Lars Juhl Jensen

Lars Juhl Jensen

professor, group leader


  1. 2022
  2. 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 articleResearchpeer-review

  3. Published

    The impact of PrsA over-expression on the Bacillus subtilis transcriptome during fed-batch fermentation of alpha-amylase production

    Geissler, Adrian Sven, Poulsen, L. D., Doncheva, Nadezhda Tsankova, Anthon, Christian, Seemann, Ernst Stefan, González-Tortuero, E., Breüner, A., Jensen, Lars Juhl, Hjort, C., Vinther, Jeppe & Gorodkin, Jan, 2022, In: Frontiers in Microbiology. 13, 17 p., 909493.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. 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 journalJournal articleResearchpeer-review

  5. Published

    U-CIE [/juː ‘siː/]: Color encoding of high-dimensional data

    Koutrouli, Mikaela, Morris, J. H. & Jensen, Lars Juhl, 2022, In: Protein Science. 31, 9, 8 p., e4388.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Phosphorylation of SHP2 at Tyr62 enables acquired resistance to SHP2 allosteric inhibitors in FLT3-ITD-driven AML

    Pfeiffer, A., Franciosa, Giulia, Locard-Paulet, Marie, Piga, I., Reckzeh, K., Vemulapalli, V., Blacklow, S. C., Theilgaard-Mønch, Kim, Jensen, Lars Juhl & Olsen, Jesper Velgaard, 2022, In: Cancer Research. 82, 11, p. 2141-2155 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    A knowledge graph to interpret clinical proteomics data

    Santos Delgado, Alberto, 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 articleResearchpeer-review

  8. 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 journalJournal articleResearchpeer-review

  9. 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 journalReviewResearchpeer-review

  10. Published

    PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

    Zafeiropoulos, H., Paragkamian, S., Ninidakis, S., Pavlopoulos, G. A., Jensen, Lars Juhl & Pafilis, E., 2022, In: Microorganisms. 10, 2, 22 p., 293.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. 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 articleResearchpeer-review

  12. 2021
  13. Published

    OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

    Baltoumas, F. A., Zafeiropoulou, S., Karatzas, E., Paragkamian, S., Thanati, F., Iliopoulos, I., Eliopoulos, A. G., Schneider, R., Jensen, Lars Juhl, Pafilis, E. & Pavlopoulos, G. A., 2021, In: NAR Genomics and Bioinformatics. 3, 4, 10 p., lqab090.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. 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 journalJournal articleResearchpeer-review

  15. 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

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    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, 2021, In: PLOS Biology. 19, 4, 22 p., e3001144.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. 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 journalJournal articleResearchpeer-review

  18. 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

  19. 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 journalJournal articleResearchpeer-review

  20. 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, Nadezhda Tsankova, 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

  21. Published

    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., 2021, In: Bioinformatics. 37, 21, p. 3865-3873

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. 2020
  23. 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

  24. Published

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

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

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. 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

  26. 2019
  27. 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

  28. 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

  29. 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

  30. 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

  31. 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 journalJournal articleResearchpeer-review

  32. 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

  33. 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

  34. 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

  35. 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, Rodriguez, C. L., Pedersen, M. K., Eriksson, R., 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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, Nadezhda Tsankova, 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

  41. 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

  42. 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, Nadezhda Tsankova, 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

  43. 2018
  44. 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

  45. 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

  46. Published

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

    Cook, H. V., Doncheva, Nadezhda Tsankova, 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. 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

  48. Published

    Quantitative metaproteomics of medieval dental calculus reveals individual oral health status

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

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. 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

  50. Published

    Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting

    Mackie, M. E., Rüther, P. L., Samodova-Sommer, Diana, Di Gianvincenzo, Fabiana, Granzotto, C., Lyon, D., Peggie, D. A., Howard, H., Harrison, L., Jensen, Lars Juhl, Olsen, Jesper Velgaard & Cappellini, E., 2018, In: Angewandte Chemie (International ed. in English). 57, 25, p. 7369-7374 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. 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, David, 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

  52. 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

  53. Published

    Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

    Pan, X., Wenzel, A., Jensen, Lars Juhl & Gorodkin, Jan, 2018, In: PLoS ONE. 13, 8, 15 p., e0202369.

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. 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

  55. 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, K., Jensen, Lars Juhl, Brunak, Søren, Pellegrini, M. & Ferro, A., 1 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D354-D359 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

Previous 1 2 3 4 5 Next

ID: 9931112