Lars Juhl Jensen

Lars Juhl Jensen

Professor, Group Leader, Professor

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    ORCID: 0000-0001-7885-715X

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    1. 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 journal › Journal article › Research › peer-review

    2. 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 journal › Journal article › Research › peer-review

    3. 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 proceeding › Book chapter › Communication

    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 journal › Journal article › Research › peer-review

    5. 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 journal › Journal article › Research › peer-review

    6. 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 journal › Journal article › Research › peer-review

    7. 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 journal › Journal article › Research › peer-review

    8. 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 journal › Journal article › Research › peer-review

    9. 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 journal › Comment/debate › Research › peer-review

    10. 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 journal › Journal article › Research › peer-review

    11. 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 journal › Comment/debate › Research › peer-review

    12. 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 journal › Journal article › Research › peer-review

    13. 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 journal › Journal article › Research › peer-review

    14. 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 journal › Journal article › Research › peer-review

    15. 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 journal › Journal article › Research › peer-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 journal › Editorial › Research

    17. 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 journal › Journal article › Research › peer-review

    18. 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 journal › Journal article › Research › peer-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 journal › Journal article › Research › peer-review

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

    21. 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 journal › Journal article › Research › peer-review

    22. 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 journal › Journal article › Research › peer-review

    23. 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 journal › Journal article › Research › peer-review

    24. 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 journal › Journal article › Research › peer-review

    25. 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 journal › Journal article › Research › peer-review

    26. 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 journal › Journal article › Research › peer-review

    27. 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 journal › Journal article › Research › peer-review

    28. 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 journal › Journal article › Research › peer-review

    29. 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 journal › Journal article › Research › peer-review

    30. 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 journal › Journal article › Research › peer-review

    31. Published

      A knowledge graph to interpret clinical proteomics data

      Santos, A., Colaço, A. R., Nielsen, A. B., 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 journal › Journal article › Research › peer-review

    32. 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 journal › Journal article › Research › peer-review

    33. 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 journal › Journal article › Research › peer-review

    34. 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 journal › Journal article › Research › peer-review

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

    36. 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 journal › Journal article › Research › peer-review

    37. 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 journal › Journal article › Research › peer-review

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