non-homologous sequence methods for assigning protein function

    Yeats, C., orengo, C., Veuthey, A. L., Boeckmann, B., Jensen, Lars Juhl, Valencia, A., Rausell, A. & Bork, P., 2009, Modern Genome Annotation: The BioSapien Network. Springer Publishing Company, p. 213-238

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

  26. Published

    Homology-directed repair protects the replicating genome from metabolic assaults

    Somyajit, K., Spies, J., Coscia, F., Kirik, U., Rask, M., Lee, J., Neelsen, K. J., Mund, Andreas, Jensen, Lars Juhl, Paull, T. T., Mann, Matthias & Lukas, Jiri, 2021, In: Developmental Cell. 56, 4, p. 461-477.e7

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

  27. Published

    Human pathways in animal models: possibilities and limitations

    Doncheva, Nadezhda Tsankova, Palasca, Oana, Yarani, R., Litman, Thomas, Anthon, Christian, Groenen, M. A. M., Stadler, P. F., Pociot, Flemming, Jensen, Lars Juhl & Gorodkin, Jan, 2021, In: Nucleic Acids Research. 49, 4, p. 1859-1871 13 p.

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

  28. Identification and analysis of evolutionarily cohesive functional modules in protein networks

    Campillos, M., von Mering, C., Jensen, Lars Juhl & Bork, P., 2006, In: Genome Research. 16, 3, p. 374-82 9 p.

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

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

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

  30. 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 journal › Journal article › peer-review

  31. 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, E. H., 20 May 2015, In: Journal of Research in Pharmacy Practice. 4, 2, p. 64-72 9 p.

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

  32. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

    Hooper, S. D., Boué, S., Krause, R., Jensen, Lars Juhl, Mason, C. E., Ghanim, M., White, K. P., Furlong, E. E. M. & Bork, P., 2007, In: Molecular Systems Biology. 3, p. 72

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

  33. Published

    Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies

    Locard-Paulet, Marie, Palasca, Oana & Jensen, Lars Juhl, 2022, In: PLOS Computational Biology. 18, 10, 20 p., e1010604.

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

  34. 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 journal › Journal article › peer-review

  35. Published

    Improved metagenome binning and assembly using deep variational autoencoders

    Nissen, J. N., Johansen, Joachim, Allesoe, R. L., Sonderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Jensen, Lars Juhl, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2021, In: Nature Biotechnology. 39, p. 555-560

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

  36. 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 journal › Journal article › peer-review

  37. 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 journal › Journal article › peer-review

  38. 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 journal › Journal article › peer-review

  39. 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 journal › Journal article › peer-review

  40. Large-scale extraction of gene regulation for model organisms in an ontological context

    Saric, J., Jensen, Lars Juhl & Rojas, I., 2005, In: In Silico Biology. 5, 1, p. 21-32 12 p.

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

  41. Published

    Large-scale prediction of drug-target relationships

    Kuhn, M., Campillos, M., González, P., Jensen, Lars Juhl & Bork, P., 2008, In: F E B S Letters. 582, 8, p. 1283-90 8 p.

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

  42. Published

    Light-induced asymmetries in embryonic retinal gene expression are mediated by the vascular system and extracellular matrix

    Versace, E., Sgadò, P., George, J., Loveland, J. L., Ward, J., Thorpe, P., Jensen, Lars Juhl, Spencer, K. A., Paracchini, S. & Vallortigara, G., 2022, In: Scientific Reports. 12, 1, 12 p., 12086.

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

  43. Published

    Linear motif atlas for phosphorylation-dependent signaling

    Miller, M. L., Jensen, Lars Juhl, Diella, F., Jørgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S. A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B. E., Yaffe, M. B., Brunak, Søren & Linding, R., 2008, In: Science Signaling. 1, 35, p. ra2

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

  44. 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, Rodriguez, C. L., Pedersen, M. K., Eriksson, R., 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 journal › Journal article › peer-review

  45. Literature mining for the biologist: from information retrieval to biological discovery

    Jensen, Lars Juhl, Saric, J. & Bork, P., 2006, In: Nature Reviews. Genetics. 7, 2, p. 119-29 11 p.

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

  46. Martini: using literature keywords to compare gene sets

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

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

  47. Published

    Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

    Bassani-Sternberg, M., Pletscher-Frankild, S., Jensen, Lars Juhl & Mann, Matthias, Mar 2015, In: Molecular and Cellular Proteomics. 14, 3, p. 658-73 16 p.

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

  48. Published

    Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level

    Danielsen, J. M. R., Sylvestersen, K. B., Bekker-Jensen, Simon Holst, Szklarczyk, D., Poulsen, J. W., Horn, H., Jensen, Lars Juhl, Mailand, Niels & Nielsen, Michael Lund, 1 Mar 2011, In: Molecular and Cellular Proteomics. 10, 3, p. M110.003590

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

  49. Published

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

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

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

  50. Published

    Microblogging the ISMB: a new approach to conference reporting

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

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

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ID: 9931112