Lars Juhl Jensen

Lars Juhl Jensen

professor, group leader


  1. 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

  2. A DNA structural atlas for Escherichia coli

    Pedersen, A. G., Jensen, Lars Juhl, Brunak, S., Staerfeldt, H. H. & Ussery, D., 2000, In : Journal of Molecular Biology. 299, 4, p. 907-30 24 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. 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

  4. 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

  5. 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

  6. A new non-linear normalization method for reducing variability in DNA microarray experiments

    Workman, C., Jensen, Lars Juhl, Jarmer, H. Ø., Berka, R., Gautier, L., Nielser, H. B., Saxild, H. H., Nielsen, C., Brunak, S. & Knudsen, S., 2002, In : Genome Biology (Online Edition). 3, 9, p. research0048

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. 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

  8. Published

    A side effect resource to capture phenotypic effects of drugs

    Kuhn, M., Campillos, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 1 Jan 2010, In : Molecular Systems Biology. 6, p. 343

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae

    Gallego, O., Betts, M. J., Gvozdenovic-Jeremic, J., Maeda, K., Matetzki, C., Aguilar-Gurrieri, C., Beltran-Alvarez, P., Bonn, S., Fernández-Tornero, C., Jensen, Lars Juhl, Kuhn, M., Trott, J., Rybin, V., Müller, C. W., Bork, P., Kaksonen, M., Russell, R. B. & Gavin, A., 2010, In : Molecular Systems Biology. 6, p. 430

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. 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

  11. 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

  12. 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

  13. 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

  14. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

    Korbel, J. O., Jensen, Lars Juhl, von Mering, C. & Bork, P., 2004, In : Nature Biotechnology. 22, 7, p. 911-7 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome

    Jensen, Lars Juhl, Skovgaard, M., Sicheritz-Pontén, T., Jørgensen, M. K., Lundegaard, C., Pedersen, C. C., Petersen, N. & Ussery, D., 2003, In : B M C Genomics. 4, 1, p. 12

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. 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

  17. ArrayProspector: a web resource of functional associations inferred from microarray expression data

    Jensen, Lars Juhl, Lagarde, J., von Mering, C. & Bork, P., 2004, In : Nucleic Acids Research. 32, Web Server issue, p. W445-8

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Assessing systems properties of yeast mitochondria through an interaction map of the organelle

    Perocchi, F., Jensen, Lars Juhl, Gagneur, J., Ahting, U., von Mering, C., Bork, P., Prokisch, H. & Steinmetz, L. M., 2006, In : P L o S Genetics (Online). 2, 10, p. e170

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation

    Jensen, Lars Juhl & Knudsen, S., 2000, In : Bioinformatics. 16, 4, p. 326-33 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. 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

  21. Published

    BioStar: an online question & answer resource for the bioinformatics community

    Parnell, L. D., Lindenbaum, P., Shameer, K., Dall'Olio, G. M., Swan, D. C., Jensen, Lars Juhl, Cockell, S. J., Pedersen, B. S., Mangan, M. E., Miller, C. A. & Albert, I., 2011, In : P L o S Computational Biology (Online). 7, 10, p. e1002216

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Biochemistry. Not comparable, but complementary

    Jensen, Lars Juhl & Bork, P., 3 Oct 2008, In : Science (New York, N.Y.). 322, 5898, p. 56-7 2 p.

    Research output: Contribution to journalComment/debateResearchpeer-review

  23. 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

  24. Published

    Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

    Csikász-Nagy, A., Kapuy, O., Tóth, A., Pál, C., Jensen, Lars Juhl, Uhlmann, F., Tyson, J. J. & Novák, B., 2009, In : Molecular Systems Biology. 5, p. 236

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Circular reasoning rather than cyclic expression

    Jensen, Lars Juhl, de Lichtenberg, U., Jensen, T. S., Brunak, Søren & Bork, P., 2008, In : Genome Biology. 9, 6, p. 403

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Co-evolution of transcriptional and post-translational cell-cycle regulation

    Jensen, Lars Juhl, Jensen, T. S., de Lichtenberg, U., Brunak, S. & Bork, P., 2006, In : Nature Study. 443, 7111, p. 594-7 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. 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

  28. Comparative genomics of four Pseudomonas species

    Jensen, Lars Juhl, Skovgaard, M., Sicheritz-Ponten, T., Hansen, N. T., Johansen, H., Jørgensen, M. K., Kiil, K. & Ussery, D. W., 2004, The Phedomonads. p. 139-164

    Research output: Chapter in Book/Report/Conference proceedingBook chapterCommunication

  29. 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

  30. Comparison of computational methods for the identification of cell cycle-regulated genes

    de Lichtenberg, U., Jensen, Lars Juhl, Fausbøll, A., Jensen, T. S., Bork, P. & Brunak, S., 2005, In : Bioinformatics. 21, 7, p. 1164-71 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. 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

  32. 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

  33. Crystal ball. Systems biology: in the broadest sense of the word

    Ussery, D., de Lichtenberg, U. & Jensen, Lars Juhl, 2005, In : Environmental Microbiology. 7, 4, p. 482-3 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. 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

  35. Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments

    Gauthier, N. P., Larsen, M. E., Wernersson, R., de Lichtenberg, U., Jensen, Lars Juhl, Brunak, S. & Jensen, T. S., 2008, In : Nucleic Acids Research. 36, Database issue, p. D854-9

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

    Gauthier, N. P., Jensen, Lars Juhl, Wernersson, R., Brunak, Søren & Jensen, T. S., 2010, In : Nucleic Acids Research. 38, Database issue, p. D699-702

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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, E. H., 2014, In : Pharmacology Research & Perspectives. 2, 3, p. 1-10 e00038.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. 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

  44. 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

  45. 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

  46. 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 journalJournal articleResearchpeer-review

  47. 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

  48. 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 journalJournal articleResearchpeer-review

  49. 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 journalJournal articleResearchpeer-review

  50. 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

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