Lars Juhl Jensen

Lars Juhl Jensen

Professor, Group Leader, Professor

Member of:


    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 articlepeer-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 articlepeer-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 Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research

      Zahoránszky-Kőhalmi, G., Siramshetty, V. B., Kumar, P., Gurumurthy, M., Grillo, B., Mathew, B., Metaxatos, D., Backus, M., Mierzwa, T., Simon, R., Grishagin, I., Brovold, L., Mathé, E. A., Hall, M. D., Michael, S. G., Godfrey, A. G., Mestres, J., Jensen, Lars Juhl & Oprea, T. I., 2022, In: Journal of Chemical Information and Modeling. 62, 3, p. 718-729

      Research output: Contribution to journalJournal articlepeer-review

    5. 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 articlepeer-review

    6. 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 articlepeer-review

    7. Published

      A knowledge graph to interpret clinical proteomics data

      Santos, A., Colaço, A. R., Nielsen, Annelaura Bach, Niu, Lili, Strauss, Maximilian, Geyer, P. E., Coscia, F., Albrechtsen, Nicolai Jacob Wewer, Mundt, F., Jensen, Lars Juhl & Mann, Matthias, 2022, In: Nature Biotechnology. 40, p. 692–702

      Research output: Contribution to journalJournal articlepeer-review

    8. 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 articlepeer-review

    9. 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 articlepeer-review

    10. E-pub ahead of print

      A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates

      Stripp, Alexandra, Hendriks, Ivo Alexander, Elsborg, Jonas Damgaard, Buch-Larsen, Sara Charlotte, Nielsen, C. H., Terslev, L., Kirsch, Rebecca, Damgaard, D., Doncheva, Nadezhda Tsankova, Lennartsson, Caroline Linnea Elin, Rykær, M., Jensen, Lars Juhl, Christophorou, M. A. & Nielsen, Michael Lund, 2024, (E-pub ahead of print) In: Nature Structural and Molecular Biology.

      Research output: Contribution to journalJournal articlepeer-review

    11. 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 articlepeer-review

    12. 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 articlepeer-review

    13. Published

      A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment

      Bernard, C., Locard-Paulet, Marie, Noël, C., Duchateau, M., Giai Gianetto, Q., Moumen, B., Rattei, T., Hechard, Y., Jensen, Lars Juhl, Matondo, M. & Samba-Louaka, A., 2022, In: Nature Communications. 13, 1, 14 p., 4104.

      Research output: Contribution to journalJournal articlepeer-review

    14. Published

      About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature

      Tantoso, E., Eisenhaber, B., Sinha, S., Jensen, Lars Juhl & Eisenhaber, F., 2023, In: Biology Direct. 18, 17 p., 7.

      Research output: Contribution to journalJournal articlepeer-review

    15. 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, Chunaram, May 2017, In: Molecular and Cellular Proteomics. 16, p. 759-769

      Research output: Contribution to journalJournal articlepeer-review

    16. 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, Chunaram, 2015, In: Nature Biotechnology. 33, p. 415–423

      Research output: Contribution to journalJournal articlepeer-review

    17. Published

      Alcoholic liver disease: A registry view on comorbidities and disease prediction

      Grissa, Dhouha, Nytoft Rasmussen, D., Krag, A., Brunak, Søren & Jensen, Lars Juhl, 2020, In: P L o S One. 16, 9, 19 p., 1008244.

      Research output: Contribution to journalJournal articlepeer-review

    18. 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

    19. 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 articlepeer-review

    20. 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 articlepeer-review

    21. 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 articlepeer-review

    22. 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 journalEditorial

    23. Published

      Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration

      Kokoli, M., Karatzas, E., Baltoumas, F. A., Schneider, R., Pafilis, E., Paragkamian, S., Doncheva, Nadezhda Tsankova, Jensen, Lars Juhl & Pavlopoulos, G. A., 2023, In: NAR Genomics and Bioinformatics. 5, 2, 8 p., lqad053.

      Research output: Contribution to journalJournal articlepeer-review

    24. 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 articlepeer-review

    25. 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 articlepeer-review

    26. 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 articlepeer-review

    27. Published

      Avoiding abundance bias in the functional annotation of posttranslationally modified proteins

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

      Research output: Contribution to journalComment/debatepeer-review

    28. 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 articlepeer-review

    29. 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/debatepeer-review

    30. 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: The Journal of Biological Databases and Curation. 2014, 9 p., bau012.

      Research output: Contribution to journalJournal articlepeer-review

    31. 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 articlepeer-review

    32. 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 articlepeer-review

    33. 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 articlepeer-review

    34. 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 articlepeer-review

    35. 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

    36. 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, 2020, In: Journal of Proteome Research. 19, 3, p. 1338-1345 8 p.

      Research output: Contribution to journalJournal articlepeer-review

    37. 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 articlepeer-review

    38. 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, e1054.

      Research output: Contribution to journalJournal articlepeer-review

    39. 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 articlepeer-review

    40. Published

      Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis

      Yarani, R., Palasca, Oana, Doncheva, Nadezhda Tsankova, Anthon, Christian, Pilecki, B., Svane, C. A. S., Mirza, A. H., Litman, Thomas, Holmskov, U., Bang-Berthelsen, C. H., Vilien, M., Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2023, In: Frontiers in Molecular Biosciences. 9, 1081176.

      Research output: Contribution to journalJournal articlepeer-review

    41. 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 articlepeer-review

    42. 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 articlepeer-review

    43. 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 articlepeer-review

    44. 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 articlepeer-review

    45. 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 articlepeer-review

    46. Published

      Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks

      Doncheva, Nadezhda Tsankova, Morris, J. H., Holze, H., Kirsch, Rebecca, Nastou, Katerina, Cuesta-Astroz, Y., Rattei, T., Szklarczyk, D., Von Mering, C. & Jensen, Lars Juhl, 2022, In: Journal of Proteome Research. 22, 2, p. 637-646

      Research output: Contribution to journalJournal articlepeer-review

    47. 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 articlepeer-review

    48. 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 articlepeer-review

    49. 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 articlepeer-review

    50. 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 articlepeer-review

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