Lars Juhl Jensen

Lars Juhl Jensen

Professor, Group Leader, Professor

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    ORCID: 0000-0001-7885-715X

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    1. Published

      Did the early full genome sequencing of yeast boost gene function discovery?

      Tantoso, E., Eisenhaber, B., Sinha, S., Jensen, Lars Juhl & Eisenhaber, F., 2023, In: Biology Direct. 18, 11 p., 46.

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

    2. Published

      Differential Expression of the β3 Subunit of Voltage-Gated Ca2+ Channel in Mesial Temporal Lobe Epilepsy

      Kjær, C., Palasca, Oana, Barzaghi, G., Bak, Lasse Kristoffer, Durhuus, R. K. J., Jakobsen, Emil, Pedersen, Louise, Bartels, Emil Daniel, Woldbye, David Paul Drucker, Pinborg, Lars Hageman & Jensen, Lars Juhl, 2023, In: Molecular Neurobiology. 60, p. 5755–5769

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

    3. Published

      Differentially Expressed miRNAs in Ulcerative Colitis and Crohn's Disease

      Yarani, R., Shojaeian, A., Palasca, Oana, Doncheva, Nadezhda Tsankova, Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2022, In: Frontiers in Immunology. 13, 21 p., 865777.

      Research output: Contribution to journal › Review › Research › peer-review

    4. Published

      Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA

      Eriksson, R., 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 journal › Journal article › Research › peer-review

    5. 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 › Research › peer-review

    6. 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 › Research › peer-review

    7. 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 › Research › peer-review

    8. 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 › Research › peer-review

    9. 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 › Research › peer-review

    10. 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-T., Jensen, L. J., 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. & 2 others, 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 › Research › peer-review

    11. 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 › Research › peer-review

    12. 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 › Research › peer-review

    13. 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 › Research › peer-review

    14. 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 › Research › peer-review

    15. 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 › Research › peer-review

    16. 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 › Research › peer-review

    17. 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 › Research › peer-review

    18. 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 › Research › peer-review

    19. 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 › Research › peer-review

    20. 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 › Research › peer-review

    21. Published

      FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data

      Koutrouli, Mikaela, Nastou, Katerina, Piera Líndez, Pau, Bouwmeester, R., Rasmussen, Simon, Martens, L. & Jensen, Lars Juhl, 2024, In: Bioinformatics. 40, 2, 11 p., btae010.

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

    22. 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 › Research › peer-review

    23. 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 › Research › peer-review

    24. 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

    25. 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 › Research › peer-review

    26. 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 › Research › peer-review

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

    28. 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 › Research › peer-review

    29. 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 › Research › peer-review

    30. 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

    31. 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 › Research › peer-review

    32. 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 › Research › peer-review

    33. Published

      Hunting for the elusive target antigen in gestational alloimmune liver disease (GALD)

      Rieneck, K., Rasmussen, K. K., Schoof, E. M., Clausen, F. B., Holze, H., Bergholt, Thomas, Jørgensen, M. H., Christensen, Vibeke Brix, Almaas, R., Jordal, P. L., Locard-Paulet, Marie, Runager, K., Nielsen, L. K., Schlotmann, Balthasar Clemens, Weischenfeldt, Joachim Lütken, Jensen, Lars Juhl & Dziegiel, Morten Hanefeld, 2023, In: PLoS ONE. 18, 10, 25 p., e0286432.

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

    34. 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 › Research › peer-review

    35. 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 › Research › peer-review

    36. 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 › Research › peer-review

    37. 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 › Research › peer-review

    38. 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 › Research › peer-review

    39. 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 › Research › peer-review

    40. E-pub ahead of print

      Impact of acute alcohol consumption on circulating microbiome in asymptomatic alcohol-related liver disease

      Israelsen, M., Alvarez Silva, Maria Camila, Madsen, B. S., Hansen, C. D., Torp, N. C., Johansen, S., Hansen, J. K., Prier Lindvig, K., Insonere, J., Riviere, V., Juel, H. B., Brejnrod, A., Jensen, Lars Juhl, Thiele, M., Lelouvier, B., Hansen, Torben, Arumugam, Mani & Krag, A., 2023, (E-pub ahead of print) In: Gut. gutjnl-2023-330360.

      Research output: Contribution to journal › Letter › Research › peer-review

    41. 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 › Research › peer-review

    42. 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 › Research › peer-review

    43. 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 › Research › peer-review

    44. 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 › Research › peer-review

    45. 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 › Research › peer-review

    46. 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 › Research › peer-review

    47. 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 › Research › peer-review

    48. 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 › Research › peer-review

    49. 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 › Research › peer-review

    50. Published

      Linear motif atlas for phosphorylation-dependent signaling

      Miller, M. L., Jensen, L. J., 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. & 3 others, Yaffe, M. B., Brunak, Søren & Linding, R., 2008, In: Science Signaling. 1, 35, p. ra2

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

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