The NNF Center for Protein Research

  1. 2011
  2. Published

    GeLCMS for in-depth protein characterization and advanced analysis of proteomes

    Lundby, Alicia & Olsen, Jesper Velgaard, 1 Jan 2011, Gel-Free Proteomics Methods and Protocols. Vol. 753. p. 143-55 13 p.

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

  3. Published

    Phospho.ELM: a database of phosphorylation sites--update 2011

    Dinkel, H., Chica, C., Via, A., Gould, C. M., Jensen, Lars Juhl, Gibson, T. J. & Diella, F., 1 Jan 2011, In : Nucleic Acids Symposium Series. 39, Database issue, p. D261-7

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    The SOCS2 Ubiquitin Ligase Complex Regulates Growth Hormone Receptor Levels

    Vesterlund, M., Zadjali, F., Persson, T., Nielsen, Michael Lund, Kessler, B. M., Norstedt, G. & Flores Morales, A., 1 Jan 2011, In : P L o S One. 6, 9, p. e25358 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1

    Blasius, M., Forment, J. V., Thakkar, N., Wagner, S. A., Choudhary, Chuna Ram & Jackson, S. P., 2011, In : Genome Biology (Online Edition). 12, 8, p. R78

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    A secretory system for bacterial production of high-profile protein targets

    Kotzsch, A., Vernet, E., Hammarström, M., Berthelsen, J., Weigelt, J., Gräslund, S. & Sundström, M., 2011, In : Protein Science. 20, 3, p. 597-609 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Allosteric and orthosteric sites in CC chemokine receptor (CCR5), a chimeric receptor approach

    Thiele, S., Steen, A., Jensen, P. C., Mokrosinski, J., Frimurer, Thomas Michael & Rosenkilde, Mette, 2011, In : Journal of Biological Chemistry. 286, 43, p. 37543-54 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    An Aboriginal Australian genome reveals separate human dispersals into Asia

    Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, Simon, Albrechtsen, Anders, Skotte, L., Lindgreen, Stinus, Metspalu, M., Jombart, T., Kivisild, T., Zhai, W., Eriksson, A., Manica, A., Orlando, L., De La Vega, F. M., Tridico, S., Metspalu, E., Nielsen, K., Avila Arcos, M. D. C., Moreno Mayar, José Victor, Muller, C., Dortch, J., Gilbert, M Thomas P, Lund, O., Wesolowska, A., Karmin, M., Weinert, L. A., Wang, B., Li, J., Tai, S., Xiao, F., Hanihara, T., van Driem, G., Jha, A. R., Ricaut, F., de Knijff, P., Migliano, A. B., Gallego Romero, I., Kristiansen, Karsten, Lambert, D. M., Brunak, Søren, Forster, P., Brinkmann, B., Nehlich, O., Bunce, M., Richards, M., Gupta, R., Bustamante, C. D., Krogh, Anders, Foley, R. A., Lahr, M. M., Balloux, F., Sicheritz-Pontén, T., Villems, R., Nielsen, Rasmus, Wang, J. & Willerslev, Eske, 2011, In : Science. 334, 6052, p. 94-98 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    An anatomically oriented breast coordinate system for mammogram analysis

    Brandt, S., Karemore, Gopal, Karssemeijer, N. & Nielsen, Mads, 2011, In : I E E E Transactions on Medical Imaging. 30, 10, p. 1841-1851 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    BioStar: an online question & answer resource for the bioinformatics community

    Parnell, L. D., Lindenbaum, P., Shameer, K., Dall'Olio, G. M., Swan, D. C., Jensen, Lars Juhl, Cockell, S. J., Pedersen, B. S., Mangan, M. E., Miller, C. A. & Albert, I., 2011, In : P L o S Computational Biology (Online). 7, 10, p. e1002216

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Cdc20 control of cell fate during prolonged mitotic arrest: do Cdc20 protein levels affect cell fate in response to antimitotic compounds?

    Nilsson, Jakob, 2011, In : BioEssays. 33, 12, p. 903-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Enterotypes of the human gut microbiome: [Plus]Corrigendum [Plus]Addendum

    Arumugam, Mani, Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J., dos Santos, M. B. Q., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, Torben, Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H. B., Nielsen, Trine, Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E. G., Wang, J., Guarner, F., Pedersen, Oluf Borbye, de Vos, W. M., Brunak, Søren, Doré, J., Antolín, M., Artiguenave, F., Blottiere, H. M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Kristiansen, Karsten & MetaHIT Consortium, M. C., 2011, In : Nature. 473, 7346, p. 174-180 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells

    Pines, A., Kelstrup, C. D., Vrouwe, M. G., Puigvert, J. C., Typas, D., Misovic, B., de Groot, A., von Stechow, L., van de Water, B., Danen, E. H. J., Vrieling, H., Mullenders, L. H. F. & Olsen, Jesper Velgaard, 2011, In : Molecular and Cellular Biology. 31, 24, p. 4964-77 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis

    Berchtold, L. A., Størling, Z. M., Ortis, F., Lage, K., Bang-Berthelsen, C., Bergholdt, R., Hald, J., Brorsson, C. A., Eizirik, D. L., Pociot, Flemming, Brunak, Søren & Størling, Joachim, 2011, In : PNAS Early Edition. 108, 37, p. E681-8

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Identification of animal species in skin clothing from museum collections

    Schmidt, A. L., Gilbert, M Thomas P, Cappellini, Enrico & Olsen, Jesper Velgaard, 2011. 8 p.

    Research output: Contribution to conferencePaperResearchpeer-review

  16. Published

    Inhibitor of apoptosis (IAP) proteins in regulation of inflammation and innate immunity

    Damgaard, R. B. & Gyrd-Hansen, M., 2011, In : Discovery Medicine. 11, 58, p. 221-31 11 p.

    Research output: Contribution to journalReviewResearchpeer-review

  17. Published

    Phosphorylation of the yeast γ-tubulin Tub4 regulates microtubule function

    Lin, T., Gombos, L., Neuner, A., Sebastian, D., Olsen, Jesper Velgaard, Hrle, A., Benda, C. & Schiebel, E., 2011, In : P L o S One. 6, 5, p. e19700

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington

    Waters, M. R., Stafford jr., T., McDonald, H. G., Gustafson, C., Rasmussen, M., Cappellini, Enrico, Olsen, Jesper Velgaard, Szklarczyk, D. M., Jensen, Lars Juhl, Gilbert, M Thomas P & Willerslev, Eske, 2011, In : Science. 334, 6054, p. 351-353 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Predictive mutagenesis of ligation-independent cloning (LIC) vectors for protein expression and site-specific chemical conjugation

    Vernet, E., Sauer, J., Andersen, P. A., Jensen, Knud Jørgen & Voldborg, B. G. R., 2011, In : Analytical Biochemistry. 414, 2, p. 312-314 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. 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

  21. Published

    Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation

    Weinert, B. T., Wagner, S. A., Horn, H., Henriksen, P., Liu, W. R., Olsen, Jesper Velgaard, Jensen, Lars Juhl & Choudhary, Chuna Ram, 2011, In : Science Signaling. 4, 183, p. ra48

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Screening of genetic parameters for soluble protein expression in Escherichia coli

    Vernet, E., Kotzsch, A., Voldborg, B. & Sundström, M., 2011, In : Protein Expression and Purification. 77, 1, p. 104-11 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    SignalP 4.0: discriminating signal peptides from transmembrane regions

    Petersen, T. N., Brunak, Søren, von Heijne, G. & Nielsen, H., 2011, In : Nature Methods. 8, 10, p. 785-6 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing

    Fedorov, O., Huber, K., Eisenreich, A., Filippakopoulos, P., King, O., Bullock, A. N., Szklarczyk, D., Jensen, Lars Juhl, Fabbro, D., Trappe, J., Rauch, U., Bracher, F. & Knapp, S., 2011, In : Chemistry & Biology. 18, 1, p. 67-76 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Structural basis for c-KIT inhibition by the suppressor of cytokine signaling 6 (SOCS6) ubiquitin ligase

    Zadjali, F., Pike, A. C. W., Vesterlund, M., Sun, J., Wu, C., Li, S. S. C., Rönnstrand, L., Knapp, S., Bullock, A. N. & Flores Morales, A., 2011, In : Journal of Biological Chemistry. 286, 1, p. 480-90 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

    Rigbolt, K. T. G., Prokhorova, T., Akimov, V., Løkkegaard, Jeanette, Johansen, P. T., Kratchmarova, I., Kassem, M. S. E., Mann, Matthias, Olsen, Jesper Velgaard & Blagoev, B., 2011, In : Science Signaling. 4, 164, p. rs3

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

    Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., Jensen, Lars Juhl & von Mering, C., 2011, In : Nucleic Acids Research. 39, Database issue, p. D561-8

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. 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

  29. Published

    The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks

    Meerang, M., Ritz, D., Paliwal, S., Garajova, Z., Bosshard, M., Mailand, Niels, Janscak, P., Hübscher, U., Meyer, H. & Ramadan, K., 2011, In : Nature Cell Biology. 13, 11, p. 1376-82 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

    Raes, J., Letunic, I., Yamada, T., Jensen, Lars Juhl & Bork, P., 2011, In : Molecular Systems Biology. 7, p. 473

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

    Chhabra, S. R., Joachimiak, M. P., Petzold, C. J., Zane, G. M., Price, M. N., Reveco, S. A., Fok, V., Johanson, A. R., Batth, Tanveer Singh, Singer, M., Chandonia, J., Joyner, D., Hazen, T. C., Arkin, A. P., Wall, J. D., Singh, A. K. & Keasling, J. D., 2011, In : PLOS ONE. 6, 6, p. e21470

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Using electronic patient records to discover disease correlations and stratify patient cohorts

    Roque, F. S., Jensen, P. B., Schmock, H., Dalgaard, M., Andreatta, M., Hansen, T., Søeby, K., Bredkjær, S., Juul, Anders, Werge, Thomas, Jensen, Lars Juhl & Brunak, Søren, 2011, In : P L o S Computational Biology. 7, 8, p. e1002141 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. 2010
  34. Published

    Assembly and function of DNA double-strand break repair foci in mammalian cells

    Bekker-Jensen, Simon Holst & Mailand, Niels, 10 Dec 2010, In : D N A Repair. 9, 12, p. 1219-28 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation

    Nagaraj, N., D'Souza, R. C. J., Cox, J., Olsen, Jesper Velgaard & Mann, M., 3 Dec 2010, In : Journal of Proteome Research. 9, 12, p. 6786-94 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Dipeptidyl peptidase-4 inhibitors administered in combination with metformin result in an additive increase in the plasma concentration of active GLP-1

    Migoya, E. M., Bergeron, R., Miller, J. L., Snyder, R. N. K., Tanen, M., Hilliard, D., Weiss, B., Larson, P., Gutierrez, M., Jiang, G., Liu, F., Pryor, K. A., Yao, J., Zhu, L., Holst, Jens Juul, Deacon, Carolyn F., Herman, G., Thornberry, N., Amatruda, J., Williams-Herman, D., Wagner, J. A. & SinhaRoy, R., 1 Dec 2010, In : Clinical Pharmacology and Therapeutics. 88, 6, p. 801-8 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Bioinformatics training: a review of challenges, actions and support requirements

    Schneider, M. V., Watson, J., Attwood, T., Rother, K., Budd, A., McDowall, J., Via, A., Fernandes, P., Nyronen, T., Blicher, T., Jones, P., Blatter, M., De Las Rivas, J., Judge, D. P., van der Gool, W. & Brooksbank, C., Nov 2010, In : Briefings in Bioinformatics. II, 6, p. 544-51 8 p.

    Research output: Contribution to journalReviewResearchpeer-review

  38. Published

    Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

    Vermeulen, M., Eberl, H. C., Matarese, F., Marks, H., Denissov, S., Butter, F., Lee, K. K., Olsen, Jesper Velgaard, Hyman, A. A., Stunnenberg, H. G. & Mann, M., 17 Sep 2010, In : Cell. 142, 6, p. 967-80 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Incentive and entrenchment effects in European ownership

    Bennedsen, Morten & Nielsen, K. M., Sep 2010, In : Journal of Banking & Finance. 34, 9, p. 2212-2229

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Variability in the incidence of miRNAs and genes in fragile sites and the role of repeats and CpG islands in the distribution of genetic material

    Laganà, A., Russo, Francesco, Sismeiro, C., Giugno, R., Pulvirenti, A. & Ferro, A., 11 Aug 2010, In : PLoS ONE. 5, 6, e11166.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Biophysical characterization of the fluorescent protein voltage probe VSFP2.3 based on the voltage-sensing domain of Ci-VSP

    Lundby, Alicia, Akemann, W. & Knöpfel, T., 6 Aug 2010, In : European Biophysics Journal. 39, 12, p. 1625-1635 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Predicting post-translational lysine acetylation using support vector machines

    Gnad, F., Ren, S., Choudhary, Chuna Ram, Cox, J. & Mann, M., 1 Jul 2010, In : Bioinformatics. 26, 13, p. 1666-8 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Quantitative phosphoproteomics dissection of 7TM receptor signaling using full and biased agonists

    Christensen, G. L., Kelstrup, C., Lyngsø, C., Sarwar, U., Bøgebo, R., Sheikh, S. P., Gammeltoft, S., Olsen, Jesper Velgaard & Hansen, J. L., Jul 2010, In : Molecular and Cellular Proteomics. 9, 7, p. 1540-53 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Reflect: a practical approach to web semantics

    O'Donoghue, S. I., Horn, H., Pafilisa, E., Haag, S., Kuhn, M., Satagopam, V. P., Schneider, R. & Jensen, Lars Juhl, Jul 2010, In : Journal of Web Semantics. 8, 2-3, p. 182-189

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    The phosphoproteome of toll-like receptor-activated macrophages

    Weintz, G., Olsen, Jesper Velgaard, Frühauf, K., Niedzielska, M., Amit, I., Jantsch, J., Mages, J., Frech, C., Dölken, L., Mann, M. & Lang, R., 8 Jun 2010, In : Molecular Systems Biology. 6, p. 371

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Crystallization and preliminary crystallographic analysis of the catalytic module of endolysin from Cp-7, a phage infecting Streptococcus pneumoniae

    Silva-Martin, N., Molina, Rafael, Angulo, I., Mancheño, J. M., García, P. & Hermoso, J. A., 1 Jun 2010, In : Acta Crystallographica Section F: Structural Biology Communications. 66, Pt 6, p. 670-3 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Decoding signalling networks by mass spectrometry-based proteomics

    Choudhary, Chuna Ram & Mann, Matthias, 1 Jun 2010, In : Nature Reviews. Molecular Cell Biology. 11, 6, p. 427-39 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    Protein annotation in the era of personal genomics

    Blicher, T., Gupta, R., Wesolowska, A., Jensen, Lars Juhl & Brunak, Søren, 1 Jun 2010, In : Current Opinion in Structural Biology. 20, 3, p. 335-41 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Nitric oxide increases cyclic GMP levels, AMP-activated protein kinase (AMPK)alpha1-specific activity and glucose transport in human skeletal muscle

    Deshmukh, Atul Shahaji, Long, Y. C., de Castro Barbosa, T., Karlsson, H. K. R., Glund, S., Zavadoski, W. J., Gibbs, E. M., Koistinen, H. A., Wallberg-Henriksson, H. & Zierath, Juleen R, Jun 2010, In : Diabetologia. 53, 6, p. 1142-50 9 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

    The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

    Stella, Stefano, Cascio, D. & Johnson, R. C., 15 Apr 2010, In : Genes and Development. 24, 8, p. 814-826 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    Suppression of water as a nucleophile in Candida antarctica lipase B catalysis

    Larsen, M. W., Zielinska, D. F., Martinelle, M., Hidalgo, A., Jensen, Lars Juhl, Bornscheuer, U. T. & Hult, K., 12 Apr 2010, In : ChemBioChem. 11, 6, p. 796-801 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review