Lars Juhl Jensen
Professor, Group Leader, Professor
Jensen Group
Blegdamsvej 3, 2200 København N., 06 Bygning 6, Building: 06-2-26
Member of:
- 2019
- 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. 2385-2396Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- Published
Linking glycemic dysregulation in diabetes to symptoms, comorbidities, and genetics through EHR data mining
Kirk, I. K., Simon, C., Banasik, K., Holm, P. C., Haue, A. D., Jensen, P. B., Jensen, L. J., Rodriguez, C. L., Pedersen, M. K., Eriksson, R., Andersen, H. U., Almdal, T., Bork-Jensen, J., Grarup, N., Borch-Johnsen, K., Pedersen, O., Pociot, F., Hansen, T., Bergholdt, R., Rossing, P. & 1 others, , 2019, In: eLife. 8, 19 p., e44941.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites
Lundby, Alicia, Franciosa, Giulia, Emdal, Kristina Bennet, Refsgaard, J. C., Gnosa, S. P., 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. 543-560Research output: Contribution to journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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 journal › Comment/debate › Research › peer-review
- 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 journal › Letter › Research › peer-review
- 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-S130Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 2018
- 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 journal › Journal article › Research › peer-review
- 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, A., 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 journal › Journal article › Research › peer-review
- 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
- 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 journal › Journal article › Research › peer-review
- 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
- 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 journal › Journal article › Research › peer-review
- 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
- Published
Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting
Mackie, Meaghan, Rüther, P. L., Samodova, D., 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 journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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. 2493-2505Research output: Contribution to journal › Journal article › Research › peer-review
- Published
TISSUES 2.0: an integrative web resource on mammalian tissue expression
Palasca, Oana, Santos, A., Stolte, C., Gorodkin, Jan & Jensen, Lars Juhl, 2018, In: Database: The Journal of Biological Databases and Curation. 2018, 1, p. 1-12Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Unexplored therapeutic opportunities in the human genome
Oprea, T. I., Bologa, C. G., Brunak, S., Campbell, A., Gan, G. N., Gaulton, A., Gomez, S. M., Guha, R., Hersey, A., Holmes, J., Jadhav, A., Jensen, L. J., Johnson, G. L., Karlson, A., Leach, A. R., Ma'ayan, A., Malovannaya, A., Mani, S., Mathias, S. L., McManus, M. T. & 21 others, , 2018, In: Nature Reviews. Drug Discovery. 17, 5, p. 317-332 16 p.Research output: Contribution to journal › Review › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 2017
- 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, , 9 Nov 2017, In: Journal of Biomedical Semantics. 8, 1, 16 p., 50.Research output: Contribution to journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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
- 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. 759-769Research output: Contribution to journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- 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 journal › Journal article › Research › peer-review
- Published
Pharos: Collating protein information to shed light on the druggable genome
Nguyen, D-T., Mathias, S., Bologa, C., Brunak, S., Fernandez, N., Gaulton, A., Hersey, A., Holmes, J., Jensen, L. J., Karlsson, A., Liu, G., Ma'ayan, A., Mandava, G., Mani, S., Mehta, S., Overington, J., Patel, J., Rouillard, A. D., Schürer, S., Sheils, T. & 10 others, , Jan 2017, In: Nucleic Acids Research. 45, D1, p. D995–D1002Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos Delgado, A., Doncheva, Nadezhda Tsankova, Roth, A., Bork, P., Jensen, Lars Juhl & von Mering, C., Jan 2017, In: Nucleic Acids Research. 45, D1, p. D362-D368Research output: Contribution to journal › Journal article › Research › peer-review
- Published
RAIN: RNA-protein Association and Interaction Networks
Junge, A., Refsgaard, J. C., Garde, C., Pan, X., Santos, A., Alkan, F., Anthon, Christian, von Mering, C., Workman, C. T., Jensen, Lars Juhl & Gorodkin, Jan, 2017, In: Database: The Journal of Biological Databases and Curation. 2017, 9 p., baw167.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification
Mullari, M., Lyon, D., Jensen, Lars Juhl & Nielsen, Michael Lund, 2017, In: Journal of Proteome Research. 16, 8, p. 2762-2772 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Structure-based discovery of novel US28 small molecule ligands with different modes of action
Lückmann, Michael, Amarandi, R., Papargyri, N., Jakobsen, M. H., Ulven, Elisabeth Rexen, Jensen, Lars Juhl, Pui, A., Schwartz, Thue W., Rosenkilde, Mette & Frimurer, Thomas Michael, 2017, In: Chemical Biology & Drug Design. 89, 3, p. 289–296Research output: Contribution to journal › Journal article › Research › peer-review
- 2016
- Published
Seqenv: linking sequences to environments through text mining
Sinclair, L., Ijaz, U. Z., Jensen, Lars Juhl, Coolen, M. J. L., Gubry-Rangin, C., Chroňáková, A., Oulas, A., Pavloudi, C., Schnetzer, J., Weimann, A., Ijaz, A., Eiler, A., Quince, C. & Pafilis, E., 20 Dec 2016, In: PeerJ. 4, p. 1-17 17 p., e2690.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells
Buch-Larsen, Sara Charlotte, Sylvestersen, K. B., Mund, Andreas, Lyon, D., Mullari, M., Madsen, M. V., Daniel, J. A., Jensen, Lars Juhl & Nielsen, Michael Lund, 30 Aug 2016, In: Science Signaling. 9, 443, 14 p., rs9.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Standardized benchmarking in the quest for orthologs
Altenhoff, A. M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D. A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L. P., Schreiber, F., da Silva, A. S., Szklarczyk, D., Train, C-M., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjölander, K., Jensen, L. J. & 8 others, , May 2016, In: Nature Methods. 13, p. 425-30 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The SIDER database of drugs and side effects
Kuhn, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 4 Jan 2016, In: Nucleic Acids Research. 44, p. D1075-9Research output: Contribution to journal › Journal article › Research › peer-review
- Published
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., Jensen, Lars Juhl, von Mering, C. & Bork, P., 4 Jan 2016, In: Nucleic Acids Research. 44, D1, p. D286-93Research output: Contribution to journal › Journal article › Research › peer-review
- 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
- 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
- Published
Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls
Midjord-Belstrøm, Daniel, Jersie-Christensen, R. R., Lyon, D., Damgaard, Christian, Jensen, Lars Juhl, Holmstrup, Palle & Olsen, Jesper Velgaard, 2016, In: PeerJ. 4, 17 p., e2433.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
One tagger, many uses: Illustrating the power of ontologies in dictionary-based named entity recognition
Jensen, Lars Juhl, 2016, In: CEUR Workshop Proceedings. 1747, 2 p.Research output: Contribution to journal › Conference article › Research › peer-review
- Published
Overview of the interactive task in BioCreative V
Wang, Q., S Abdul, S., Almeida, L., Ananiadou, S., Balderas-Martínez, Y. I., Batista-Navarro, R., Campos, D., Chilton, L., Chou, H-J., Contreras, G., Cooper, L., Dai, H-J., Ferrell, B., Fluck, J., Gama-Castro, S., George, N., Gkoutos, G., Irin, A. K., Jensen, L. J., Jimenez, S. & 36 others, , 2016, In: Database: The Journal of Biological Databases and Curation. 2016, 18 p., baw119.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data
Szklarczyk, D., Santos Delgado, A., von Mering, C., Jensen, Lars Juhl, Bork, P. & Kuhn, M., 2016, In: Nucleic Acids Research. 44, D1, p. D380-84 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles
Franceschini, A., Lin, J., von Mering, C. & Jensen, Lars Juhl, 2016, In: Bioinformatics. 32, 7, p. 1085-7 3 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics
Refsgaard, J. C., Munk, S. & Jensen, Lars Juhl, 2016, Phospho-Proteomics: Methods and Protocols. Stechow, L. V. (ed.). Springer Publishing Company, Vol. 1355. p. 323-39 17 p. (Methods in molecular biology (Clifton, N.J.)).Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
- 2015
- 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
ID: 9931112
Most downloads
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714
downloads
TISSUES 2.0: an integrative web resource on mammalian tissue expression
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
518
downloads
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
478
downloads
Drug target ontology to classify and integrate drug discovery data
Research output: Contribution to journal › Journal article › Research › peer-review
Published