Lars Juhl Jensen

Lars Juhl Jensen

professor, group leader


  1. 2021
  2. E-pub ahead of print

    TIGA: Target illumination GWAS analytics

    Yang, J. J., Grissa, Dhouha, Lambert, C. G., Bologa, C. G., Mathias, S. L., Waller, A., Wild, D. J., Jensen, Lars Juhl & Oprea, T. I., 4 Jun 2021, (E-pub ahead of print) In: Bioinformatics (Oxford, England).

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. E-pub ahead of print

    Quantitative proteome comparison of human hearts with those of model organisms

    Linscheid, N., Santos Delgado, Alberto, Poulsen, P. C., Mills, Robert William, Callø, Kirstine, Leurs, U., Ye, J. Z., Stolte, C., Thomsen, Morten Bækgaard, Bentzen, Bo Hjorth, Lundegaard, Pia Rengtved, Olesen, Morten Steen Salling, Jensen, Lars Juhl, Olsen, Jesper Velgaard & Lundby, Alicia, Apr 2021, (E-pub ahead of print) In: PLOS Biology. e3001144.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. E-pub ahead of print

    Improved metagenome binning and assembly using deep variational autoencoders

    Nissen, J. N., Johansen, Joachim, Allesøe, Rosa Lundbye, Sonderby, C. K., Armenteros, J. J. A., Grønbech, Christopher Heje, Jensen, Lars Juhl, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, Jan 2021, (E-pub ahead of print) In: Nature Biotechnology. 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. 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., 2021, In: bioRxiv.

    Research output: Contribution to journalJournal articleResearch

  6. Published

    Homology-directed repair protects the replicating genome from metabolic assaults

    Somyajit, K., Spies, Julian, 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 journalJournal articleResearchpeer-review

  7. Published

    Human pathways in animal models: possibilities and limitations

    Doncheva, N. T., 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 journalJournal articleResearchpeer-review

  8. Published

    TCRD and Pharos 2021: mining the human proteome for disease biology

    Sheils, T. K., Mathias, S. L., Kelleher, K. J., Siramshetty, V. B., Nguyen, D. T., Bologa, C. G., Jensen, Lars Juhl, Vidović, D., Koleti, A., Schürer, S. C., Waller, A., Yang, J. J., Holmes, J., Bocci, G., Southall, N., Dharkar, P., Mathé, E., Simeonov, A. & Oprea, T. I., 2021, In: Nucleic Acids Research. 49, D1, p. D1334-D1346 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

    Szklarczyk, D., Gable, A. L., Nastou, Katerina, Lyon, D., Kirsch, Rebecca, Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., Jensen, Lars Juhl & von Mering, C., 2021, In: Nucleic Acids Symposium Series. 49, D1, p. D605-D612 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures

    Jensen, P. S. H., Johansen, M., Bak, Lasse Kristoffer, Jensen, Lars Juhl & Kjær, C., 2021, In: Neurochemical Research. 46, p. 447-454 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. 2020
  12. 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 articleResearchpeer-review

  13. 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 articleResearchpeer-review

  14. Published

    Visualize omics data on networks with Omics Visualizer, a Cytoscape App

    Legeay, M., Doncheva, N. T., Morris, J. H. & Jensen, Lars Juhl, 2020, In: F1000Research. 9, 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. 2019
  16. 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

  17. 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

  18. 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

  19. Published

    Cytoscape stringApp: Network analysis and visualization of proteomics data

    Doncheva, N. T., 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

  20. 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

  21. 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, D. & Brunak, Søren, 2019, In: npj Systems Biology and Applications. 5, 10 p., 27.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. 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

  23. 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

  24. 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, A. D., 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, P. & Brunak, Søren, 2019, In: eLife. 8, 19 p., e44941.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites

    Lundby, Alicia, Franciosa, Giulia, Emdal, K. B., 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

  26. Published

    ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins

    Tagore, S., Gorohovski, A., Jensen, Lars Juhl & Frenkel-Morgenstern, M., 2019, In: PLOS Computational Biology. 15, 8, 16 p., e1007239.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

    Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., Jensen, Lars Juhl & von Mering, C., 2019, In: Nucleic Acids Research. 47, D1, p. D607-D613 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    SnapShot: S-Phase Entry and Exit

    Burgess, A., Vuong, J., Marzec, K. A., de Lichtenberg, U. N., O'Donoghue, S. I. & Jensen, Lars Juhl, 2019, In: Cell. 179, 3, p. 802-802.e1 2 p.

    Research output: Contribution to journalComment/debateResearchpeer-review

  29. Published

    Transcriptome analysis in patients with temporal lobe epilepsy

    Kjær, C., Barzaghi, G., Bak, Lasse Kristoffer, Goetze, Jens P. , Yde, C. W., Woldbye, David Paul Drucker, Pinborg, Lars Hageman & Jensen, Lars Juhl, 2019, In: Brain. 142, 10, p. 49-64 16 p., e55.

    Research output: Contribution to journalLetterResearchpeer-review

  30. Published

    Transcriptome landscape of protein-coding genes and long noncoding RNAs in the colon and blood of DSS-induced mouse model of Acute ulcerative colitis

    Yarani, R., Palasca, Oana, Doncheva, N. T., Anthon, Christian, Pilecki, B., Litman, Thomas, Holmskov, U., Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2019, In: Journal of Crohn's and Colitis. 13, p. S129-S130

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  31. Published

    eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

    Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunic, I., Rattei, T., Jensen, Lars Juhl, von Mering, C. & Bork, P., 2019, In: Nucleic Acids Research. 47, D1, p. D309-D314 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. 2018
  33. Published

    WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

    Pan, X., Xiong, K., Anthon, Christian, Hyttel, P., Freude, Kristine, Jensen, Lars Juhl & Gorodkin, Jan, 6 Nov 2018, In: Genes. 9, 11, 11 p., 536.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    miRandola 2017: a curated knowledge base of non-invasive biomarkers

    Russo, F., Di Bella, S., Vannini, F., Berti, G., Scoyni, F., Cook, H. V., Santos Delgado, Alberto, Nigita, G., Bonnici, V., Laganà, A., Geraci, F., Pulvirenti, A., Giugno, R., De Masi, F., Belling, Kirstine G, Jensen, Lars Juhl, Brunak, Søren, Pellegrini, M. & Ferro, A., 4 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D354-D359 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. 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

  36. Published

    A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

    Westergaard, D., 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. Published

    Quantitative metaproteomics of medieval dental calculus reveals individual oral health status

    Jersie-Christensen, R. R., Lanigan, Liam Thomas, Lyon, D., Mackie, Meaghan, Midjord-Belstrøm, Daniel, Kelstrup, C. D., Fotaki, Anna Katerina, Willerslev, Eske, Lynnerup, Niels, Jensen, Lars Juhl, Cappellini, Enrico & Olsen, Jesper Velgaard, 2018, In: Nature Communications. 9, p. 1-12 4744.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Site-specific characterization of endogenous SUMOylation across species and organs

    Hendriks, Ivo Alexander, Lyon, D., Su, D., Skotte, Niels Henning, Daniel, J. A., Jensen, Lars Juhl & Nielsen, Michael Lund, 2018, In: Nature Communications. 9, p. 1-17 2456.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Systems-wide Analysis of Serine ADP-Ribosylation Reveals Widespread Occurrence and Site-Specific Overlap with Phosphorylation

    Buch-Larsen, Sara Charlotte, Hendriks, Ivo Alexander, Lyon, D., Jensen, Lars Juhl & Nielsen, Michael Lund, 2018, In: Cell Reports. 24, 9, p. 2493-2505

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    TISSUES 2.0: an integrative web resource on mammalian tissue expression

    Palasca, Oana, Santos Delgado, Alberto, Stolte, C., Gorodkin, Jan & Jensen, Lars Juhl, 2018, In: Database: The Journal of Biological Databases and Curation. 2018, 1, p. 1-12

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Unexplored therapeutic opportunities in the human genome

    Oprea, T. I., Bologa, C. G., Brunak, Søren, Campbell, A., Gan, G. N., Gaulton, A., Gomez, S. M., Guha, R., Hersey, A., Holmes, J., Jadhav, A., Jensen, Lars Juhl, Johnson, G. L., Karlson, A., Leach, A. R., Ma'ayan, A., Malovannaya, A., Mani, S., Mathias, S. L., McManus, M. T., Meehan, T. F., von Mering, C., Muthas, D., Nguyen, D., Overington, J. P., Papadatos, G., Qin, J., Reich, C., Roth, B. L., Schürer, S. C., Simeonov, A., Sklar, L. A., Southall, N., Tomita, S., Tudose, I., Ursu, O., Vidovic, D., Waller, A., Westergaard, D., Yang, J. J. & Zahoránszky-Köhalmi, G., 2018, In: Nature Reviews. Drug Discovery. 17, 5, p. 317-332 16 p.

    Research output: Contribution to journalReviewResearchpeer-review

  46. Published

    Viruses.STRING: A Virus-Host Protein-Protein Interaction Database

    Cook, H. V., Doncheva, N. T., Szklarczyk, D., von Mering, C. & Jensen, Lars Juhl, 2018, In: Viruses. 10, 10, p. 1-11 519.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. 2017
  48. 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

  49. Published

    TIN-X: target importance and novelty explorer

    Cannon, D. C., Yang, J. J., Mathias, S. L., Ursu, O., Mani, S., Waller, A., Schürer, S. C., Jensen, Lars Juhl, Sklar, L. A., Bologa, C. G. & Oprea, T. I., 15 Aug 2017, In: Bioinformatics. 33, 16, p. 2601-2603 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. 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

  51. 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 articleResearchpeer-review

  52. 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

  53. Published

    Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

    Hendriks, Ivo Alexander, Lyon, D., Young, C., Jensen, Lars Juhl, Vertegaal, A. C. O. & Nielsen, Michael Lund, Mar 2017, In: Nature Structural and Molecular Biology. 24, 3, p. 325-336 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. Published

    miRNAs in Human Subcutaneous Adipose Tissue: Effects of Weight Loss Induced by Hypocaloric Diet and Exercise

    Kristensen, M. M., Davidsen, P. K., Vigelso, A., Hansen, C. N., Jensen, Lars Juhl, Jessen, N., Bruun, J. M., Dela, Flemming & Helge, Jørn Wulff, Mar 2017, In: Obesity. 25, 3, p. 572-580 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  55. 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

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ID: 9931112