The NNF Center for Protein Research

  1. 2006
  2. Published

    Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli

    Kruse, Thomas, Blagoev, B., Løbner-Olesen, Anders, Wachi, M., Sasaki, K., Iwai, N., Mann, Matthias & Gerdes, K., 1 Jan 2006, In : Genes & Development. 20, 1, p. 113-124 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. 2007
  4. Published

    Breast cancer cells with acquired antiestrogen resistance are sensitized to cisplatin-induced cell death

    Yde, C. W., Gyrd-Hansen, M., Lykkesfeldt, A. E., Issinger, O. & Stenvang, Jan, Jun 2007, In : Molecular Cancer Therapeutics. 6, 6, p. 1869-1876 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. 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

  6. 2008
  7. Published

    A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

    Hansen, K. L., Hansen, N. T., Karlberg, E. O., Eklund, A. C., Roque, F. S., Donahoe, P. K., Szallasi, Z., Jensen, T. S. & Brunak, Søren, 2008, In : Proceedings of the National Academy of Science of the United States of America. 105, 52, p. 20870-5 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. 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

  9. 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

  10. Published

    Drug target identification using side-effect similarity

    Campillos, M., Kuhn, M., Gavin, A., Jensen, Lars Juhl & Bork, P., 2008, In : Science. 321, 5886, p. 263-6 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    HCLK2 is required for activity of the DNA damage response kinase ATR

    Rendtlew Danielsen, J. M., Larsen, D. H., Schou, K. B., Freire, R., Falck, J., Bartek, J. & Lukas, Jiri, 2008, In : Journal of Biological Chemistry. 284, 7, p. 4140-7 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Large-scale prediction of drug-target relationships

    Kuhn, M., Campillos, M., González, P., Jensen, Lars Juhl & Bork, P., 2008, In : F E B S Letters. 582, 8, p. 1283-90 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Linear motif atlas for phosphorylation-dependent signaling

    Miller, M. L., Jensen, Lars Juhl, Diella, F., Jørgensen, Claus Bøttcher, Tinti, M., Li, L., Hsiung, M., Parker, S. A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B. E., Yaffe, M. B., Brunak, Søren & Linding, R., 2008, In : Science signaling. 1, 35, p. ra2

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Predicting biological networks from genomic data

    Harrington, E. D., Jensen, Lars Juhl & Bork, P., 2008, In : F E B S Letters. 582, 8, p. 1251-8 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. 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

  16. Published

    Text mining for biology--the way forward: opinions from leading scientists

    Altman, R. B., Bergman, C. M., Blake, J., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, Lars Juhl, Krallinger, M., Mons, B., O'Donoghue, S. I., Peitsch, M. C., Rebholz-Schuhmann, D., Shatkay, H. & Valencia, A., 2008, In : Genome Biology (Online Edition). 9 Suppl 2, p. S7

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    A pilot project to generate affinity reagents to human proteins

    Uhlen, M., Gräslund, S. & Sundström, M., 1 Jan 2008, In : Nature Methods. 5, 10, p. 854-855 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. 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

  19. 2009
  20. Published

    A variant in the G6PC2/ABCB11 locus is associated with increased fasting plasma glucose, increased basal hepatic glucose production and increased insulin release after oral and intravenous glucose loads

    Rose, C. S., Grarup, Niels, Krarup, N. T., Poulsen, P., Wegner, L., Nielsen, Trine, Banasik, Karina, Færch, Kristine, Andersen, G., Albrechtsen, Anders, Borch-Johnsen, K., Clausen, J. O., Jørgensen, T., Vaag, A., Pedersen, Oluf Borbye & Hansen, Torben, 2009, In : Diabetologia. 52, 10, p. 2122-2129 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

    Csikász-Nagy, A., Kapuy, O., Tóth, A., Pál, C., Jensen, Lars Juhl, Uhlmann, F., Tyson, J. J. & Novák, B., 2009, In : Molecular Systems Biology. 5, p. 236

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    G-allele of intronic rs10830963 in MTNR1B confers increased risk of impaired fasting glycemia and type 2 diabetes through an impaired glucose-stimulated insulin release: studies involving 19,605 Europeans

    Sparsø, T., Bonnefond, A., Andersson, E., Bouatia-Naji, N., Holmkvist, J., Wegner, L., Grarup, Niels, Gjesing, Anette Marianne Prior, Banasik, Karina, Cavalcanti-Proença, C., Marchand, M., Vaxillaire, M., Charpentier, G., Jarvelin, M., Tichet, J., Balkau, B., Marre, M., Lévy-Marchal, C., Faerch, K., Borch-Johnsen, K., Jørgensen, T., Madsbad, Sten, Poulsen, P., Vaag, A., Dina, C., Hansen, T., Pedersen, Oluf Borbye, Froguel, P., Sparsø, T., Bonnefond, A., Andersson, E., Bouatia-Naji, N., Holmkvist, J., Wegner, L., Grarup, N., Gjesing, A. P., Banasik, K., Cavalcanti-Proença, C., Marchand, M., Vaxillaire, M., Charpentier, G., Jarvelin, M., Tichet, J., Balkau, B., Marre, M., Lévy-Marchal, C., Faerch, K., Borch-Johnsen, K., Jørgensen, T., Madsbad, Sten, Poulsen, P., Vaag, A., Dina, C., Hansen, T., Pedersen, O. & Froguel, P., 2009, In : Diabetes. 58, 6, p. 1450-6 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Global analysis of the yeast osmotic stress response by quantitative proteomics

    Soufi, B., Kelstrup, C. D., Stoehr, G., Fröhlich, F., Walther, T. C. & Olsen, Jesper Velgaard, 2009, In : Molecular BioSystems. 5, 11, p. 1337-46 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics

    Pan, C., Olsen, Jesper Velgaard, Daub, H. & Mann, Matthias, 2009, In : Molecular and Cellular Proteomics. 8, 12, p. 2796-808 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast

    Gnad, F., de Godoy, L. M. F., Cox, J., Neuhauser, N., Ren, S., Olsen, Jesper Velgaard & Mann, Matthias, 2009, In : Proteomics. 9, 20, p. 4642-4652 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Homologous and non-homologous sequence methods for assigning protein function

    Yeats, C., orengo, C., Veuthey, A. L., Boeckmann, B., Jensen, Lars Juhl, Valencia, A., Rausell, A. & Bork, P., 2009, Modern Genome Annotation: The BioSapien Network. Springer Publishing Company, p. 213-238

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

  27. Published

    ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization

    Pappalardo, F., Halling-Brown, M. D., Rapin, N., Zhang, P., Alemani, D., Emerson, A., Paci, P., Duroux, L. P., Pennisi, M., Palladini, A., Miotto, O., Churchill, D., Rossi, E., Shepherd, A. J., Moss, D. S., Castiglione, F., Bernaschi, M., Lefranc, M., Brunak, Søren, Motta, S., Lollini, P., Basford, K. E. & Brusic, V., 2009, In : Briefings in Bioinformatics. 10, 3, p. 330-40 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Lysine acetylation targets protein complexes and co-regulates major cellular functions

    Choudhary, Chuna Ram, Kumar, C., Gnad, F., Nielsen, Michael Lund, Rehman, M., Walther, T. C., Olsen, Jesper Velgaard & Mann, Matthias, 2009, In : Science. 325, 5942, p. 834-40 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Microblogging the ISMB: a new approach to conference reporting

    Saunders, N., Beltrão, P., Jurczak, D., Krause, R., Kuhn, M., Wu, S. & Jensen, Lars Juhl, 2009, In : PloS Computational Biology. 5, 1, p. e1000263

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Mislocalization of the MRN complex prevents ATR signaling during adenovirus infection

    Carson, C. T., Orazio, N. I., Lee, D. V., Suh, J., Bekker-Jensen, Simon Holst, Araujo, F. D., Lakdawala, S. S., Lilley, C. E., Bartek, J., Lukas, Jiri & Weitzman, M. D., 2009, In : EMBO Journal. 28, 6, p. 652-62 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes

    Choudhary, Chuna Ram, Olsen, Jesper Velgaard, Brandts, C., Cox, J., Reddy, P. N. G., Böhmer, F. D., Gerke, V., Schmidt-Arras, D., Berdel, W. E., Müller-Tidow, C., Mann, Matthias & Serve, H., 2009, In : Molecular Cell. 36, 2, p. 326-39 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Protein-protein interactions: analysis and prediction

    Frishman, D., Albert, M., Blankenburg, H., Bork, P., Harrington, E. D., Hermjakob, H., Jensen, Lars Juhl, Juan, D. A., Pagel, P., Schachter, V. & Valencia, A., 2009, Modern Genome Annotation: The BioSapien Network. Springer Publishing Company, p. 353-410 (Modern Genome Annotation: The BioSapiens network).

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

  33. Published

    Quantifying environmental adaptation of metabolic pathways in metagenomics

    Gianoulis, T. A., Raes, J., Patel, P. V., Bjornson, R., Korbel, J. O., Letunic, I., Yamada, T., Paccanaro, A., Snyder, M., Bork, P., Gerstein, M. B. & Jensen, Lars Juhl, 2009, In : Proceedings of the National Academy of Science of the United States of America. 106, 5, p. 1374-9 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Reflect: augmented browsing for the life scientist

    Pafilis, E., O'Donoghue, S. I., Jensen, Lars Juhl, Horn, H., Kuhn, M., Brown, N. P. & Schneider, R., 2009, In : Nature Biotechnology. 27, 6, p. 508-10 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    The binding of NCAM to FGFR1 induces a specific cellular response mediated by receptor trafficking

    Francavilla, C., Cattaneo, P., Berezin, V., Bock, E., Ami, D., de Marco, A., Christofori, G. & Cavallaro, U., 2009, In : Journal of Cell Biology. 187, 7, p. 1101-16 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published
  37. 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

  38. Published

    Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

    Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie, C. S. & Marks, D. S., 2009, In : Nature Biotechnology. 27, 6, p. 549-55 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Crystal structure of CbpF, a bifunctional choline-binding protein and autolysis regulator from Streptococcus pneumoniae

    Molina, Rafael, Gonzalez, Ana Valeria, Stelter, M., Pérez-Dorado, I., Kahn, R., Morales, M., Moscoso, M., Campuzano, S., Campillo, N. E., Mobashery, S., García, J. L., García, P. & Hermoso, J. A., Mar 2009, In : EMBO Reports. 10, 3, p. 246-51 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Characterization of gadolinium complexes for SAD phasing in macromolecular crystallography: application to CbpF

    Molina, Rafael, Stelter, M., Kahn, R. & Hermoso, J. A., Aug 2009, In : Acta crystallographica. Section D, Biological crystallography. 65, Pt 8, p. 823-31 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Role of the AMPKgamma3 isoform in hypoxia-stimulated glucose transport in glycolytic skeletal muscle

    Deshmukh, Atul Shahaji, Glund, S., Tom, R. Z. & Zierath, Juleen R, Dec 2009, In : American Journal of Physiology: Endocrinology and Metabolism. 297, 6, p. E1388-94

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Novel selective thiazoleacetic acids as CRTH2 antagonists developed from in silico derived hits. Part 1

    Rist, O., Grimstrup, M., Receveur, J., Frimurer, Thomas Michael, Ulven, Trond, Kostenis, E. & Högberg, T., 4 Dec 2009, In : Bioorganic & Medicinal Chemistry Letters. 20, 3, p. 1177-1180 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. 2010
  44. Published

    A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host.

    Lyngsø, C., Kjaerulff, S., Muller, S., Bratt, T., Mortensen, U. H. & Dal Degan, F., 2010, In : Protein Science. 19, 3, p. 579-592 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

    Gauthier, N. P., Jensen, Lars Juhl, Wernersson, R., Brunak, Søren & Jensen, T. S., 2010, In : Nucleic Acids Research. 38, Database issue, p. D699-702

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Dissecting spatio-temporal protein networks driving human heart development and related disorders

    Hansen, K. L., Møllgård, Kjeld, Greenway, S., Wakimoto, H., Gorham, J. M., Workman, C. T., Bendsen, E., Hansen, N. T., Rigina, O., Roque, F. S., Wiese, C., Christoffels, V. M., Roberts, A. E., Smoot, L. B., Pu, W. T., Donahoe, P. K., Tommerup, Niels, Brunak, Søren, Seidman, C. E., Seidman, J. G. & Larsen, Lars Allan, 2010, In : Molecular Systems Biology. 6, p. 381

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Ezrin mediates c-Myc actions in prostate cancer cell invasion

    Chuan, Y. C., Iglesias Gato, Diego, Fernandez-Perez, L., Cedazo-Minguez, A., Pang, S., Norstedt, G., Pousette, A. & Flores-Morales, A., 2010, In : Oncogene. 29, 10, p. 1531-42 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    Prediction of human targets for viral-encoded microRNAs by thermodynamics and empirical constraints

    Laganá, A., Forte, S., Russo, Francesco, Giugno, R., Pulvirenti, A. & Ferro, A., 2010, In : Journal of RNAi and Gene Silencing.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

    Olsen, Jesper Velgaard, Vermeulen, M., Santamaria, A., Kumar, C., Miller, M. L., Jensen, Lars Juhl, Gnad, F., Cox, J., Jensen, T. S., Nigg, E. A., Brunak, Søren & Mann, Matthias, 2010, In : Science Signaling. 3, 104, p. ra3 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    STITCH 2: an interaction network database for small molecules and proteins

    Kuhn, M., Szklarczyk, D., Franceschini, A., Campillos, M., von Mering, C., Jensen, Lars Juhl, Beyer, A. & Bork, P., 2010, In : Nucleic Acids Research. 38, Database issue, p. D552-6

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    Structural basis for KV7.1/KCNEx interactions in the IKs channel complex

    Lundby, Alicia, Tseng, G. & Schmitt, Nicole, 2010, In : Heart Rhythm. 7, 5, p. 708-713

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. Published

    Understanding the proteome - the missing link for successful drug discovery

    Sundström, M., 2010, In : Bioforum Europe. 1-2, p. 12-13

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Published

    A side effect resource to capture phenotypic effects of drugs

    Kuhn, M., Campillos, M., Letunic, I., Jensen, Lars Juhl & Bork, P., 1 Jan 2010, In : Molecular Systems Biology. 6, p. 343

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. 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

  55. 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

  56. Published

    High-resolution transcription atlas of the mitotic cell cycle in budding yeast

    Granovskaia, M. V., Jensen, Lars Juhl, Ritchie, M. E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L. M., 1 Jan 2010, In : Genome Biology (Online Edition). 11, 3, p. R24

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    Yeast expression proteomics by high-resolution mass spectrometry

    Walther, T. C., Olsen, Jesper Velgaard & Mann, Matthias, 1 Jan 2010, In : Methods in Enzymology. 470, p. 259-80 22 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  58. Published

    eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

    Muller, J., Szklarczyk, D., Julien, P., Letunic, I., Roth, A., Kuhn, M., Powell, S., von Mering, C., Doerks, T., Jensen, Lars Juhl & Bork, P., 1 Jan 2010, In : Nucleic Acids Symposium Series. 38, Database issue, p. D190-5

    Research output: Contribution to journalJournal articleResearchpeer-review

  59. Published

    Novel selective thiazoleacetic acids as CRTH2 antagonists developed from in silico derived hits. Part 2

    Grimstrup, M., Rist, Ø., Receveur, J., Frimurer, Thomas Michael, Ulven, Trond, Mathiesen, Jesper M., Kostenis, E. & Högberg, T., 1 Feb 2010, In : Bioorganic & Medicinal Chemistry Letters. 20, 3, p. 1181-1185 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  60. Published

    Ancient human genome sequence of an extinct Palaeo-Eskimo

    Rasmussen, M., Li, Y., Lindgreen, Stinus, Pedersen, J. S., Albrechtsen, Anders, Moltke, Ida, Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, M Thomas P, Wang, Y., Raghavan, M., Campos, P., Kamp, Hanne Louise Munkholm, Wilson, A. S., Gledhill, A., Tridico, S., Bunce, M., Lorenzen, Eline, Binladen, J. K. M. A., Guo, X., Zhao, J., Zhang, X., Zhang, H., Li, Z., Chen, M., Orlando, L. A. A., Kristiansen, Karsten, Bak, Mads, Tommerup, Niels, Bendixen, C., Pierre, T. L., Grønnow, B., Meldgaard, Morten, Andreasen, C., Fedorova, S. A., Osipova, L. P., Higham, T. F. G., Ramsey, C. B., Hansen, T. V. O., Nielsen, Finn Cilius, Crawford, M. H., Brunak, Søren, Sicheritz-Pontén, T., Villems, R., Nielsen, Rasmus, Krogh, Anders, Wang, J. & Willerslev, Eske, 11 Feb 2010, In : Nature. 463, 7282, p. 757-762 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  61. Published

    Evolution and regulation of cellular periodic processes: a role for paralogues

    Trachana, K., Jensen, Lars Juhl & Bork, P., 1 Mar 2010, In : E M B O Reports. 11, 3, p. 233-8 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  62. Published

    Exploration of SAR features by modifications of thiazoleacetic acids as CRTH2 antagonists

    Grimstrup, M., Receveur, J. M., Rist, Ø., Frimurer, Thomas Michael, Nielsen, P. A., Mathiesen, Jesper M. & Högberg, T., 1 Mar 2010, In : Bioorganic and Medicinal Chemistry Letters. 20, 5, p. 1638-1641 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    Interdependence of AMPK and SIRT1 for metabolic adaptation to fasting and exercise in skeletal muscle

    Cantó, C., Jiang, L. Q., Deshmukh, Atul Shahaji, Mataki, C., Coste, A., Lagouge, M., Zierath, Juleen R & Auwerx, J., 3 Mar 2010, In : Cell Metabolism. 11, 3, p. 213-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  64. Published

    4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement

    Cong, Y., Baker, M. L., Jakana, J., Woolford, D., Miller, E. J., Reissmann, S., Kumar, R. N., Redding-Johanson, A. M., Batth, Tanveer Singh, Mukhopadhyay, A., Ludtke, S. J., Frydman, J. & Chiu, W., 16 Mar 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 11, p. 4967-72 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. 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

  66. 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

  67. 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

  68. 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

  69. 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

  70. 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

  71. 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

  72. 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

  73. 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

  74. 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

  75. 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

  76. 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

  77. 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

  78. 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

  79. 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

  80. 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

  81. 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

  82. 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

  83. 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

  84. 2011
  85. 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

  86. 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

  87. 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

  88. 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

  89. 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

  90. 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

  91. 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

  92. 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

  93. 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

  94. 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

  95. 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

  96. 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

  97. 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

  98. 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

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

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