The NNF Center for Protein Research

  1. 2014
  2. Published

    Proteomic analysis of arginine methylation sites in human cells reveals dynamic regulation during transcriptional arrest

    Sylvestersen, K. B., Horn, H., Jungmichel, S., Jensen, Lars Juhl & Nielsen, Michael Lund, 21 Feb 2014, In : Molecular & Cellular Proteomics. 13, p. 2072-2088 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds

    Geertz-Hansen, H. M., Blom, N., Feist, A., Brunak, Søren & Petersen, T. N., 13 Feb 2014, In : Proteins: Structure, Function, and Bioinformatics. 82, 9, p. 1819-1828 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. 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

  5. Published

    Gibberellic acid-induced aleurone layers responding to heat shock or tunicamycin provide insight into the N-glycoproteome, protein secretion, and endoplasmic reticulum stress

    Barba-Espín, G., Dedvisitsakul, P., Hägglund, Per Mårten, Svensson, B. & Finnie, C., 1 Feb 2014, In : Plant Physiology. 164, 2, p. 951-965 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Compass: A hybrid method for clinical and biobank data mining

    Krysiak-Baltyn, K., Nordahl Petersen, T., Audouze, K. M. L., Jørgensen, N., Ängquist, Lars & Brunak, Søren, Feb 2014, In : Journal of Biomedical Informatics. 47, p. 160-170

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI from Chlorella vulgaris in complex with its target DNA

    Redondo, P., Merino, N., Villate, M., Blanco, F. J., Montoya, Guillermo & Molina, Rafael, Feb 2014, In : Acta crystallographica. Section F, Structural biology communications. 70, Pt 2, p. 256-9 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism

    Zhao, B., Yang, Y., Wang, X., Chong, Z., Yin, R., Song, S., Zhao, C., Li, C., Huang, H., Sun, B., Wu, D., Jin, K., Song, M., Zhu, B., Jiang, G., Danielsen, J. M. R., Xu, G., Yang, Y. & Wang, H., Feb 2014, In : Nucleic Acids Research. 42, 3, p. 1593-1605 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

    Weinert, B. T., Iesmantavicius, V., Moustafa, T., Schölz, C., Wagner, S. A., Magnes, C., Zechner, R. & Choudhary, Chuna Ram, 31 Jan 2014, In : Molecular Systems Biology. 10, 1, p. 716 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    A direct role of Mad1 in the spindle assembly checkpoint beyond Mad2 kinetochore recruitment

    Kruse, Thomas, Larsen, M. S. Y., Sedgwick, G. G., Sigurdsson, J. O., Streicher, W., Olsen, Jesper Velgaard & Nilsson, Jakob, 29 Jan 2014, In : E M B O Reports. 15, p. 282-290

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Stable MCC binding to the APC/C is required for a functional spindle assembly checkpoint

    bmk286, bmk286 & Nilsson, Jakob, 25 Jan 2014, In : E M B O Reports. 15, p. 264-272

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Protein Interaction Screening for the Ankyrin Repeats and Suppressor of Cytokine Signaling (SOCS) Box (ASB) Family Identify Asb11 as a Novel Endoplasmic Reticulum Resident Ubiquitin Ligase

    Andresen, C. A., Smedegaard, S., Sylvestersen, K. B., Svensson, C., Iglesias Gato, Diego, Cazzamali, G., Nielsen, T. K., Nielsen, Michael Lund & Flores Morales, A., 24 Jan 2014, In : The Journal of Biological Chemistry. 289, 4, p. 2043-2054 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification

    Tessarz, P., Santos-Rosa, H., Robson, S. C., Sylvestersen, K. B., Nelson, C. J., Nielsen, Michael Lund & Kouzarides, T., 23 Jan 2014, In : Nature. 505, p. 564-568

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    New histone supply regulates replication fork speed and PCNA unloading

    Mejlvang, J., Feng, Y., Alabert, C., Neelsen, K. J., Jasencakova, Zuzana, Zhao, X., Lees, M., Sandelin, Albin Gustav, Pasero, P., Lopes, M. & Groth, Anja, 6 Jan 2014, In : Journal of Cell Biology. 204, 1, p. 29-43 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs

    Russo, Francesco, Di Bella, S., Bonnici, V., Laganà, A., Rainaldi, G., Pellegrini, M., Pulvirenti, A., Giugno, R. & Ferro, A., 1 Jan 2014, In : BMC Genomics. 15, S4.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    BuD, a helix-loop-helix DNA-binding domain for genome modification

    Stella, Stefano, Molina, Rafael, López-Méndez, B., Juillerat, A., Bertonati, C., Daboussi, F., Campos-Olivas, R., Duchateau, P. & Montoya, Guillermo, 1 Jan 2014, In : Acta Crystallographica Section D: Biological Crystallography. 70, 7, p. 2042-2052 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Comprehensive reconstruction and visualization of non-coding regulatory networks in human

    Bonnici, V., Russo, Francesco, Bombieri, N., Pulvirenti, A. & Giugno, R., 1 Jan 2014, In : Frontiers in Bioengineering and Biotechnology. 2, DEC, 69.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Expression, purification, crystallization and preliminary X-ray diffraction analysis of the novel modular DNA-binding protein BurrH in its apo form and in complex with its target DNA

    Stella, Stefano, Molina, Rafael, Bertonatti, C., Juillerrat, A. & Montoya, Guillermo, 1 Jan 2014, In : Acta Crystallographica Section F:Structural Biology Communications. 70, 1, p. 87-91 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Numb-dependent integration of pre-TCR and p53 function in T-cell precursor development

    Martin-Blanco, N. M., Checquolo, S., Del Gaudio, F., Palermo, R., Franciosa, Giulia, Di Marcotullio, L., Gulino, A., Canelles, M. & Screpanti, I., 1 Jan 2014, In : Cell Death and Disease. 5, e1472.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Purification, characterization and crystallization of the human 80S ribosome

    Khatter, H., Myasnikov, A. G., Mastio, L., Billas, I. M. L., Birck, C., Stella, Stefano & Klaholz, B. P., 1 Jan 2014, In : Nucleic Acids Research. 42, 6

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Create and preserve: proteostasis in development and aging is governed by Cdc48/p97/VCP

    Franz, A., Ackermann, Leena & Hoppe, T., Jan 2014, In : B B A - Reviews on Cancer. 1843, 1, p. 205-15 11 p.

    Research output: Contribution to journalReviewResearchpeer-review

  22. Published

    A comparison of protein kinases inhibitor screening methods using both enzymatic activity and binding affinity determination

    Rudolf, A. F., Skovgaard, T., Knapp, S., Jensen, Lars Juhl & Berthelsen, J., 2014, In : PloS one. 9, 6, p. 1-5 6 p., e98800.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations

    Bønnelykke, K., Sleiman, P., Nielsen, K., Kreiner-Møller, E., Mercader, J. M., Belgrave, D., den Dekker, H. T., Husby, A., Sevelsted, A., Faura-Tellez, G., Paternoster, L., Flaaten, R., Mølgaard, A., Smart, D. E., Thomsen, P. F., Rasmussen, Morten Arendt, Bonàs-Guarch, S., Holst, C., Nohr, E. A., Yadav, R., March, M. E., Blicher, T. H., Lackie, P. M., Jaddoe, V. W. V., Simpson, A., Holloway, J. W., Duijts, L., Custovic, A., Davies, D. E., Torrents, D., Gupta, R., Hollegaard, M. V., Hougaard, D. M., Hakonarson, H. & Bisgaard, Hans, 2014, In : Nature Genetics. 46, p. 51-55 5 p.

    Research output: Contribution to journalLetterResearchpeer-review

  24. Published

    Analogues of the natural product Sinefungin as inhibitors of EHMT1 and EHMT2

    Devkota, K., Lohse, Brian, Liu, Q., Wang, M., Stærk, Dan, Berthelsen, J. & Clausen, Rasmus Prætorius, 2014, In : A C S Medicinal Chemistry Letters. 5, 4, p. 293-297

    Research output: Contribution to journalLetterResearchpeer-review

  25. Published

    COMPARTMENTS: unification and visualization of protein subcellular localization evidence

    Binder, J. X., Pletscher-Frankild, S., Tsafou, K., Stolte, C., O'Donoghue, S. I., Schneider, R. & Jensen, Lars Juhl, 2014, In : Database. 2014, 9 p., bau012.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Development of a native Escherichia coli induction system for ionic liquid tolerance

    Frederix, M., Hütter, K., Leu, J., Batth, Tanveer Singh, Turner, W. J., Rüegg, T. L., Blanch, H. W., Simmons, B. A., Adams, P. D., Keasling, J. D., Thelen, M. P., Dunlop, M. J., Petzold, C. J. & Mukhopadhyay, A., 2014, In : PLOS ONE. 9, 7, p. e101115

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    Direct evidence of milk consumption from ancient human dental calculus

    Warinner, C., Hendy, J., Speller, C., Cappellini, Enrico, Fischer, R., Trachsel, C., Arneborg, J., Lynnerup, Niels, Craig, O. E., Swallow, D. M., Fotaki, Anna Katerina, Jersie-Christensen, R. R., Olsen, Jesper Velgaard, Liebert, A., Montalva, N., Fiddyment, S., Charlton, S., Mackie, Meaghan, Canci, A., Bouwman, A., Rühli, F., Gilbert, M Thomas P & Collins, M. J., 2014, In : Scientific Reports. 4, 6 p., 7104.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA

    Eriksson, Robert, Aagaard, L., Jensen, Lars Juhl, Borisova, L., Hørlück, D., Brunak, Søren & Hansen, E. H., 2014, In : Pharmacology Research & Perspectives. 2, 3, p. 1-10 e00038.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Helical propensity in an intrinsically disordered protein accelerates ligand binding

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

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Human chitotriosidase CHIT1 cross reacts with mammalian-like substrates

    Larsen, T., Yoshimura, Y., Voldborg, B. G. R., Cazzamali, G., Bovin, N. V., Westerlind, U., Palcic, M. M. & Leisner, Jørgen, 2014, In : F E B S Letters. 588, 5, p. 746-751 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. 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

  32. Published

    Lipid profiling and transcriptomic analysis reveals a functional interplay between estradiol and growth hormone in liver

    Fernández-Pérez, L., Santana-Farré, R., Mirecki-Garrido, M. D., García, I., Guerra, B., Mateo-Diaz, C., Iglesias Gato, Diego, Díaz-Chico, J. C., Flores Morales, A. & Díaz, M., 2014, In : P L o S One. 9, 19 p., e96305.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Molecular basis and regulation of OTULIN-LUBAC interaction

    Elliott, P. R., Nielsen, Sofie Vincents, Marco-Casanova, P., Fiil, B. K., Keusekotten, K., Mailand, Niels, Freund, S. M. V., Gyrd-Hansen, M. & Komander, D., 2014, In : Molecular Cell. 54, 3, p. 335-348 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Pathogens and host immunity in the ancient human oral cavity

    Warinner, C., Rodrigues, J. F. M., Vyas, R., Trachsel, C., Shved, N., Grossmann, J., Radini, A., Hancock, Y., Tito, R. Y., Fiddyment, S., Speller, C., Hendy, J., Charlton, S., Luder, H. U., Salazar-García, D. C., Eppler, E., Seiler, R., Hansen, Lars Hestbjerg, Samaniego Castruita, J. A., Barkow-Oesterreicher, S., Teoh, K. Y., Kelstrup, C., Olsen, Jesper Velgaard, Nanni, P., Kawai, T., Willerslev, Eske, von Mering, C., Lewis, C. M., Collins, M. J., Gilbert, M Thomas P, Rühli, F. & Cappellini, Enrico, 2014, In : Nature Genetics. 46, p. 336-344 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Predicting Kinase Activity in Angiotensin Receptor Phosphoproteomes Based on Sequence-Motifs and Interactions

    Bøgebo, R., Horn, H., Olsen, Jesper Velgaard, Gammeltoft, S., Jensen, Lars Juhl, Hansen, J. L. & Christensen, G. L., 2014, In : PLOS ONE. 9, 4, p. 1-9 9 p., e94672.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Protein-driven inference of miRNA-disease associations

    Mørk, S., Pletscher-Frankild, S., Palleja, A., Gorodkin, Jan & Jensen, Lars Juhl, 2014, In : Bioinformatics (Oxford, England). 30, 3, p. 392-397 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    REST mediates androgen receptor actions on gene repression and predicts early recurrence of prostate cancer

    Svensson, C., Ceder, J., Iglesias Gato, Diego, Chuan, Y. C., Pang, S. T., Bjartell, A., Martinez, R. M., Bott, L., Helczynski, L., Ulmert, D., Wang, Y., Niu, Y., Collins, C. & Flores Morales, A., 2014, In : Nucleic Acids Research. 42, 2, p. 999-1015 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)

    Cappellini, Enrico, Gentry, A., Palkopoulou, E., Ishida, Y., Cram, D., Roos, A., Watson, M., Johansson, U. S., Fernholm, B., Agnelli, P., Barbagli, F., Littlewood, D. T. J., Kelstrup, C., Olsen, Jesper Velgaard, Lister, A. M., Roca, A. L., Dalén, L. & Gilbert, M Thomas P, 2014, In : Zoological Journal of the Linnean Society. 170, 1, p. 222-232 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    SILAC-Based Temporal Phosphoproteomics

    Francavilla, C., Hekmat, O., Blagoev, B. & Olsen, Jesper Velgaard, 2014, Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC): Methods and Protocols. Warscheid, B. (ed.). Vol. 1188. p. 125-48 24 p. (Methods in molecular biology (Clifton, N.J.)).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterEducation

  40. 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

  41. 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

  42. Published

    Semantic Relation Discovery by using Co-occurrence Information

    Schulz, S., Catalina, M. C., Kreuzthaler, M., Minarro-Gimenez, J. A., Andersen, U., Jensen, A. B. & Maegaard, Bente, 2014. 6 p.

    Research output: Contribution to conferencePaperResearchpeer-review

  43. Published

    Species identification of archaeological skin objects from Danish bogs: comparison between mass spectrometry-based peptide sequencing and microscopy-based methods

    Brandt, Luise Ørsted, Schmidt, A. L., Mannering, U., Sarret, M., Kelstrup, C., Olsen, Jesper Velgaard & Cappellini, Enrico, 2014, In : PloS one. 9, 9, 10 p., e106875.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Systematic Analysis of the Crosstalk between Mitosis and DNA Damage by a Live Cell siRNA Screen

    Pedersen, R. S., 2014, Faculty of Science, University of Copenhagen. 143 p.

    Research output: Book/ReportPh.D. thesisResearch

  45. Published

    The impact of structural integrity and route of administration on the antibody specificity against three cow's milk allergens - a study in Brown Norway rats

    Madsen, J. L., Kroghsbo, S., Madsen, C. B., Pozdnyakova, I., Barkholt, V. & Bøgh, K. L., 2014, In : Clinical and Translational Allergy. 4, 12 p., 25.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    The use of combined heart rate response and accelerometry to assess the level and predictors of physical activity in tuberculosis patients in Tanzania

    Faurholt-Jepsen, M., Faurholt-Jepsen, D., Range, N., Praygod, G., Jeremiah, K., Aabye, M. G., Changalucha, J., Krarup, H., Christensen, Dirk Lund, Andersen, A. B., Brage, S. & Friis, Henrik, 2014, In : Epidemiology and Infection. 142, 6, p. 1334-1342 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. 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

  48. Published

    UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells

    Oka, Y., Varmark, H., Vitting-Seerup, Kristoffer, Beli, P., Waage, J. E., Hakobyan, A., Mistrik, M., Choudhary, Chuna Ram, Rohde, M., Bekker-Jensen, Simon Holst & Mailand, Niels, 2014, In : E M B O Reports. 15, 9, p. 956-964 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. 2013
  50. Published

    A minimal number of MELT repeats supports all functions of KNL1 in chromosome segregation

    Zhang, G., Lischetti, T. & Nilsson, Jakob, 20 Dec 2013, In : Journal of Cell Science. 127, p. 871-884

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    Heterologous expression and purification of an active human TRPV3 ion channel

    Kol, S., Braun, C. S., Thiel, G., Doyle, D. A., Sundström, M., Gourdon, Pontus Emanuel & Nissen, P., 1 Dec 2013, In : The F E B S Journal (Online). 280, 23, p. 6010-6021 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    eggNOG v4.0: nested orthology inference across 3686 organisms

    Powell, S., Forslund, K., Szklarczyk, D. M., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, Lars Juhl, von Mering, C. & Bork, P., 1 Dec 2013, In : Nucleic Acids Research. 42, D1, p. D231-D239 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Published

    STITCH 4: integration of protein-chemical interactions with user data

    Kuhn, M., Szklarczyk, D. M., Pletscher-Frankild, S., Blicher, T. H., von Mering, C., Jensen, Lars Juhl & Bork, P., 28 Nov 2013, In : Nucleic Acids Research. 42, D1, p. D401-D407 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. Published

    ATR Prohibits Replication Catastrophe by Preventing Global Exhaustion of RPA

    Toledo Lazaro, Luis Ignacio, Altmeyer, M., Rask, M., Lukas, Claudia, Larsen, D. H., Povlsen, L. K., Bekker-Jensen, Simon Holst, Mailand, Niels, Bartek, J. & Lukas, Jiri, 21 Nov 2013, In : Cell. 155, 5, p. 1088-1103 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  55. Published

    JMJD1C demethylates MDC1 to regulate the RNF8 and BRCA1-mediated chromatin response to DNA breaks

    Watanabe, S., Watanabe, K., Akimov, V., Bartkova, J., Blagoev, B., Lukas, Jiri & Bartek, J., 17 Nov 2013, In : Nature Structural and Molecular Biology. 20, p. 1425-1433

    Research output: Contribution to journalJournal articleResearchpeer-review

  56. Published

    ATR-Chk1-APC/C-dependent stabilization of Cdc7-ASK (Dbf4) kinase is required for DNA lesion bypass under replication stress

    Yamada, M., Watanabe, K., Mistrik, M., Vesela, E., Protivankova, I., Mailand, Niels, Lee, M. H., Masai, H., Lukas, Jiri & Bartek, J., 15 Nov 2013, In : Genes & Development. 27, 22, p. 2459-2472 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    The PI3-kinase isoform p110δ is essential for cell transformation induced by the D816V mutant of c-Kit in a lipid-kinase-independent manner

    Sun, J., Mohlin, S., Lundby, Alicia, Kazi, J. U., Hellman, U., Påhlman, S., Olsen, Jesper Velgaard & Rönnstrand, L., 11 Nov 2013, In : Oncogene.

    Research output: Contribution to journalJournal articleResearchpeer-review

  58. Published

    Hvordan når kvinderne toppen?

    Lundby, Alicia, Gerken, M., Jess, T. & Dahl, Tais Wittchen, 5 Nov 2013, In : Berlingske Tidende.

    Research output: Contribution to journalContribution to newspaper - Comment/debateCommunication

  59. Published

    Status of large-scale analysis of post-translational modifications by mass spectrometry

    Olsen, Jesper Velgaard & Mann, Matthias, 1 Nov 2013, In : Molecular & Cellular Proteomics. 12, p. 3444-52

    Research output: Contribution to journalJournal articleResearchpeer-review

  60. Published

    The DNA damage checkpoint precedes activation of ARF in response to escalating oncogenic stress during tumorigenesis

    Evangelou, K., Bartkova, J., Kotsinas, A., Pateras, I. S., Liontos, M., Velimezi, G., Kosar, M., Liloglou, T., Trougakos, I. P., Dyrskjot, L., Andersen, C. L., Papaioannou, M., Drosos, Y., Papafotiou, G., Hodny, Z., Sosa-Pineda, B., Wu, X., Klinakis, A., Ørntoft, T. F., Lukas, Jiri, Bartek, J. & Gorgoulis, V. G., 1 Nov 2013, In : Cell Death and Differentiation. 20, 11, p. 1485-1497 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  61. 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

  62. Published

    The Chromatin Scaffold Protein SAFB1 Renders Chromatin Permissive for DNA Damage Signaling

    Altmeyer, M., Toledo Lazaro, Luis Ignacio, Gudjónsson, Thorkell, Grøfte, M., Rask, M., Lukas, Claudia, Akimov, V., Blagoev, B., Bartek, J. & Lukas, Jiri, 24 Oct 2013, In : Molecular Cell. 52, 2, p. 206-220

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    Are graph databases ready for bioinformatics?

    Have, C. T. & Jensen, Lars Juhl, 21 Oct 2013, In : Bioinformatics (Online). 2 p.

    Research output: Contribution to journalEditorialResearch

  64. Published

    How unfinished business from S-phase affects mitosis and beyond

    Mankouri, H. W., Huttner, D. & Hickson, Ian David, 16 Oct 2013, In : EMBO Journal. 32, 20, p. 2661-71 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. Published

    A new cellular stress response that triggers centriolar satellite reorganization and ciliogenesis

    Villumsen, B. H., Danielsen, J. R., Povlsen, L., Sylvestersen, K. B., Merdes, A., Beli, P., Yang, Y., Choudhary, Chuna Ram, Nielsen, Michael Lund, Mailand, Niels & Bekker-Jensen, Simon Holst, 11 Oct 2013, In : E M B O Journal. 32, 23, p. 3029-3040

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. Published

    X-linked inhibitor of apoptosis (XIAP) deficiency: The spectrum of presenting manifestations beyond hemophagocytic lymphohistiocytosis

    Speckmann, C., Lehmberg, K., Albert, M. H., Damgaard, R. B., Fritsch, M., Gyrd-Hansen, M., Rensing-Ehl, A., Vraetz, T., Grimbacher, B., Salzer, U., Fuchs, I., Ufheil, H., Belohradsky, B. H., Hassan, A., Cale, C. M., Elawad, M., Strahm, B., Schibli, S., Lauten, M., Kohl, M., Meerpohl, J. J., Rodeck, B., Kolb, R., Eberl, W., Soerensen, J., von Bernuth, H., Lorenz, M., Schwarz, K., zur Stadt, U. & Ehl, S., 1 Oct 2013, In : Clinical Immunology. 149, 1, p. 133-141 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  67. 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

  68. Published

    Small Angle X-Ray Scattering Studies of Mitochondrial Glutaminase C Reveal Extended Flexible Regions, and Link Oligomeric State with Enzyme Activity

    Møller, M., Nielsen, S. S., Ramachandran, S., Li, Y., Tria, G., Streicher, W., Petoukhov, M. V., Cerione, R. A., Gillilan, R. E. & Vestergaard, Bente, 30 Sep 2013, In : P L o S One. 8, 9, e74783.

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk

    Blair, D. R., Lyttle, C. S., Mortensen, J. M., Bearden, C. F., Jensen, A. B., Khiabanian, H., Melamed, R., Rabadan, R., Bernstam, E. V., Brunak, Søren, Jensen, Lars Juhl, Nicolae, D., Shah, N. H., Grossman, R. L., Cox, N. J., White, K. P. & Rzhetsky, A., 26 Sep 2013, In : Cell. 155, 1, p. 70-80 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. Published

    Functional Proteomics Defines the Molecular Switch Underlying FGF Receptor Trafficking and Cellular Outputs

    Francavilla, C., Rigbolt, K. T. G., Emdal, Kristina Bennet, Carraro, G., Vernet, E., Bekker-Jensen, D. B., Streicher, W., Wikström, M., Sundström, M., Bellusci, S., Cavallaro, U., Blagoev, B. & Olsen, Jesper Velgaard, 26 Sep 2013, In : Molecular Cell. 51, 6, p. 707-22 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  71. Published

    A computational approach to chemical etiologies of diabetes

    Audouze, K. M. L., Brunak, Søren & Grandjean, P., 19 Sep 2013, In : Scientific Reports. 3, p. 2712 2712.

    Research output: Contribution to journalJournal articleResearchpeer-review

  72. Published

    Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells

    Galli, G. G., Carrara, M., Francavilla, C., Honnens de Lichtenberg, Kristian, Olsen, Jesper Velgaard, Calogero, R. A. & Lund, Anders H., 16 Sep 2013, In : Molecular and Cellular Biology.

    Research output: Contribution to journalJournal articleResearchpeer-review

  73. Published

    Covalent Trapping of Methyllycaconitine at the α4-α4 Interface of the α4β2 Nicotinic Acetylcholine Receptor: ANTAGONIST BINDING SITE AND MODE OF RECEPTOR INHIBITION REVEALED

    Absalom, N. L., Quek, G., Lewis, T. M., Qudah, T., von Arenstorff, I., Ambrus, J. I., Harpsøe, Kasper, Karim, N., Balle, T., McLeod, M. D. & Chebib, M., 13 Sep 2013, In : The Journal of Biological Chemistry. 288, 37, p. 26521-32 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  74. Published

    PICH: A DNA Translocase Specially Adapted for Processing Anaphase Bridge DNA

    Biebricher, A., Hirano, S., Enzlin, J., Wiechens, N., Streicher, W., Huttner, D., Wang, L., Nigg, E., Owen-Hughes, T., Liu, Ying, Peterman, E., Wuite, G. & Hickson, Ian David, 12 Sep 2013, In : Molecular Cell. 51, 5, p. 691-701 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. Published

    Extracellular circulating viral microRNAs: Current knowledge and perspectives

    Laganà, A., Russo, Francesco, Veneziano, D., Bella, S. D., Giugno, R., Pulvirenti, A., Croce, C. M. & Ferro, A., 11 Sep 2013, In : Frontiers in Genetics. 4, JUN, Article 120.

    Research output: Contribution to journalReviewResearchpeer-review

  76. Published

    Phosphoproteomics taken to heart

    Lundby, Alicia & Olsen, Jesper Velgaard, 1 Sep 2013, In : Cell Cycle. 12, 17, p. 2707-2708 2 p.

    Research output: Contribution to journalEditorialResearchpeer-review

  77. Published

    Best practices in bioinformatics training for life scientists

    Via, A., Blicher, T., Bongcam-Rudloff, E., Brazas, M. D., Brooksbank, C., Budd, A., De Las Rivas, J., Dreyer, J., Fernandes, P. L., van Gelder, C., Jacob, J., Jimenez, R. C., Loveland, J., Moran, F., Mulder, N., Nyrönen, T., Rother, K., Schneider, M. V. & Attwood, T. K., Sep 2013, In : Briefings in Bioinformatics. 14, 5, p. 528-37 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  78. Published

    Functional intersection of ATM and DNA-dependent protein kinase catalytic subunit in coding end joining during V(D)J recombination

    Lee, B., Gapud, E. J., Zhang, S., Dorsett, Y., Bredemeyer, A., George, R., Callen, E., Daniel, J. A., Osipovich, O., Oltz, E. M., Bassing, C. H., Nussenzweig, A., Lees-Miller, S., Hammel, M., Chen, B. P. C. & Sleckman, B. P., Sep 2013, In : Molecular and Cellular Biology. 33, 18, p. 3568-79 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. 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

  80. Published

    Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation

    Weinert, B. T., Schölz, C., Wagner, S. A., Iesmantavicius, V., Su, D., Daniel, J. A. & Choudhary, Chuna Ram, 29 Aug 2013, In : Cell Reports. 4, 4, p. 842-51 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  81. Published

    Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

    Börnigen, D., Pers, T. H., Thorrez, L., Huttenhower, C., Moreau, Y. & Brunak, Søren, 5 Aug 2013, In : Nucleic Acids Research. 41, 18, p. e171

    Research output: Contribution to journalJournal articleResearchpeer-review

  82. Published

    TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells

    Hekmat, O., Munk, S., Fogh, L., Yadav, R., Francavilla, C., Horn, H., Würtz, S. Ø., Schrohl, A., Damsgaard, B., Romer, M. U., Belling, Kirstine G, Jensen, N. F., Gromova, I., Bekker-Jensen, D. B., Moreira, José, Jensen, Lars Juhl, Gupta, R., Lademann, U. A., Brünner, Nils, Olsen, Jesper Velgaard & Stenvang, Jan, 5 Aug 2013, In : Journal of Proteome Research. 12, 9, p. 4136-4151 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

    Kouskoumvekaki, I., Shublaq, N. & Brunak, Søren, 1 Aug 2013, In : Briefings in Bioinformatics. 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  84. Published

    Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

    Weinert, B. T., Iesmantavicius, V., Wagner, S. A., Schölz, C., Gummesson, Bertil, Beli, P., Nyström, T. & Choudhary, Chuna Ram, 25 Jul 2013, In : Molecular Cell. 51, 2, p. 265-272 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  85. Published

    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

    Orlando, L. A. A., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, Anders, Stiller, M., Schubert, M., Cappellini, Enrico, Petersen, Bent, Moltke, Ida, Johnson, P. L. F., Fumagalli, M., Mouatt, J. T. V., Raghavan, M., Korneliussen, Thorfinn Sand, Malaspinas, A. S., Vogt, J., Szklarczyk, D. M., Kelstrup, C., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A. M. V., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G. D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J. F., Weinstock, J., Gregersen, K., Røed, K. H., Eisenmann, V., Rubin, C. J., Miller, D. C., Antczak, D. F., Bertelsen, M. F., Brunak, S., Al-Rasheid, K. A. S., Ryder, O., Andersson, L., Mundy, J., Krogh, Anders, Gilbert, M Thomas P, Kjær, Kurt H., Sicheritz-Pontén, T., Jensen, Lars Juhl, Olsen, Jesper Velgaard, Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J. & Willerslev, Eske, 4 Jul 2013, In : Nature. 499, 7456, p. 74-78 5 p.

    Research output: Contribution to journalLetterResearchpeer-review

  86. Published

    CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer

    Cepeda, D., Ng, H., Sharifi, H. R., Mahmoudi, S., Cerrato, V. S., Fredlund, E., Magnusson, K., Nilsson, H., Malyukova, A., Rantala, J., Klevebring, D., Viñals, F., Bhaskaran, N., Zakaria, S. M., Rahmanto, A. S., Grotegut, S., Nielsen, Michael Lund, Szigyarto, C. A., Sun, D., Lerner, M., Navani, S., Widschwendter, M., Uhlén, M., Jirström, K., Pontén, F., Wohlschlegel, J., Grandér, D., Spruck, C., Larsson, L. & Sangfelt, O., 3 Jul 2013, In : E M B O Molecular Medicine (Online). 5, 7, p. 1067-1086 20 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  87. Published

    Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

    Nguyen, E. D., Meiler, J., Norn, Christoffer & Frimurer, Thomas Michael, 2 Jul 2013, In : PLOS ONE. 8, 7, p. e67302 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  88. Published

    Disease-causing mutations in the XIAP BIR2 domain impair NOD2-dependent immune signalling

    Damgaard, R. B., Fiil, B. K., Speckmann, C., Yabal, M., Stadt, U. Z., Bekker-Jensen, Simon Holst, Jost, P. J., Ehl, S., Mailand, Niels & Gyrd-Hansen, M., 1 Jul 2013, In : E M B O Journal. 5, p. 1278-1295 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  89. Published

    MetaRanker 2.0: a web server for prioritization of genetic variation data

    Pers, T. H., Dworzynski, P., Thomas, C. E., Hansen, K. L. & Brunak, Søren, 1 Jul 2013, In : Nucleic Acids Research. 41, W1, p. W104-W108

    Research output: Contribution to journalJournal articleResearchpeer-review

  90. 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

  91. Published

    OTULIN Restricts Met1-Linked Ubiquitination to Control Innate Immune Signaling

    Fiil, B. K., Damgaard, R. B., Wagner, S. A., Keusekotten, K., Fritsch, M., Bekker-Jensen, Simon Holst, Mailand, Niels, Choudhary, Chuna Ram, Komander, D. & Gyrd-Hansen, M., 27 Jun 2013, In : Molecular Cell. 50, 6, p. 818-30 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  92. Published

    Guarding against Collateral Damage during Chromatin Transactions

    Altmeyer, M. & Lukas, Jiri, 20 Jun 2013, In : Cell. 153, 7, p. 1431-4 4 p.

    Research output: Contribution to journalReviewResearchpeer-review

  93. Published

    The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

    Pafilis, E., Pletscher-Frankild, S., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, A., Arvanitidis, C. & Jensen, Lars Juhl, 18 Jun 2013, In : PloS one. 8, 6, p. e65390

    Research output: Contribution to journalJournal articleResearchpeer-review

  94. Published

    RNF111/Arkadia is a SUMO-targeted ubiquitin ligase that facilitates the DNA damage response

    Poulsen, S. L., Hansen, R. K., Wagner, S. A., van Cuijk, L., van Belle, G. J., Streicher, W., Wikström, M., Choudhary, Chuna Ram, Houtsmuller, A. B., Marteijn, J. A., Bekker-Jensen, Simon Holst & Mailand, Niels, 10 Jun 2013, In : Journal of Cell Biology. 201, 6, p. 797-807 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    53BP1 mediates productive and mutagenic DNA repair through distinct phosphoprotein interactions

    Callen, E., Wong, N., Chen, H., Faryabi, R. B., Polato, F., Santos, M., Nussenzweig, A., Kruhlak, M. J., Di Virgilio, M., Nussenzweig, M. C., Nieto-Soler, M., Fernandez-Capetillo, O., Starnes, L. M., Daniel, J. A., Wesemann, D. R., Alt, F. W., Lee, J., Ge, K., Tubbs, A. & Sleckman, B. P., 6 Jun 2013, In : Cell. 153, 6, p. 1266-1280 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    OTULIN antagonizes LUBAC signaling by specifically hydrolyzing met1-linked polyubiquitin

    Keusekotten, K., Elliott, P. R., Kulathu, Y., Wauer, T., Hospenthal, M. K., Komander, D., Glockner, L., Krappmann, D., Fiil, B. K., Damgaard, R. B., Gyrd-Hansen, M. & Hofmann, K., 6 Jun 2013, In : Cell. 153, 6, p. 1312-1326 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. 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

  98. Published

    In Vivo Phosphoproteomics Analysis Reveals the Cardiac Targets of β-Adrenergic Receptor Signaling

    Lundby, Alicia, Andersen, M. N., Steffensen, Annette Buur, Horn, H., Kelstrup, C. D., Francavilla, C., Jensen, Lars Juhl, Schmitt, Nicole, Thomsen, Morten Bækgaard & Olsen, Jesper Velgaard, 4 Jun 2013, In : Science Signaling. 6, 278, p. rs11 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  99. Published

    Structures of down syndrome kinases, DYRKs, reveal mechanisms of kinase activation and substrate recognition

    Soundararajan, M., Roos, A. K., Savitsky, P., Filippakopoulos, P., Kettenbach, A. N., Olsen, Jesper Velgaard, Gerber, S., Eswaran, J., Knapp, S. & Elkins, J. M., 4 Jun 2013, In : Structure. 21, 6, p. 986-996 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. Published

    Estrogens regulate the hepatic effects of growth hormone, a hormonal interplay with multiple fates

    Fernández-Pérez, L., Guerra, B., Díaz-Chico, J. C. & Flores Morales, A., 2 Jun 2013, In : Frontiers in Endocrinology. 4, 12 p., 66.

    Research output: Contribution to journalReviewResearchpeer-review

  101. Published

    Acetylation dynamics of human nuclear proteins during the ionizing radiation-induced DNA damage response

    Bennetzen, M., Andersen, J. S., Lasen, D. H., Dinant, C., Watanabe, S., Bartek, J. & Lukas, Jiri, 1 Jun 2013, In : Cell Cycle. 12, 11, p. 1688-1695 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  102. 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