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, A., 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, A., 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, A., 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

  51. 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

  52. 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 journalJournal articleResearchpeer-review

  53. 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

  54. 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 journalJournal articleResearchpeer-review

  55. 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 journalJournal articleResearchpeer-review

  56. 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 journalJournal articleResearchpeer-review

  57. 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 journalJournal articleResearchpeer-review

  58. 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

  59. 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 journalJournal articleResearchpeer-review

  60. 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

  61. 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 journalJournal articleResearchpeer-review

  62. 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

  63. 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

  64. 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

  65. 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 journalJournal articleResearchpeer-review

  66. 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 proceedingBook chapterResearchpeer-review

  67. 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 journalJournal articleResearchpeer-review

  68. 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

  69. 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

  70. 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 journalJournal articleResearchpeer-review

  71. 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 journalJournal articleResearchpeer-review

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

  77. 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 journalJournal articleResearchpeer-review

  78. 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 journalJournal articleResearchpeer-review

  79. Published

    Linear motif atlas for phosphorylation-dependent signaling

    Miller, M. L., Jensen, Lars Juhl, Diella, F., Jørgensen, Claus Bøttcher, 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 journalJournal articleResearchpeer-review

  80. 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

  81. 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 journalJournal articleResearchpeer-review

  82. 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 journalJournal articleResearchpeer-review

  83. 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

  84. 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 journalJournal articleResearchpeer-review

  85. 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

  86. 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 journalJournal articleResearchpeer-review

  87. 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

  88. 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

  89. NetworKIN: a resource for exploring cellular phosphorylation networks

    Linding, R., Jensen, Lars Juhl, Pasculescu, A., Olhovsky, M., Colwill, K., Bork, P., Yaffe, M. B. & Pawson, T., 2008, In : Nucleic Acids Research. 36, Database issue, p. D695-9

    Research output: Contribution to journalJournal articleResearchpeer-review

  90. Published

    On the total number of genes and their length distribution in complete microbial genomes

    Skovgaard, M., Jensen, Lars Juhl, Brunak, Søren, Ussery, D. & Krogh, Anders, 2001, In : Trends in Genetics. 17, 8, p. 425-8 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  91. 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

  92. 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

  93. Published

    Ontologies in quantitative biology: a basis for comparison, integration, and discovery

    Jensen, Lars Juhl & Bork, P., 1 May 2010, In : PLoS Biology. 8, 5, p. e1000374

    Research output: Contribution to journalJournal articleResearchpeer-review

  94. Origin of replication in circular prokaryotic chromosomes

    Worning, P., Jensen, Lars Juhl, Hallin, P. F., Staerfeldt, H. & Ussery, D., 2006, In : Environmental Microbiology. 8, 2, p. 353-61 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Orphan protein function and its relation to glycosylation

    Gupta, R., Jensen, Lars Juhl & Brunak, S., 2002, In : Ernst Schering Foundation Symposium Proceedings. 38, p. 276-94 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. 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

  97. 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

  98. 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

  99. Published

    Phospho.ELM: a database of phosphorylation sites--update 2011

    Dinkel, H., Chica, C., Via, A., Gould, C. M., Jensen, Lars Juhl, Gibson, T. J. & Diella, F., 1 Jan 2011, In : Nucleic Acids Symposium Series. 39, Database issue, p. D261-7

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. 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

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