The NNF Center for Protein Research

  1. 2010
  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 2009
  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. Published
  45. 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

  46. 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

  47. 2008
  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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