The NNF Center for Protein Research

  1. 2012
  2. Published

    Histone deacetylases 1 and 3 but not 2 mediate cytokine-induced beta cell apoptosis in INS-1 cells and dispersed primary islets from rats and are differentially regulated in the islets of type 1 diabetic children

    Lundh, M., Christensen, D. P., Damgaard Nielsen, M., Richardson, S. J., Dahllöf, M. S., Skovgaard, T., Berthelsen, J., Dinarello, C. A., Stevenazzi, A., Mascagni, P., Grunnet, L. G., Morgan, N. G. & Mandrup-Poulsen, Thomas, 2012, In : Diabetologia. 55, 9, p. 2421-31

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks

    Poulsen, M., Lukas, C., Lukas, J., Bekker-Jensen, Simon Holst & Mailand, Niels, 2012, In : Journal of Cell Biology. 197, 2, p. 189-99 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    ICLs: a chicken without an egg

    Bekker-Jensen, Simon Holst & Mailand, Niels, 2012, In : Nature Reviews. Molecular Cell Biology. 13, 6, p. 342

    Research output: Contribution to journalReviewResearchpeer-review

  5. Published

    Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression

    Bergholdt, R., Brorsson, C., Palleja, A., Berchtold, L. A., Fløyel, T., Bang-Berthelsen, C. H., Frederiksen, K. S., Jensen, Lars Juhl, Størling, J. & Pociot, F., 2012, In : Diabetes. 61, 4, p. 954-62 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Influence of neonatal hypothyroidism on hepatic gene expression and lipid metabolism in adulthood

    Santana-Farré, R., Mirecki-Garrido, M., Bocos, C., Henríquez-Hernández, L. A., Kahlon, N., Herrera, E., Norstedt, G., Parini, P., Flores Morales, A. & Fernández-Pérez, L., 2012, In : PLOS ONE. 7, 5, p. e37386 e37386.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. 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

  8. Published

    Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

    Croft, L. J., Szklarczyk, D., Jensen, Lars Juhl & Gorodkin, Jan, 2012, In : B M C Systems Biology. 6, 1, p. 90

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer

    Kelstrup, C. D., Young, C., Lavallee, R., Nielsen, Michael Lund & Olsen, Jesper Velgaard, 2012, In : Journal of Proteome Research. p. 3487-3497 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Pdx1 is post-translationally modified in vivo and serine 61 is the principal site of phosphorylation

    Frogne, T., Sylvestersen, K. B., Kubicek, S., Nielsen, Michael Lund & Hecksher-Sørensen, J., 2012, In : P L o S One. 7, 4, p. e35233

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Pharmacological characterization and modeling of the binding sites of novel 1,3-bis(pyridinylethynyl)benzenes as metabotropic glutamate receptor 5-selective negative allosteric modulators

    Mølck, C., Harpsøe, Kasper, Gloriam, David E., Clausen, Rasmus Prætorius, Madsen, Ulf, Pedersen, L., Jimenez, H. N., Nielsen, S. M., Mathiesen, Jesper M. & Bräuner-Osborne, Hans, 2012, In : Molecular Pharmacology. 82, 5, p. 929-37 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae

    Henriksen, P., Wagner, S. A., Weinert, B. T., Sharma, S., Bacinskaja, G., Rehman, M., Juffer, A. H., Walther, T. C., Lisby, Michael & Choudhary, Chuna Ram, 2012, In : Molecular & Cellular Proteomics. 11, 11, p. 1510-1522 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Proteomic analyses reveal divergent ubiquitylation site patterns in murinetissues

    Wagner, S. A., Beli, P., Weinert, B. T., Schölz, C. F., Kelstrup, C. D., Young, C., Nielsen, Michael Lund, Olsen, Jesper Velgaard, Brakebusch, Cord Herbert & Choudhary, Chuna Ram, 2012, In : Molecular & Cellular Proteomics.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins

    Cappellini, Enrico, Jensen, Lars Juhl, Szklarczyk, D. M., Ginolhac, A., Rodrigues da Fonseca, Rute Andreia, Stafford jr., T., Holen, S. R., Collins, M. J., Orlando, L. A. A., Willerslev, Eske, Gilbert, M Thomas P & Olsen, Jesper Velgaard, 2012, In : Journal of Proteome Research. 11, 2, p. 917-926 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response

    Beli, P., Lukashchuk, N., Wagner, S. A., Weinert, B. T., Olsen, Jesper Velgaard, Baskcomb, L., Mann, Matthias, Jackson, S. P. & Choudhary, Chuna Ram, 2012, In : Molecular Cell. 46, 2, p. 212-25 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    RNF8 and RNF168 but not HERC2 are required for DNA damage-induced ubiquitylation in chicken DT40 cells

    Østergaard, Vibe Hallundbæk, Pentzold, C., Pedersen, R. T., Iosif, S., Alpi, A., Bekker-Jensen, Simon Holst, Mailand, Niels & Lisby, Michael, 2012, In : D N A Repair. 11, 11, p. 892–905 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    SOCS2 deletion protects against hepatic steatosis but worsens insulin resistance in high-fat-diet-fed mice

    Zadjali, F., Santana-Farre, R., Vesterlund, M., Carow, B., Mirecki-Garrido, M., Hernandez-Hernandez, I., Flodström-Tullberg, M., Parini, P., Rottenberg, M., Norstedt, G., Fernandez-Perez, L. & Flores Morales, A., 2012, In : FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 26, 8, p. 3282-91 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    STITCH 3: zooming in on protein-chemical interactions

    Kuhn, M., Szklarczyk, D., Franceschini, A., von Mering, C., Jensen, Lars Juhl & Bork, P., 2012, In : Nucleic Acids Research. 40, Database issue, p. D876-80

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. 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

  20. Published

    The DNA damage- and transcription-associated protein Paxip1 controls thymocyte development and emigration

    Callen, E., Faryabi, R. B., Daniel, J. A., Nussenzweig, A., Luckey, M., Park, J., Hao, B., Krangel, M. S., Yang, W., Peng, W., Sun, H., Dressler, G., Chi, H. & Ge, K., 2012, In : Immunity. 37, 6, p. 971-985 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    The Ndc80 internal loop is required for recruitment of the Ska complex to establish end-on microtubule attachment to kinetochores

    Zhang, G., Kelstrup, C. D., Hu, X., Hansen, M. J. K., Singleton, M. R., Olsen, Jesper Velgaard & Nilsson, Jakob, 2012, In : Journal of Cell Science. p. 3243-3253 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    The Ubiquitin Ligase XIAP Recruits LUBAC for NOD2 Signaling in Inflammation and Innate Immunity

    Damgaard, R. B., Nachbur, U., Yabal, M., Wong, W. W., Fiil, B. K., Kastirr, M., Rieser, E., Rickard, J. A., Bankovacki, A., Peschel, C., Ruland, J., Bekker-Jensen, Simon Holst, Mailand, Niels, Kaufmann, T., Strasser, A., Walczak, H., Silke, J., Jost, P. J. & Gyrd-Hansen, M., 2012, In : Molecular Cell. 46, 6, p. 746-58 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Transcriptional regulation is a major controller of cell cycle transition dynamics

    Romanel, A., Jensen, Lars Juhl, Cardelli, L. & Csikász-Nagy, A., 2012, In : P L o S One. 7, 1, p. e29716

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges

    Powell, S., Trachana, K., Letunic, I., Doerks, T., Bork, P., Szklarczyk, D., Jensen, Lars Juhl, Roth, A., Von Mering, C., Kuhn, M., Muller, J., Arnold, R. & Rattei, T., 2012, In : Nucleic Acids Research. 40, D1, p. D284-9

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. 2011
  26. Published

    The AAA-ATPase VCP/p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks

    Acs, K., Luijsterburg, M. S., Ackermann, Leena, Salomons, F. A., Hoppe, T. & Dantuma, N. P., 27 Nov 2011, In : Nature Structural & Molecular Biology. 18, 12, p. 1345-50 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing

    Schjoldager, Katrine Ter-Borch Gram, Vester-Christensen, M. B., Goth, Christoffer Knak, Petersen, T. N., Brunak, Søren, Bennett, Eric Paul, Levery, S. B. & Clausen, Henrik, 18 Nov 2011, In : Journal of Biological Chemistry. 286, 46, p. 40122-32 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Structure of a Blinkin-BUBR1 complex reveals an interaction crucial for kinetochore-mitotic checkpoint regulation via an unanticipated binding Site

    Bolanos-Garcia, V. M., Lischetti, T., Matak-Vinković, D., Cota, E., Simpson, P. J., Chirgadze, D. Y., Spring, D. R., Robinson, C. V., Nilsson, Jakob & Blundell, T. L., 9 Nov 2011, In : Structure. 19, 11, p. 1691-700 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Liver X receptor agonist downregulates growth hormone signaling in the liver

    Zadjali, F., Santana-Farre, R., Mirecki-Garrido, M., Ellis, E., Norstedt, G., Fernandez-Perez, L. & Flores-Morales, A., 1 Nov 2011, In : Hormone Molecular Biology and Clinical Investigation. 8, 2, p. 471-8 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

    Wagner, S. A., Beli, P., Weinert, B. T., Nielsen, Michael Lund, Cox, J., Mann, Matthias & Choudhary, Chuna Ram, 1 Oct 2011, In : Molecular and Cellular Proteomics. 10, 10, p. M111.013284

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Ten simple rules for getting help from online scientific communities

    Dall'olio, G. M., Marino, J., Schubert, M., Keys, K. L., Stefan, M. I., Gillespie, C. S., Poulain, P., Shameer, K., Sugar, R., Invergo, B. M., Jensen, Lars Juhl, Bertranpetit, J. & Laayouni, H., 1 Sep 2011, In : P L o S Computational Biology. 7, 9, p. e1002202

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Binding Mode of a Novel MPEP-Derived Metabotropic Glutamate Receptor Subtype 5 (mGluR5) NAM, 1,3-Bis(pyridin-2-ylethynyl)Benzene

    Molck, C., Harpsøe, Kasper, Gloriam, David E., Kaae, B. H., Jimenez, H. N., Uberti, M. A., Topiol, S., Clausen, Rasmus Prætorius, Madsen, Ulf, Nielsen, S. M., Mathiesen, Jesper M. & Bräuner-Osborne, Hans, Sep 2011, In : Current Neuropharmacology. 9, p. 43-43

    Research output: Contribution to journalConference abstract in journalResearch

  33. Published

    Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases

    Ma, S. M., Garcia, D. E., Redding-Johanson, A. M., Friedland, G. D., Chan, R., Batth, Tanveer Singh, Haliburton, J. R., Chivian, D., Keasling, J. D., Petzold, C. J., Lee, T. S. & Chhabra, S. R., Sep 2011, In : Metabolic Engineering. 13, 5, p. 588-97 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth

    Wild, P., Farhan, H., McEwan, D. G., Wagner, S., Rogov, V. V., Brady, N. R., Richter, B., Korac, J., Waidmann, O., Choudhary, Chuna Ram, Dötsch, V., Bumann, D. & Dikic, I., 8 Jul 2011, In : Science. 333, 6039, p. 228-33 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Quantitative, high-resolution proteomics for data-driven systems biology

    Cox, J. & Mann, Matthias, 7 Jul 2011, In : Annual Review of Biochemistry. 80, p. 273-299 27 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Pinpointing Phosphorylation Sites: Quantitative Filtering and a Novel Site-specific x-Ion Fragment

    Kelstrup, C. D., Hekmat, O., Francavilla, C. & Olsen, Jesper Velgaard, 1 Jul 2011, In : Journal of Proteome Research. 10, 7, p. 2937-48 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    The association between anxiety and measures of glycaemia in a population-based diabetes screening programme

    Aujla, N., Davies, Michael Jonathan, Skinner, Timothy, Gray, L. J., Webb, D. R., Srinivasan, Balaji & Khunti, K., 1 Jul 2011, In : Diabetic Medicine. 28, 7, p. 785-788 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    Separation of the gluconeogenic and mitochondrial functions of pgc-1α through s6 kinase

    Lustig, Y., Ruas, J. L., Estall, J. L., Lo, J. C., Devarakonda, S., Laznik, D., Choi, J. H., Spiegelman, B. M., Ono, H. & Olsen, Jesper Velgaard, 15 Jun 2011, In : Genes & Development. 25, 12, p. 1232-1244 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    The ubiquitin- and SUMO-dependent signaling response to DNA double-strand breaks

    Bekker-Jensen, Simon Holst & Mailand, Niels, 12 Jun 2011, In : FEBS letters. 585, p. 2914-2919 6 p.

    Research output: Contribution to journalReviewResearchpeer-review

  40. Published

    Unique interaction pattern for a functionally biased ghrelin receptor agonist

    Sivertsen, B. B., Lang, M., Frimurer, T. M., Holliday, N. D., Bach, Anders, Els, S., Engelstoft, M. S., Petersen, P. S., Madsen, A. N., Schwartz, Thue W., Beck-Sickinger, A. G. & Holst, Birgitte, 10 Jun 2011, In : The Journal of Biological Chemistry. 286, 23, p. 20845-20860 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Pathogenesis and biomarkers of carcinogenesis in ulcerative colitis

    Thorsteinsdottir, S., Gudjónsson, Thorkell, Nielsen, Ole Haagen, Vainer, B. & Seidelin, Jakob Benedict, 7 Jun 2011, In : Nature Reviews. Gastroenterology & Hepatology. 8, 7, p. 395-404 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia

    Wesolowska, A., Gautier, L., Weinhold, N., Audouze, K. M. L., Brunak, Søren, Sicheritz-Ponten, T., Gupta, R., Dalgaard, M. D., Nielsen, B. F., Leffers, H., Borst, L., Helt, L. R., Nersting, J., Schmiegelow, Kjeld, Bak, Mads & Tommerup, Niels, 1 Jun 2011, In : Leukemia. 25, 6, p. 1001-1006 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes

    Pers, Tune H, Hansen, N. T., Hansen, K. L., Koefoed, P., Dworzynski, P., Miller, M. L., Flint, T. J., Mellerup, Erling Thyge, Dam, Henrik, Andreassen, O. A., Djurovic, S., Melle, I., Børglum, A. D., Werge, Thomas, Purcell, S., Ferreira, M. A., Kouskoumvekaki, I., Workman, C., Hansen, Torben, Mors, O. & Brunak, Søren, 11 Apr 2011, In : Genetic Epidemiology. 35, 5, p. 318-332 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. 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

  45. Published

    Andromeda - a peptide search engine integrated into the MaxQuant environment

    Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, Jesper Velgaard & Mann, Matthias, 1 Apr 2011, In : Journal of Proteome Research. 10, 4, p. 1794-805 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress

    Lukas, Claudia, Savic, V., Bekker-Jensen, Simon Holst, Doil, C., Neumann, B., Pedersen, R. S., Grøfte, M., Chan, K. L., Hickson, Ian David, Bartek, J. & Lukas, Jiri, 1 Mar 2011, In : Nature Cell Biology. 13, 3, p. 243-53 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level

    Danielsen, J. M. R., Sylvestersen, K. B., Bekker-Jensen, Simon Holst, Szklarczyk, D., Poulsen, J. W., Horn, H., Jensen, Lars Juhl, Mailand, Niels & Nielsen, Michael Lund, 1 Mar 2011, In : Molecular and Cellular Proteomics. 10, 3, p. M110.003590

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    Direct effects of FGF21 on glucose uptake in human skeletal muscle: implications for type 2 diabetes and obesity

    Mashili, F. L., Austin, R. L., Deshmukh, Atul Shahaji, Fritz, T., Caidahl, K., Bergdahl, K., Zierath, Juleen R, Chibalin, A. V., Moller, D. E., Kharitonenkov, A. & Krook, A., Mar 2011, In : Diabetes - Metabolism: Research and Reviews (Print Edition). 27, 3, p. 286-97 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Targeted proteomics for metabolic pathway optimization: application to terpene production

    Redding-Johanson, A. M., Batth, Tanveer Singh, Chan, R., Krupa, R., Szmidt, H. L., Adams, P. D., Keasling, J. D., Lee, T. S., Mukhopadhyay, A. & Petzold, C. J., Mar 2011, In : Metabolic Engineering. 13, 2, p. 194-203 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    Evidence that OGG1 glycosylase protects neurons against oxidative DNA damage and cell death under ischemic conditions

    Liu, D., Croteau, D. L., Souza-Pinto, N., Pitta, M., Tian, J., Wu, C., Jiang, H., Mustafa, K., Keijzers, Guido, Bohr, Vilhelm & Mattson, M. P., Feb 2011, In : Journal of Cerebral Blood Flow and Metabolism. 31, 2, p. 680-692 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    Bioinformatics-driven identification and examination of candidate genes for non-alcoholic fatty liver disease

    Banasik, Karina, Justesen, Johanne Marie, Hornbak, M., Krarup, N. T., Gjesing, Anette Marianne Prior, Sandholt, C. H., Søndergaard Jensen, T., Grarup, Niels, Andersson, Å., Jørgensen, T., Witte, D. R., Sandbæk, A., Lauritzen, T., Thorens, B., Brunak, Søren, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye & Hansen, Torben, 1 Jan 2011, In : P L o S One. 6, 1, p. e16542

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    Effective representation and storage of mass spectrometry-based proteomic data sets for the scientific community

    Olsen, Jesper Velgaard & Mann, Matthias, 1 Jan 2011, In : Science Signaling. 4, 160, p. pe7

    Research output: Contribution to journalJournal articleResearchpeer-review