The NNF Center for Protein Research

  1. Published

    SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability (vol 46, pg 9484, 2018)

    Hjorth-Jensen, K., Maya-Mendoza, A., Dalgaard, Nanna, Sigurosson, J. O., Bartek, J., Iglesias Gato, Diego, Olsen, Jesper Velgaard & Flores-Morales, A., 2018, In : Nucleic Acids Symposium Series. 46, 18, p. 9891-9891

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability

    Hjorth-Jensen, K., Maya-Mendoza, A., Dalgaard, Nanna, Sigurðsson, J. O., Bartek, J., Iglesias Gato, Diego, Olsen, Jesper Velgaard & Flores-Morales, A., 2018, In : Nucleic Acids Research. 46, 18, p. 9484-9495

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Cyprus Women's Health Research (COHERE) initiative: determining the relative burden of women's health conditions and related co-morbidities in an Eastern Mediterranean population

    Hocaoglu, M. B., Gurkas, S., Karaderi, Tugce, Taneri, B., Erguler, K., Barin, B., Bilgin, E. M., Eralp, G., Allison, M., Findikli, N., Boynukalin, K., Bahceci, M., Naci, H., Vincent, K., Missmer, S. A., Becker, C. M., Zondervan, K. T. & Rahmioglu, N., 2019, In : BMC Women's Health. 19, 7 p., 50.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress

    Hoffmann, Saskia, Smedegaard, S., Nakamura, Kyosuke, Mortuza, G. B., Räschle, M., Ibañez de Opakua, A., Oka, Y., Feng, Y., Blanco, F. J., Mann, Matthias, Montoya, Guillermo, Groth, Anja, Bekker-Jensen, Simon Holst & Mailand, Niels, 4 Jan 2016, In : The Journal of Cell Biology. 212, 1, p. 63-75

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Sweet google O’ mine - The importance of online search engines for MS-facilitated, database-independent identification of peptide-encoded book prefaces: A EUPA YPIC challenge entry

    Hogrebe, A. & Jersie-Christensen, R. R., 2019, In : EuPA Open Proteomics. 22-23, p. 14-18 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Benchmarking common quantification strategies for large-scale phosphoproteomics

    Hogrebe, A., von Stechow, L., Bekker-Jensen, D. B., Weinert, B. T., Kelstrup, C. D. & Olsen, Jesper Velgaard, 2018, In : Nature Communications. 9, 1, p. 1-13 1045.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Selective autophagy maintains centrosome integrity and accurate mitosis by turnover of centriolar satellites

    Holdgaard, S. G., Cianfanelli, V., Pupo, E., Lambrughi, M., Lubas, M., Nielsen, J. C., Eibes, S., Maiani, E., Harder, L. M., Wesch, N., Foged, M. M., Maeda, K., Nazio, F., de la Ballina, L. R., Dötsch, V., Brech, A., Frankel, Lisa, Jäättelä, M., Locatelli, F., Barisic, Marin, Andersen, J. S., Bekker-Jensen, Simon Holst, Lund, Anders H., Rogov, V. V., Papaleo, Elena, Lanzetti, L., De Zio, D. & Cecconi, F., 2019, In : Nature Communications. 10, 1, p. 1-19 19 p., 4176.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    The type 2 diabetes associated minor allele of rs2237895 KCNQ1 associates with reduced insulin release following an oral glucose load

    Holmkvist, J., Banasik, K., Andersen, G., Unoki, H., Jensen, T. S., Pisinger, Charlotta Holm, Borch-Johnsen, K., Sandbaek, A., Lauritzen, T., Brunak, Søren, Maeda, S., Hansen, T. & Pedersen, Oluf Borbye, 2009, In : PLoS ONE. 4, 6, p. e5872

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Methods and Guidelines for Measurement of Glucagon in Plasma

    Holst, Jens Juul & Albrechtsen, Nicolai Jacob Wewer, 2019, In : International Journal of Molecular Sciences (Online). 20, 10 p., 5416.

    Research output: Contribution to journalReviewResearchpeer-review

  10. 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 journalJournal articleResearchpeer-review

  11. 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 journalJournal articleResearchpeer-review

  12. Published

    A Primer on Concepts and Applications of Proteomics in Neuroscience

    Hosp, F. & Mann, Matthias, 1 Nov 2017, In : Neuron. 96, 3, p. 558-571 14 p.

    Research output: Contribution to journalReviewResearchpeer-review

  13. Published

    Arginine Methylation by PRMT2 Controls the Functions of the Actin Nucleator Cobl

    Hou, W., Nemitz, S., Schopper, S., Nielsen, Michael Lund, Kessels, M. M. & Qualmann, B., 2018, In : Developmental Cell. 45, 2, p. 262-275.E8

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    A large-cohort, longitudinal study determines pre-cancer disease routes across different cancer types

    Hjaltelin, Jessica Xin, Helleberg, M., Jensen, A. B., Brunak, Søren & Lundgren, Jens, 2019, In : Cancer Research. 79, 4, p. 864-872

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Network biology concepts in complex disease comorbidities

    Hjaltelin, Jessica Xin, Thomas, C. E. & Brunak, Søren, Oct 2016, In : Nature Reviews. Genetics. 17, p. 615–629

    Research output: Contribution to journalReviewResearchpeer-review

  16. 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. D286-93

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. 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

  18. 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

  19. Published

    High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

    Humphrey, S. J., Karayel, O., James, D. E. & Mann, Matthias, 2018, In : Nature Protocols (Print). 13, p. 1897-1916 20 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Identification of thioredoxin target disulfides using isotope-coded affinity tags

    Hägglund, Per Mårten, Bunkenborg, J., Maeda, K., Finnie, C. & Svensson, B., 2014, Plant Proteomics: Methods and Protocols. Humana Press, p. 677-685 9 p. (Methods in Molecular Biology, Vol. 1072).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  21. Published

    Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags

    Hägglund, Per Mårten, Bunkenborg, J., Maeda, K. & Svensson, B., 1 Dec 2008, In : Journal of Proteome Research. 7, 12, p. 5270-5276 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Seed thioredoxin h

    Hägglund, Per Mårten, Finnie, C., Yano, H., Shahpiri, A., Buchanan, B. B., Henriksen, A. & Svensson, B., 1 Aug 2016, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1864, 8, p. 974-982 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Identification of thioredoxin target disulfides in proteins released from barley aleurone layers

    Hägglund, Per Mårten, Bunkenborg, J., Yang, F., Harder, L. M., Finnie, C. & Svensson, B., 18 Apr 2010, In : Journal of Proteomics. 73, 6, p. 1133-1136 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Melanin concentrating hormone receptor 1 (MCHR1) antagonists - Still a viable approach for obesity treatment?

    Högberg, T., Frimurer, Thomas Michael & Sasmal, P. K., 1 Oct 2012, In : Bioorganic & Medicinal Chemistry Letters. 22, 19, p. 6039-6047 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Helical propensity in an intrinsically disordered protein accelerates ligand binding

    Iesmantavicius, V., Dogan, J., Jemth, P., Teilum, Kaare & Kjærgaard, M., 2014, In : Angewandte Chemie (International ed. in English). 53, 6, p. 1548-1551 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-Treated Yeast Cells

    Iesmantavicius, V., Weinert, B. T. & Choudhary, Chuna Ram, 24 Jun 2014, In : Molecular & Cellular Proteomics. 13, 8, p. 1979-92 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    SOCS2 mediates the cross talk between androgen and growth hormone signaling in prostate cancer

    Iglesias Gato, Diego, Chuan, Y. C., Wikström, P., Augsten, S., Jiang, N., Niu, Y., Seipel, A., Danneman, D., Vermeij, M., Fernandez-Perez, L., Jenster, G., Egevad, L., Norstedt, G. & Flores Morales, A., 2014, In : Carcinogenesis. 35, 1, p. 24-33

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    The proteome of prostate cancer bone metastasis reveals heterogeneity with prognostic implications

    Iglesias Gato, Diego, Thysell, E., Tyanova, S., Crnalic, S., Santos Delgado, Alberto, Lima, T. S., Geiger, T., Cox, J., Widmark, A., Bergh, A., Mann, Matthias, Flores-Morales, A. & Wikström, P., 2018, In : Clinical Cancer Research. 24, 21, p. 5433-5444 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    OTUB1 de-ubiquitinating enzyme promotes prostate cancer cell invasion in vitro and tumorigenesis in vivo: [Plus] erratum

    Iglesias Gato, Diego, Chuan, Y., Jiang, N., Lavallee, C., Bao, J., Paul, I., Egevad, L., Kessler, B. M., Wikström, P., Niu, Y. & Flores-Morales, A., 27 Jan 2015, In : Molecular Cancer. 14, 14 p., 8.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    The Proteome of Primary Prostate Cancer

    Iglesias Gato, Diego, Wikström, P., Tyanova, S., Lavallee, C., Thysell, E., Carlsson, J., Hägglöf, C., Cox, J., Andrén, O., Stattin, P., Egevad, L., Widmark, A., Bjartell, A., Collins, C. C., Bergh, A., Geiger, T., Mann, Matthias & Flores-Morales, A., May 2016, In : European Urology. 69, 5, p. 942-952 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Androgen-independent effects of Serenoa repens extract (Prostasan®) on prostatic epithelial cell proliferation and inflammation

    Iglesias Gato, Diego, Carsten, T., Vesterlund, M., Pousette, A., Schoop, R. & Norstedt, G., Feb 2012, In : Phytotherapy Research. 26, 2, p. 259-64 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

    Ignjatovic, V., Geyer, P. E., Palaniappan, K. K., Chaaban, J. E., Omenn, G. S., Baker, M. S., Deutsch, E. W. & Schwenk, J. M., 2019, In : Journal of Proteome Research. 18, 12, p. 4085-4097

    Research output: Contribution to journalReviewResearchpeer-review

  33. Published

    Transcriptome and metabolite changes during hydrogen cyanamide-induced floral bud break in sweet cherry

    Ionescu, I. A., Lopez-Ortega, G., Burow, Meike, Bayo-Canha, A., Junge, A., Gericke, Oliver, Møller, Birger Lindberg & Sánchez Pérez, R., 2017, In : Frontiers in Plant Science. 8, 17 p., 1233.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. 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 journalJournal articleResearchpeer-review

  35. Published

    The bio.tools registry of software tools and data resources for the life sciences

    Ison, J., Ienasescu, H., Chmura, Piotr Jaroslaw, Rydza, E., Ménager, H., Kalaš, M., Schwämmle, V., Grüning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Vařeková, R. S., Raček, T., Vondrášek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyrönen, T., Valencia, A., Capella, S., Gelpí, J., Zambelli, F., Savakis, B., Leskošek, B., Rapacki, K., Blanchet, C., Jimenez, R., Oliveira, A., Vriend, G., Collin, O., van Helden, J., Løngreen, P. & Brunak, Søren, 2019, In : Genome Biology. 20, 1, 4 p., 164.

    Research output: Contribution to journalLetterResearchpeer-review

  36. Published

    Tools and data services registry: a community effort to document bioinformatics resources

    Ison, J., Rapacki, K., Ménager, H., Kalaš, M., Rydza, E., Chmura, P., Anthon, Christian, Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G. D., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Grüning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M. C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J., Licata, L., Mareuil, F., Mičetić, I., Friborg, R. M., Moretti, S., Morris, C., Möller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwämmle, V., Smith, C., Sperotto, M. M., Stockinger, H., Vařeková, R. S., Tosatto, S. C. E., de la Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Løngreen, P. & Brunak, Søren, 2016, In : Nucleic Acids Research. 44, D1, p. D38-D47 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism

    Ito, J., Batth, Tanveer Singh, Petzold, C. J., Redding-Johanson, A. M., Mukhopadhyay, A., Verboom, R., Meyer, E. H., Millar, A. H. & Heazlewood, J. L., 1 Apr 2011, In : Journal of Proteome Research. 10, 4, p. 1571-82 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    SILAC-based quantitative mass spectrometry-based proteomics quantifies endoplasmic reticulum stress in whole HeLa cells

    Itzhak, D. N., Sacco, F., Nagaraj, N., Tyanova, S., Mann, Matthias & Murgia, M., 2019, In : Disease Models & Mechanisms. 12, 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii

    Iversen, Katrine Højholt, Rasmussen, L. H., Al-Nakeeb, K., Armenteros, J. J. A., Jensen, C. S., Dargis, R., Lukjancenko, O., Justesen, U. S., Moser, Claus Ernst, Rosenvinge, F. S., Nielsen, X. C., Christensen, J. J. & Rasmussen, Simon, 17 Feb 2020, In : Scientific Reports. 10, 1, p. 2728

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-β

    J D'Souza, R. C., Knittle, A. M., Nagaraj, N., van Dinther, M., Choudhary, Chuna Ram, Ten Dijke, P., Mann, Matthias & Sharma, K., Jul 2014, In : Science signaling. 7, 335, p. rs5 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    The dual methyltransferase METTL13 targets N terminus and Lys55 of eEF1A and modulates codon-specific translation rates

    Jakobsson, Magnus Erik, Małecki, J. M., Halabelian, L., Nilges, B. S., Pinto, R., Kudithipudi, S., Munk, S., Davydova, E., Zuhairi, F. R., Arrowsmith, C. H., Jeltsch, A., Leidel, S. A., Olsen, Jesper Velgaard & Falnes, P. Ø., 2018, In : Nature Communications. 9, 1, 3411.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Regulation of eukaryotic elongation factor 1 alpha (eEF1A) by dynamic lysine methylation

    Jakobsson, Magnus Erik, Małecki, J. & Falnes, P. Ø., 2018, In : RNA biology. 15, 3, p. 314-319 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Glucagon Receptor Signaling and Glucagon Resistance

    Janah, L., Kjeldsen, Sasha Alexandra Sampson, Galsgaard, Katrine Douglas, Winther-Sørensen, Marie, Stojanovska, E., Pedersen, J., Knop, Filip Krag, Holst, Jens Juul & Albrechtsen, Nicolai Jacob Wewer, 2019, In : International Journal of Molecular Sciences. 20, 13, 27 p., 3314.

    Research output: Contribution to journalReviewResearchpeer-review

  44. Published

    Increase in clinically recorded type 2 diabetes after colectomy

    Jensen, A. B., Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Jess, T., Brunak, Søren & Allin, Kristine Højgaard, 2018, In : eLife. 7, e37420.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

    Jensen, A. B., Moseley, Pope Lloyd, Oprea, T. I., Ellesøe, S. G., Eriksson, Robert, Schmock, H., Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 24 Jun 2014, In : Nature Communications. 5, 10 p., 4022.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014

    Jensen, A. B., Ajslev, T. A., Brunak, Søren & Sørensen, Thorkild I.A., 15 Dec 2015, In : B M J Open. 5, 8 p., e008702.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Assembly and analysis of 100 full MHC haplotypes from the Danish population

    Jensen, J. M., Villesen, P., Friborg, R. M., Mailund, T., Besenbacher, S., Sørensen, L. M., Petersen, Bent, Sibbesen, J. A., Liu, S., Skov, L., Belling, Kirstine G, Have, C. T., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R., Ye, W., Rao, J., Guo, X., Sun, J., Cao, H., Ye, C., Beusekom, J. V., Espeseth, T., Flindt, E., Halager, A. E., Hellard, S. L., Hultman, C. M., Lescai, F., Li, S., Lund, O., Løngren, P., Matey-Hernandez, M. L., Mors, O., Pedersen, C. N. S., Sicheritz-Pontén, T., Sullivan, P., Syed, A., Westergaard, D., Yadav, R., Li, N., Xu, X., Hansen, Torben, Bolund, L., Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Gupta, R., Rasmussen, Simon, Børglum, A. D., Wang, Jun, Eiberg, Hans Rudolf Lytchoff, Kristiansen, Karsten, Brunak, Søren & Schierup, M. H., Sep 2017, In : Genome Research. 27, 9, p. 1597-1607 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    Inactivation of barley limit dextrinase inhibitor by thioredoxin-catalysed disulfide reduction

    Jensen, J. M., Hägglund, Per Mårten, Christensen, H. E. M. & Svensson, B., 30 Jul 2012, In : FEBS letters. 586, 16, p. 2479-2482 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Analysis of a gene panel for targeted sequencing of colorectal cancer samples

    Jensen, K. H., Izarzugaza, J. M. G., Juncker, A. S., Hansen, R. B., Hansen, T. F., Timshel, P., Blondal, T., Jensen, T. S., Rygaard-Hjalsted, E., Mouritzen, P., Thorsen, M., Wernersson, R., Nielsen, H. B., Jakobsen, A., Brunak, Søren & Sørensen, F. B., 2018, In : OncoTarget. 9, 10, p. 9043-9060 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    Ontologies in quantitative biology: a basis for comparison, integration, and discovery

    Jensen, Lars Juhl & Bork, P., 1 May 2010, In : PLoS Biology. 8, 5, p. e1000374

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. 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 journalComment/debateResearchpeer-review

  52. Published

    STRING 8--a global view on proteins and their functional interactions in 630 organisms

    Jensen, Lars Juhl, Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., Bork, P. & von Mering, C., 2008, In : Nucleic Acids Research. 37, suppl 1, p. D412-D416 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. 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 journalJournal articleResearchpeer-review

  54. Published

    The rise and fall of supervised machine learning techniques

    Jensen, Lars Juhl & Bateman, A., 2011, In : Bioinformatics (Online). 27, 24, p. 3331-2 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  55. 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 journalConference articleResearchpeer-review

  56. Published

    Protein interaction-based genome-wide analysis of incident coronary heart disease

    Jensen, Majken Karoline, Pers, Tune H, Dworzynski, P., Girman, C. J., Brunak, Søren & Rimm, E. B., 2011, In : Circulation: Cardiovascular Genetics. 4, 5, p. 549-56 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    Early detection of response to experimental chemotherapeutic Top216 with [18F]FLT and [18F]FDG PET in human ovary cancer xenografts in mice

    Wessel, Mette Munk, Erichsen, K. D., Björkling, Fredrik, Madsen, J., Jensen, P. B., Højgaard, Liselotte, Sehested, M. & Kjær, Andreas, 1 Jan 2010, In : P L o S One. 5, 9, p. e12965

    Research output: Contribution to journalJournal articleResearchpeer-review

  58. Published

    Reversed binding of a small molecule ligand in homologous chemokine receptors - differential role of extracellular loop 2

    Jensen, Per Claudi, Thiele, S., Steen, A., Elder, A., Kolbeck, R., Ghosh, S., Frimurer, Thomas Michael & Rosenkilde, Mette, May 2012, In : British Journal of Pharmacology. 166, 1, p. 258-75 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  59. Published

    Mining electronic health records: towards better research applications and clinical care

    Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 2012, In : Nature Reviews. Genetics. 13, 6, p. 395-405 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  60. Published

    Reply to 'Mining electronic health records: An additional perspective'

    Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 1 Jan 2013, In : Nature Reviews. Genetics. 14, 1 p.

    Research output: Contribution to journalComment/debateResearchpeer-review

  61. Published
  62. Published

    The biomolecular characterization of a finger ring contextually dated to the emergence of the Early Neolithic from Syltholm, Denmark

    Jensen, Theis Zetner Trolle, Mackie, Meaghan, Taurozzi, Alberto John, Lanigan, Liam Thomas, Gundelach, C., Olsen, J., Sørensen, S. A., Collins, Matthew James, Sørensen, Mikkel & Schroeder, Hannes, 2020, In : Royal Society Open Science. 7, 1, 16 p., 191172.

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    Quantitative metaproteomics of medieval dental calculus reveals individual oral health status

    Jersie-Christensen, R. R., Lanigan, Liam Thomas, Lyon, D., Mackie, Meaghan, 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

  64. Published

    Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity

    Jersie-Christensen, R. R., Sultan, A. & Olsen, Jesper Velgaard, 2016, Phospho-Proteomics: Methods and Protocols. Stechow, L. V. (ed.). p. 251-60 10 p. (Methods in molecular biology (Clifton, N.J.), Vol. 1355).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  65. Published

    Heterogeneity in the perirenal region of humans suggests presence of dormant brown adipose tissue that contains brown fat precursor cells

    Jespersen, N. Z., Feizi, A., Andersen, E. S., Heywood, S., Hattel, H. B., Daugaard, S., Peijs, Lone, Bagi, P., Feldt-Rasmussen, Bo, Schultz, H. S., Hansen, N. S., Krogh-Madsen, Rikke, Pedersen, Bente Klarlund, Petrovic, N., Nielsen, S. & Schéele, Camilla Charlotte, 2019, In : Molecular Metabolism. 24, p. 30-43 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. Published

    Estimating heritability and genetic correlations from large health datasets in the absence of genetic data

    Jia, G., Li, Y., Zhang, H., Chattopadhyay, I., Jensen, A. B., Blair, D. R., Davis, L., Robinson, P. N., Dahlen, T., Brunak, Søren, Benson, M., Edgren, G., Cox, N. J., Gao, X. & Rzhetsky, A., 2019, In : Nature Communications. 10, 11 p., 5508.

    Research output: Contribution to journalJournal articleResearchpeer-review

  67. Published

    Conflicting associations between dietary patterns and changes of anthropometric traits across subgroups of middle-aged women and men

    Jiang, L., Audouze, K., Romero Herrera, Jose Alejandro, Ängquist, Lars, Kjærulff, S. K., Izarzugaza, J. M. G., Tjønneland, Anne, Halkjær, J., Overvad, K., Sørensen, Thorkild I.A. & Brunak, Søren, 2020, In : Clinical Nutrition. 39, 1, p. 265-275

    Research output: Contribution to journalJournal articleResearchpeer-review

  68. Published

    In vivo quantitative phosphoproteomic profiling identifies novel regulators of castration-resistant prostate cancer growth

    Jiang, N., Hjorth-Jensen, K., Hekmat, O., Iglesias Gato, Diego, Kruse, Thomas, Wang, C., Wei, W., Ke, B., Yan, B., Niu, Y., Olsen, Jesper Velgaard & Flores Morales, A., 2015, In : Oncogene. 34, p. 2764–2776 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    iAnn: an event sharing platform for the life sciences

    Jimenez, R. C., Albar, J. P., Bhak, J., Blatter, M., Blicher, T., Brazas, M. D., Brooksbank, C., Budd, A., De Las Rivas, J., Dreyer, J., van Driel, M. A., Dunn, M. J., Fernandes, P. L., van Gelder, C. W. G., Hermjakob, H., Ioannidis, V., Judge, D. P., Kahlem, P., Korpelainen, E., Kraus, H., Loveland, J., Mayer, C., McDowall, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Salazar, G. A., Schneider, R., Via, A., Villaveces, J. M., Yu, P., Schneider, M. V., Attwood, T. K. & Corpas, M., 5 Jun 2013, In : Bioinformatics (Online). 29, 15, p. 1919-1921

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. Published

    Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP

    Johansen, M. B., Izarzugaza, J. M. G., Brunak, Søren, Petersen, T. N. & Gupta, R., Jul 2013, In : P L o S One. 8, 7, p. e68370

    Research output: Contribution to journalJournal articleResearchpeer-review

  71. Published

    Investigating Intestinal Glucagon after Roux-en-Y Gastric Bypass Surgery

    Jorsal, T., Albrechtsen, Nicolai Jacob Wewer, Christensen, M. M., Mortensen, B., Wandall, E., Langholz, E., Friis, S., Worm, D., Ørskov, Cathrine, Støving, R. K., Andries, A., Juhl, C. B., Sørensen, F., Forman, Julie Lyng, Falkenhahn, M., Musholt, P. B., Theis, S., Larsen, P. J., Holst, Jens Juul, Vrang, N., Jelsing, J., Vilsbøll, Tina & Knop, Filip Krag, 2019, In : Journal of Clinical Endocrinology and Metabolism. 104, 12, p. 6403–6416 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  72. Published

    Endogenous Nuclear RNAi Mediates Behavioral Adaptation to Odor

    Juang, B., Gu, C., Starnes, L., Palladino, F., Goga, A., Kennedy, S. & L'etoile, N. D., 29 Aug 2013, In : Cell. 154, 5, p. 1010-22 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  73. Published

    Comprehensive analysis of the specificity of transcription activator-like effector nucleases

    Juillerat, A., Dubois, G., Valton, J., Thomas, S., Stella, Stefano, Maréchal, A., Langevin, S., Benomari, N., Bertonati, C., Silva, G. H., Daboussi, F., Epinat, J., Montoya, Guillermo, Duclert, A. & Duchateau, P., Apr 2014, In : Nucleic Acids Research. 42, 8, p. 5390-402 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  74. Published

    Toppar: an interactive browser for viewing association study results

    Juliusdottir, T., Banasik, Karina, Robertson, N. R., Mott, R. & McCarthy, M. I., 2018, In : Bioinformatics. 34, 11, p. 1922-1924 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. Published

    Modular engineering of L-tyrosine production in Escherichia coli

    Juminaga, D., Baidoo, E. E. K., Redding-Johanson, A. M., Batth, Tanveer Singh, Burd, H., Mukhopadhyay, A., Petzold, C. J. & Keasling, J. D., Jan 2012, In : Applied and Environmental Microbiology. 78, 1, p. 89-98 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  76. 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

  77. Published

    RAIN: RNA-protein Association and Interaction Networks

    Junge, A., Refsgaard, J. C., Garde, C., Pan, X., Santos Delgado, Alberto, Alkan, F., Anthon, Christian, von Mering, C., Workman, C. T., Jensen, Lars Juhl & Gorodkin, Jan, 2017, In : Database. 2017, 9 p., baw167.

    Research output: Contribution to journalJournal articleResearchpeer-review

  78. Published

    Proteome-wide Identification of Poly(ADP-Ribosyl)ation Targets in Different Genotoxic Stress Responses

    Jungmichel, S., Rosenthal, F., Altmeyer, M., Lukas, Jiri, Hottiger, M. O. & Nielsen, Michael Lund, 24 Oct 2013, In : Molecular Cell. 52, 2, p. 272-285 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. Published

    Specificity and commonality of the phosphoinositide-binding proteome analyzed by quantitative mass spectrometry

    Jungmichel, S., Sylvestersen, K. B., Choudhary, Chuna Ram, Nguyen, S., Mann, Matthias & Nielsen, Michael Lund, 13 Feb 2014, In : Cell Reports. 6, 3, p. 578-91 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  80. Published

    The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator.

    Jungmichel, S., Clapperton, J. A., Janette, L., Hari, F. J., Spycher, C., Pavic, L., Li, J., Haire, L. F., Bonalli, M., Larsen, D. H., Lukas, C., Lukas, J., MacMillan, D., Nielsen, Michael Lund, Stucki, M. & Smerdon, S. J., 10 Jan 2012, In : Nucleic Acids Research. 40, 9, p. 4913-4928 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  81. Published

    Rapid and transient protein acetylation changes in response to DNA damage

    Jungmichel, S. & Blasius, M., 1 Jun 2013, In : Cell Cycle. 12, 13, p. 1993-1994 2 p.

    Research output: Contribution to journalJournal articleCommunication

  82. Published

    Increasing insulin resistance accentuates the effect of triglyceride-associated loci on serum triglycerides during 5 years

    Justesen, Johanne Marie, Andersson, E. A., Allin, Kristine Højgaard, Sandholt, C. H., Jørgensen, T., Linneberg, Allan René, Jørgensen, M. E., Hansen, Torben, Pedersen, Oluf Borbye & Grarup, Niels, Dec 2016, In : Journal of Lipid Research. 57, 12, p. 2193-2199 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    The normal cultivable microflora in upper jejunal fluid in healthy adults

    Justesen, Torkild, Nielsen, Ole Haagen, Jacobsen, I. E., Lave, J. & Rasmussen, Simon, Mar 1984, In : Scandinavian Journal of Gastroenterology. 19, 2, p. 279-82 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  84. Published

    Comorbidity landscape of the Danish patient population affected by chromosome abnormalities

    Jørgensen, Isabella Friis, Russo, Francesco, Jensen, A. B., Westergaard, David, zmw894, zmw894, Hjaltelin, Jessica Xin, Brunak, Søren & Belling, Kirstine G, 2019, In : Genetics In Medicine. 21, 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  85. Published

    Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo

    Jørgensen, J. R., Fransson, A., Fjord-Larsen, L., Thompson, L. H., Houchins, J. P., Andrade, N., Torp, M., Kalkkinen, N., Andersson, E., Lindvall, O., Ulfendahl, M., Brunak, Søren, Johansen, T. E. & Wahlberg, L. U., 2012, In : Experimental Neurology. 233, 1, p. 172-81 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  86. Published

    Design and characterization of dimeric ligands cross-linking two identical modulatory AMPA receptor sites

    Kaae, B. H., Harpsøe, Kasper, Sanz, A. C., Pickering, Darryl S, Sauerberg, P., Clausen, Rasmus Prætorius, Kastrup, Jette Sandholm Jensen, Liljefors, T. & Madsen, Ulf, 19 Aug 2007, In : American Chemical Society. Abstracts of Papers (at the National Meeting). 234

    Research output: Contribution to journalConference abstract in journalResearch

  87. Published

    Retraction

    Kaidi, A., Weinert, B. T., Choudhary, C. & Jackson, S. P., 2019, In : Science. 364, 6437, p. 247 1 p.

    Research output: Contribution to journalComment/debateResearch

  88. Published

    Tousled-like kinases phosphorylate Asf1 to promote histone supply during DNA replication

    Kamalyukova, I. M., Young, C., Strømme, C. B., Ménard, Patrice, Jasencakova, Zuzana, Mejlvang, J., Ask, K., Ploug, Michael, Nielsen, Michael Lund, Jensen, O. N. & Groth, Anja, 2014, In : Nature Communications. 5, p. 3394

    Research output: Contribution to journalJournal articleResearchpeer-review

  89. Published

    Prediction of pancreatic fat and analysis of its determining factors using multi-omics datasets: an IMI DIRECTstudy

    Karaderi, Tugce, Mazzoni, Gianluca, Brorsson, Caroline Anna, Westergaard, David, Banasik, Karina, Koivula, R., Thomas, L., Bell, J., Franks, P., Pearson, E. & Brunak, Søren, 2019, In : Diabetologia. 62, p. S166-S166

    Research output: Contribution to journalConference abstract in journalResearch

  90. Published

    Classification of Laser Induced Fluorescence Spectra from Normal and Malignant bladder tissues using Learning Vector Quantization Neural Network in Bladder Cancer Diagnosis

    Karemore, Gopal, Mascarenhas, K. K., Patil, C., V.K, U., Prabhu, V., Chowla, A., Nielsen, Mads & C, S., 2008, BIBE 2008: 8th. IEEE International Conference on Bioinformatics and BioEngineering, 8-10 October 2008. IEEE Communications Society, p. 1-6 6 p.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  91. Published

    Loss of CHD1 causes DNA repair defects and enhances prostate cancer therapeutic responsiveness

    Kari, V., Mansour, W. Y., Raul, S. K., Baumgart, S. J., Mund, Andreas, Grade, M., Sirma, H., Simon, R., Will, H., Dobbelstein, M., Dikomey, E. & Johnsen, S. A., 1 Nov 2016, In : E M B O Reports. 17, 11, p. 1609-1623

    Research output: Contribution to journalJournal articleResearchpeer-review

  92. Published

    Structure of dimeric and tetrameric complexes of the BAR domain protein PICK1 determined by small-angle X-Ray scattering

    Karlsen, M. L., Thorsen, Thor Seneca, Johner, N., Ammendrup-Johnsen, I., Erlendsson, Simon, Tian, X., Simonsen, J. B., Hoiberg-Nielsen, R., Christensen, N. M., Khelashvili, G., Streicher, W., Teilum, Kaare, Vestergaard, Bente, Weinstein, H., Gether, Ulrik, Arleth, Lise & Madsen, Kenneth Lindegaard, 7 Jul 2015, In : Structure. 23, 7, p. 1258-1270 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  93. Published

    NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ

    Karosiene, E., Rasmussen, M., Blicher, T., Lund, O., Buus, Søren & Nielsen, M., Oct 2013, In : Immunogenetics. 65, 10, p. 711-24 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  94. Published

    The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies

    Katayama, T., Wilkinson, M. D., Micklem, G., Kawashima, S., Yamaguchi, A., Nakao, M., Yamamoto, Y., Okamoto, S., Oouchida, K., Chun, H., Aerts, J., Afzal, H., Antezana, E., Arakawa, K., Aranda, B., Belleau, F., Bolleman, J., Bonnal, R. J., Chapman, B., Cock, P., Eriksson, T., Gordon, P., Goto, N., Hayashi, K., Horn, H., Ishiwata, R., Kaminuma, E., Kasprzyk, A., Kawaji, H., Kido, N., Kim, Y. J., Kinjo, A. R., Konishi, F., Kwon, K., Labarga, A., Lamprecht, A., Lin, Y., Lindenbaum, P., McCarthy, L., Morita, H., Murakami, K., Nagao, K., Nishida, K., Nishimura, K., Nishizawa, T., Ogishima, S., Ono, K., Oshita, K., Park, K., Prins, P., Saito, T. L., Samwald, M., Satagopam, V. P., Shigemoto, Y., Smith, R., Splendiani, A., Sugawara, H., Taylor, J., Vos, R., Withers, D., Yamasaki, C., Zmasek, C. M., Kawamoto, S., Okubo, K., Asai, K. & Takagi, T., 11 Feb 2013, In : Journal of Biomedical Semantics. 4, 1, p. 6 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    Suppressor of Cytokine Signaling 6 (SOCS6) Negatively Regulates Flt3 Signal Transduction through Direct Binding to Phosphorylated Tyrosines 591 and 919 of Flt3

    Kazi, J. U., Sun, J., Phung, B., Zadjali, F., Flores Morales, A. & Rönnstrand, L., 2012, In : The Journal of Biological Chemistry. 287, 43, p. 36509-17 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    SOCS proteins in regulation of receptor tyrosine kinase signaling

    Kazi, J. U., Kabir, N. N., Flores Morales, A. & Rönnstrand, L., 2014, In : Cellular and Molecular Life Sciences. 71, 17, p. 3297-3310 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. Published

    Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

    Kelstrup, C. D., Jersie-Christensen, R. R., Batth, Tanveer Singh, Arrey, T. N., Kuehn, A., Kellmann, M. & Olsen, Jesper Velgaard, 28 Oct 2014, In : Journal of Proteome Research. 13, 12, p. 6187-95 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  98. Published

    Performance evaluation of the Q Exactive HF-X for shotgun proteomics

    Kelstrup, C. D., Bekker-Jensen, D. B., Arrey, T. N., Hogrebe, A., Harder, A. & Olsen, Jesper Velgaard, Jan 2018, In : Journal of Proteome Research. 17, 1, p. 727-738 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  99. Published

    Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID)

    Kelstrup, C. D., Freese, C., Heck, A. J. R., Olsen, Jesper Velgaard & Nielsen, Michael Lund, 3 Jun 2014, In : Molecular & Cellular Proteomics. 13, 8, p. 1914-1924 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. Published

    Limits for resolving isobaric tandem mass tag reporter ions using phase constrained spectrum deconvolution

    Kelstrup, C. D., Aizikov, K., Batth, Tanveer Singh, Kreutzman, A., Grinfeld, D., Lange, O., Mourad, D., Makarov, A. A. & Olsen, Jesper Velgaard, 2018, In : Journal of Proteome Research. 17, 11, p. 4008-4016 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

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