The NNF Center for Protein Research

  1. 2015
  2. Published

    Optimisation of in silico derived 2-aminobenzimidazole hits as unprecedented selective kappa opioid receptor agonists

    Sasmal, P. K., Krishna, C. V., Sudheerkumar Adabala, S., Rawoof, K. A., Thadi, A., Sukumar, K. P., Cheera, S., Abbineni, C., Rao, K. V. L. N., Prasanthi, A., Nijhawan, K., Jaleel, M., Ramachandran Iyer, L., Chaitanya, T. K., Tiwari, N. K., Krishna, N. L., Potluri, V., Khanna, I., Frimurer, Thomas Michael, Lückmann, Michael, Rist, Ø., Elster, L. & Högberg, T., 15 Feb 2015, In : Bioorganic & Medicinal Chemistry Letters. 25, 4, p. 887-92 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Important options available--from start to finish--for translating proteomics results to clinical chemistry

    Heegaard, N. H. H., Østergaard, Ole, Bahl, J. M. C., Overgaard, M., Beck, H. C., Rasmussen, L. M. & Larsen, M. R., Feb 2015, In : Proteomics - Clinical Applications. 9, 1-2, p. 235-52 18 p.

    Research output: Contribution to journalReviewResearchpeer-review

  4. Published

    STRING v10: protein-protein interaction networks, integrated over the tree of life

    Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos Delgado, A., Tsafou, K. P., Kuhn, M., Bork, P., Jensen, Lars Juhl & von Mering, C., 28 Jan 2015, In : Nucleic Acids Research. 43, D1, p. D447-52 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    OTUB1 de-ubiquitinating enzyme promotes prostate cancer cell invasion in vitro and tumorigenesis in vivo: [Plus] erratum

    Iglesias Gato, Diego, Chuan, Y., Jiang, N., Lavallee, C., Bao, J., Paul, I., Egevad, L., Kessler, B. M., Wikström, P., Niu, Y. & Flores-Morales, A., 27 Jan 2015, In : Molecular Cancer. 14, 14 p., 8.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Computational design of artificial RNA molecules for gene regulation

    Laganà, A., Veneziano, D., Russo, Francesco, Pulvirenti, A., Giugno, R., Croce, C. M. & Ferro, A., 10 Jan 2015, RNA Bioinformatics. Springer New York LLC, p. 393-412 20 p.

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

  7. Published

    SLX4: not SIMply a nuclease scaffold?

    Gibbs-Seymour, I. & Mailand, Niels, 8 Jan 2015, In : Molecular Cell. 57, 1, p. 3-5 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Computational design of artificial RNA molecules for gene regulation

    Laganà, A., Veneziano, D., Russo, Francesco, Pulvirenti, A., Giugno, R., Croce, C. M. & Ferro, A., 1 Jan 2015, In : Methods in Molecular Biology. 1269, p. 393-410 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Extracellular vesicle-mediated transfer of micrornas in atherosclerosis

    Vannini, F. & Russo, Francesco, 1 Jan 2015, In : Forum on Immunopathological Diseases and Therapeutics. 6, 3-4, p. 157-161 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Identification of BRAF 3'UTR isoforms in melanoma

    Marranci, A., Tuccoli, A., Vitiello, M., Mercoledi, E., Sarti, S., Lubrano, S., Evangelista, M., Fogli, A., Valdes, C., Russo, Francesco, Dal Monte, M., Caligo, M. A., Pellegrini, M., Capobianco, E., Tsinoremas, N. & Poliseno, L., 1 Jan 2015, In : Journal of Investigative Dermatology. 135, 6, p. 1694-1697 4 p.

    Research output: Contribution to journalLetterResearchpeer-review

  11. Published

    Preface: Microvesicles in human diseases and their role in intercellular communication and signaling

    Vannini, F. & Russo, Francesco, 1 Jan 2015, In : Forum on Immunopathological Diseases and Therapeutics. 6, 3-4, p. v

    Research output: Contribution to journalEditorialResearchpeer-review

  12. Published

    Regulation of mitotic progression by the spindle assembly checkpoint

    Lischetti, T. & Nilsson, Jakob, 1 Jan 2015, In : Molecular & Cellular Oncology. 2, 1, p. e970484

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Centriolar satellites: key mediators of centrosome functions

    Tollenaere, M. A. X., Mailand, Niels & Bekker-Jensen, Simon Holst, Jan 2015, In : Cellular and molecular life sciences : CMLS. 73, 1, p. 11-23 13 p.

    Research output: Contribution to journalReviewResearchpeer-review

  14. Published

    Ctk1 function is necessary for full translation initiation activity in Saccharomyces cerevisiae

    Coordes, B., Brünger, K. M., Burger, K., Soufi, B., Horenk, J., Eick, D., Olsen, Jesper Velgaard & Sträßer, K., Jan 2015, In : Eukaryotic Cell (Online Edition). 14, 1, p. 86 95 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

    Santos Delgado, A., Wernersson, R. & Jensen, Lars Juhl, Jan 2015, In : Nucleic Acids Research. 43, D1, p. D1140-4 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine

    Borodina, I., Kildegaard, K. R., Jensen, N. B., Blicher, T. H., Maury, J., Sherstyk, S., Schneider, K., Lamosa, P., Herrgård, M. J., Rosenstand, I., Oberg, F., Forster, J. & Nielsen, J., Jan 2015, In : Metabolic Engineering. 27, p. 57-64 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells

    Bursomanno, S., Beli, P., Khan, A. M., Minocherhomji, S., Wagner, S. A., Bekker-Jensen, Simon Holst, Mailand, Niels, Choudhary, Chuna Ram, Hickson, Ian David & Liu, Ying, Jan 2015, In : DNA Repair. 25, p. 84-96 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Ubiquitin-SUMO Circuitry Controls Activated Fanconi Anemia ID Complex Dosage in Response to DNA Damage

    Gibbs-Seymour, I., Oka, Y., Rajendra, E., Weinert, B. T., Passmore, L. A., Patel, K. J., Olsen, Jesper Velgaard, Choudhary, Chuna Ram, Bekker-Jensen, Simon Holst & Mailand, Niels, Jan 2015, In : Molecular Cell. 57, 1, p. 150-64 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Visualizing phosphodiester-bond hydrolysis by an endonuclease

    Molina, Rafael, Stella, Stefano, Redondo, P., Gomez, H., Marcaida, M. J., Orozco, M., Prieto, J. & Montoya, Guillermo, Jan 2015, In : Nature Structural and Molecular Biology. 22, 1, p. 65-72 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    In vivo quantitative phosphoproteomic profiling identifies novel regulators of castration-resistant prostate cancer growth

    Jiang, N., Hjorth-Jensen, K., Hekmat, O., Iglesias Gato, Diego, Kruse, Thomas, Wang, C., Wei, W., Ke, B., Yan, B., Niu, Y., Olsen, Jesper Velgaard & Flores Morales, A., 2015, In : Oncogene. 34, p. 2764–2776 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

    Olsen, L. R., Simon, C., Kudahl, U. J., Bagger, F. O., Winther, Ole, Reinherz, E. L., Zhang, G. L. & Brusic, V., 2015, In : B M C Medical Genomics. 8, Suppl 4, 6 p., 5.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    A two-step protein quality control pathway for a misfolded DJ-1 variant in fission yeast

    Mathiassen, S. G., Larsen, I. B., Poulsen, E. G., Madsen, C. T., Papaleo, Elena, Lindorff-Larsen, Kresten, Kragelund, Birthe Brandt, Nielsen, Michael Lund, Kriegenburg, F. & Hartmann-Petersen, Rasmus, 2015, In : The Journal of Biological Chemistry. 290, 34, p. 21141-21153 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Acetylation site specificities of lysine deacetylase inhibitors in human cells

    Schölz, C., Weinert, B. T., Wagner, S. A., Beli, P., Miyake, Y., Qi, J., Jensen, Lars Juhl, Streicher, W., McCarthy, A. R., Westwood, N. J., Lain, S., Cox, J., Matthias, P., Mann, M., Bradner, J. E. & Choudhary, Chuna Ram, 2015, In : Nature Biotechnology. 33, p. 415–423

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Acquisition of docetaxel resistance in breast cancer cells reveals upregulation of ABCB1 expression as a key mediator of resistance accompanied by discrete upregulation of other specific genes and pathways

    Hansen, S. N., Westergaard, David, Thomsen, M. B. H., Vistesen, M. V., Do, K. N., Fogh, L., Belling, Kirstine G, Wang, J., Yang, H., Gupta, R., Ditzel, H. J., Moreira, José, Brünner, Nils, Stenvang, Jan & Rasmussen, A. S., 2015, In : Tumor Biology. 36, 6, p. 4327-4338 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p

    Madsen, C. T., Sylvestersen, K. B., Young, C., Buch-Larsen, Sara Charlotte, Poulsen, J. W., Andersen, M. A., Palmqvist, E. A., Hey-Mogensen, M., Jensen, P. B., Treebak, Jonas Thue, Lisby, Michael & Nielsen, Michael Lund, 2015, In : Nature Communications. 6, 12 p., 7726.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Comprehensive comparison of large-scale tissue expression datasets

    Santos Delgado, A., Tsafou, K., Stolte, C., Pletscher-Frankild, S., O'Donoghue, S. I. & Jensen, Lars Juhl, 2015, In : PeerJ. 3, p. e1054

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    Development of Computational Methods for Cancer Research: Strategies for closing the feedback loop in omics workflows

    Kirik, U., 2015, Lund University Publications.

    Research output: Book/ReportPh.D. thesisResearch

  28. 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., Swallow, D. M., Fotaki, Anna Katerina, Christensen, R. J., Olsen, Jesper Velgaard, Liebert, A., Montalva, N., Fiddyment, S., Mackie, M., Canci, A., Bouwman, A., Ruhli, F., Gilbert, M Thomas P & Collins, M. J., 2015, In : American Journal of Physical Anthropology. 156, Suppl. 60, p. 319 1 p.

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  29. Published

    Direct neuronal glucose uptake Heralds activity-dependent increases in cerebral metabolism

    Lundgaard, I., Li, B., Xie, L., Kang, H., Sanggaard, S., Haswell, J. D. R., Sun, W., Goldman, S., Blekot, S., Nielsen, Michael Lund, Takano, T., Deane, R. & Nedergaard, Maiken, 2015, In : Nature Communications. 6, 12 p., 6807.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

    Forslund, K., Hildebrand, F., Nielsen, Trine, Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Pedersen, H. K., Arumugam, Mani, Kristiansen, Karsten, Yvonne Voigt, A., drb459, drb459, Hercog, R., Igor Costea, P., Roat Kultima, J., Li, J., Jørgensen, T., Levenez, F., Dore, J., Nielsen, H. B., Brunak, Søren, Raes, J., Hansen, Torben, Wang, J., Dusko Ehrlich, S., Bork, P. & Pedersen, Oluf Borbye, 2015, In : Nature. 528, 7581, p. 262-266 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

    Pafilis, E., Pletscher-Frankild, S., Schnetzer, J., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, K., Leary, P., Hammock, J., Schulz, K., Parr, C. S., Arvanitidis, C. & Jensen, Lars Juhl, 2015, In : Bioinformatics. 31, 11, p. 1872-1874

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation

    Knudsen, K. J., Rehn, Matilda Carolina, Hasemann, M. S., Rapin, N. P. J., Bagger, F. O., Ohlsson, E. K., Willer, A., Frank, Anne-Katrine, Søndergaard, Elisabeth, Jendholm, L. J., Thorén, L. A. M., Lee, J., Rak, J., Theilgaard-Mønch, Kim & Porse, Bo Torben, 2015, In : Genes & Development. 29, p. 1915-1929 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago

    Rasmussen, Simon, Allentoft, Morten Erik, Nielsen, K., Orlando, L. A. A., Sikora, Martin, Sjögren, K., Pedersen, A. G., Schubert, M., Van Dam, A., Kapel, Christian, Nielsen, H. B., Brunak, Søren, Avetisyan, P., Epimakhov, A., Khalyapin, M. V., Gnuni, A., Kriiska, A., Lasak, I., Metspalu, M., Moiseyev, V., Gromov, A., Pokutta, D., Saag, L., Varul, L., Yepiskoposyan, L., Sicheritz-Ponten, T., Foley, R. A., Lahr, M. M., Nielsen, R., Kristiansen, K. & Willerslev, Eske, 2015, In : Cell. 163, 3, p. 571-582 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold

    Molina, Rafael, Marcaida, M. J., Redondo, P., Marenchino, M., Duchateau, P., D'Abramo, M., Montoya, Guillermo & Prieto, J., 2015, In : The Journal of Biological Chemistry. 290, 30, p. 18534-18544 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    FBH1 influences DNA replication fork stability and homologous recombination through ubiquitylation of RAD51

    Chu, W. K., Payne, M. J., Beli, P., Hanada, K., Choudhary, C. & Hickson, Ian David, 2015, In : Nature Communications. 6, 7 p., 5931.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    FluKB: a knowledge-based system for influenza vaccine target discovery and analysis of the immunological properties of influenza viruses

    Simon, C., Kudahl, U. J., Sun, J., Olsen, L. R., Zhang, G. L., Reinherz, E. L. & Brusic, V., 2015, In : Clinical & Developmental Immunology. 2015, 11 p., 380975.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Genome-wide association study identifies three novel genetic markers associated with elite endurance performance

    Ahmetov, I., Kulemin, N., Popov, D., Naumov, V., Akimov, E., Bravy, Y., Egorova, E., Galeeva, A., Generozov, E., Kostryukova, E., Larin, A., Mustafina, L., Ospanova, E., Pavlenko, A., Starnes, L. M., Żmijewski, P., Alexeev, D., Vinogradova, O. & Govorun, V., 2015, In : Biology of Sport. 32, 1, p. 3-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases

    Palleja, A. & Jensen, Lars Juhl, 2015, In : PeerJ. 3, p. 1-10 10 p., e1057.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Heat shock response and autophagy - cooperation and control

    Dokladny, K., Myers, O. B. & Moseley, Pope Lloyd, 2015, In : Autophagy. 11, 2, p. 200-213 14 p.

    Research output: Contribution to journalReviewResearchpeer-review

  40. Published

    Immunologic manifestations of autophagy

    Deretic, V., Kimura, T., Timmins, G., Moseley, Pope Lloyd, Chauhan, S. & Mandell, M., 2015, In : Journal of Clinical Investigation. 125, 1, p. 75-84 10 p.

    Research output: Contribution to journalReviewResearchpeer-review

  41. Published

    Molecular evidence of use of hide glue in 4th millennium BC Europe

    Bleicher, N., Kelstrup, C., Olsen, Jesper Velgaard & Cappellini, Enrico, 2015, In : Journal of Archaeological Science. 63, p. 65-71 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Mutation-Guided Unbiased Modeling of the Fat Sensor GPR119 for High-Yield Agonist Screening.

    Norn, Christoffer, Pedersen, Maria Hauge, Engelstoft, M. S., Kim, S. H., Lehmann, J., Jones, R. M., Schwartz, Thue W. & Frimurer, Thomas Michael, 2015, In : Structure. 23, 12, p. 2377-2386 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    PICH promotes sister chromatid disjunction and co-operates with topoisomerase II in mitosis

    Nielsen, Christian Thomas Friberg, Huttner, D., Bizard, Anna Helene, Hirano, S., Li, T., Palmai-Pallag, T., Bjerregaard, V. A., Liu, Ying, Nigg, E. A., Wang, L. H. & Hickson, Ian David, 2015, In : Nature Communications. 6, 15 p., 8962.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Population genomics of bronze age Eurasia

    Allentoft, Morten Erik, Sikora, Martin, Sjogren, K., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. D. B., Schroeder, Hannes, Ahlstrom, T., Vinner, Lasse, Malaspinas, A. S., Margaryan, Ashot, Higham, T., Chivall, D., Lynnerup, Niels, Harvig, L. L., Baron, J., Della Casa, P., Dabrowski, P., Duffy, P. R., Ebel, A. V., Epimakhov, A., Frei, K., Furmanek, M., Gralak, T., Gromov, A., Gronkiewicz, S., Grupe, G., Hajdu, T., Jarysz, R., Khartanovich, V., Khokhlov, A., Kiss, V., Kolar, J., Kriiska, A., Lasak, I., Longhi, C., McGlynn, G., Merkevicius, A., Merkyte, I., Metspalu, M., Mkrtchyan, R., Moiseyev, V., Paja, L., Palfi, G., Pokutta, D., Pospieszny, L., Price, T. D., Saag, L., Sablin, M., Shishlina, N., Smrcka, V., Soenov, V. I., Szeverenyi, V., Toth, G., Trifanova, S. V., Varul, L., Vicze, M., Yepiskoposyan, L., Zhitenev, V., Orlando, L. A. A., Sicheritz-Ponten, T., Brunak, Søren, Nielsen, Rasmus, Kristiansen, K. & Willerslev, Eske, 2015, In : Nature Genetics. 522, 7555, p. 167-172 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Protein-Protein Interaction Databases

    Szklarczyk, D. & Jensen, Lars Juhl, 2015, Protein-Protein Interactions: Methods and Applications. Meyerkord, C. L. & Fu, H. (eds.). 2 ed. New York: Springer Publishing Company, Vol. 1278. p. 39-56 18 p. (Methods in Molecular Biology, Vol. 1278).

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

  46. Published

    Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

    Räschle, M., Smeenk, G., Hansen, R. K., Temu, T., Oka, Y., Hein, M. Y., Nagaraj, N., Long, D. T., Walter, J. C., Hofmann, K., Storchova, Z., Cox, J., Bekker-Jensen, Simon Holst, Mailand, Niels & Mann, Matthias, 2015, In : Science. 348, 6234, p. 539- 10 p., 1253671.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Recent findings and technological advances in phosphoproteomics for cells and tissues

    von Stechow, L., Francavilla, C. & Olsen, Jesper Velgaard, 2015, In : Expert Review of Proteomics. 12, 5, p. 469-87 19 p.

    Research output: Contribution to journalReviewResearchpeer-review

  48. Published

    Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation

    Satpathy, S., Wagner, S. A., Beli, P., Gupta, R., Kristiansen, T. A., Malinova, D., Francavilla, C., Tolar, P., Bishop, G. A., Hostager, B. S. & Choudhary, Chuna Ram, 2015, In : Molecular Systems Biology. 11, 6, 810.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemia

    Willer, A., Jakobsen, J. S., Ohlsson, E., Rapin, N., Waage, J., Billing, M., Bullinger, L., Karlsson, S. & Porse, Bo Torben, 2015, In : Leukemia. 29, p. 1018-31 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation

    Emdal, Kristina Bennet, Pedersen, A., Bekker-Jensen, D. B., Tsafou, K. P., Horn, H., Lindner, S., Schulte, J. H., Eggert, A., Jensen, Lars Juhl, Francavilla, C. & Olsen, Jesper Velgaard, 2015, In : Science signaling. 8, 374, ra40.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    TopBP1 is required at mitosis to reduce transmission of DNA damage to G1 daughter cells

    Pedersen, R. T., Kruse, Thomas, Nilsson, Jakob, Østergaard, Vibe Hallundbæk & Lisby, Michael, 2015, In : Journal of Cell Biology. 210, 4, p. 565-582 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. 2014
  53. Published

    Lactococcus lactis TrxD represents a subgroup of thioredoxins prevalent in Gram-positive bacteria containing WCXDC active site motifs

    Björnberg, O., Efler, P., Ebong, E. D., Svensson, B. & Hägglund, Per Mårten, 15 Dec 2014, In : Archives of Biochemistry and Biophysics. 564, p. 164-172 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. Published

    The internal Cdc20 binding site in BubR1 facilitates both spindle assembly checkpoint signalling and silencing

    Lischetti, T., Zhang, G., Sedgwick, G. G., Bolanos-Garcia, V. M. & Nilsson, Jakob, Dec 2014, In : Nature Communications. 5, p. 1-12 12 p., 5563.

    Research output: Contribution to journalJournal articleResearchpeer-review

  55. Published

    Insight in the multilevel regulation of NER

    Dijk, M., Typas, Dimitris, Mullenders, L. & Pines, A., 15 Nov 2014, In : Experimental Cell Research. 329, 1, p. 116-23 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  56. E-pub ahead of print

    Predicting protein-RNA interaction amino acids using random forest based on submodularity subset selection

    Pan, X., Zhu, L., Fan, Y. & Yan, J., 13 Nov 2014, In : Computational Biology and Chemistry. 53PB, p. 324-330 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

    Batth, Tanveer Singh, Francavilla, C. & Olsen, Jesper Velgaard, 4 Nov 2014, In : Journal of Proteome Research. 13, 12, p. 6176-86 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  58. Published

    A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins

    Batth, Tanveer Singh, Singh, P., Ramakrishnan, V. R., Sousa, M. M. L., Chan, L. J. G., Tran, H. M., Luning, E. G., Pan, E. H. Y., Vuu, K. M., Keasling, J. D., Adams, P. D. & Petzold, C. J., Nov 2014, In : Metabolic Engineering. 26, p. 48-56 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  59. Published

    Renal-Retinal Ciliopathy Gene Sdccag8 Regulates DNA Damage Response Signaling

    Airik, R., Slaats, G. G., Guo, Z., Weiss, A., Khan, N., Ghosh, A., Hurd, T. W., Bekker-Jensen, Simon Holst, Schrøder, J. M., Elledge, S. J., Andersen, J. S., Kispert, A., Castelli, M., Boletta, A., Giles, R. H. & Hildebrandt, F., Nov 2014, In : Journal of the American Society of Nephrology:JASN. 25, 11, p. 2573-83 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  60. Published

    Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

    Kelstrup, C. D., Jersie-Christensen, R. R., Batth, Tanveer Singh, Arrey, T. N., Kuehn, A., Kellmann, M. & Olsen, Jesper Velgaard, 28 Oct 2014, In : Journal of Proteome Research. 13, 12, p. 6187-95 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  61. Published

    Met1-linked Ubiquitination in Immune Signalling

    Fiil, B. K. & Gyrd-Hansen, M., Oct 2014, In : F E B S Journal. 81, 19, p. 4337-50 14 p.

    Research output: Contribution to journalReviewResearchpeer-review

  62. Published

    Modules, networks and systems medicine for understanding disease and aiding diagnosis

    Gustafsson, M., Nestor, C. E., Zhang, H., Barabási, A., Baranzini, S., Brunak, Søren, Chung, K. F., Federoff, H. J., Gavin, A., Meehan, R. R., Picotti, P., Pujana, M. À., Rajewsky, N., Smith, K. G., Sterk, P. J., Villoslada, P. & Benson, M., Oct 2014, In : Genome Medicine. 6, 10, p. 82

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    SUMOylation of the ING1b tumor suppressor regulates gene transcription

    Satpathy, S., Guérillon, C., Kim, T., Bigot, N., Thakur, S., Bonni, S., Riabowol, K. & Pedeux, R., Oct 2014, In : Carcinogenesis. 35, 10, p. 2214-23 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  64. Published

    mGluR5: Exploration of Orthosteric and Allosteric Ligand Binding Pockets and Their Applications to Drug Discovery

    Mølck, C., Harpsøe, Kasper, Gloriam, David E., Mathiesen, Jesper M., Nielsen, S. M. & Bräuner-Osborne, Hans, Oct 2014, In : Neurochemical Research. 39, 10, p. 1862-1875 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. Published

    XTACC3-XMAP215 association reveals an asymmetric interaction promoting microtubule elongation

    Mortuza, G. B., Cavazza, T., Garcia-Mayoral, M. F., Hermida, D., Peset, I., Pedrero, J. G., Merino, N., Blanco, F. J., Lyngsø, J., Bruix, M., Pedersen, J. S., Vernos, I. & Montoya, Guillermo, 29 Sep 2014, In : Nature Communications. 5, p. 1-12 12 p., 5072.

    Research output: Contribution to journalJournal articleResearchpeer-review

  66. Published

    Neurophysiological evidence for the presence of cannabinoid CB1 receptors in the laterodorsal tegmental nucleus.

    Soni, N., Satpathy, S. & Kohlmeier, Kristi Anne, 23 Sep 2014, In : European Journal of Neuroscience. 40, 11, p. 3635-3652 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  67. Published

    Patient stratification and identification of adverse event correlations in the space of 1190 drug related adverse events

    Roitmann, E., Eriksson, Robert & Brunak, Søren, 11 Sep 2014, In : Frontiers in Physiology. 5, 14 p., 332.

    Research output: Contribution to journalJournal articleResearchpeer-review

  68. Published

    A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response

    Blasius, M., Wagner, S. A., Choudhary, Chuna Ram, Bartek, J. & Jackson, S. P., 4 Sep 2014, In : Genes & Development. 28, 18, p. 1977-1982 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    Analysis of Changes in SUMO-2/3 Modification during Breast Cancer Progression and Metastasis

    Subramonian, D., Raghunayakula, S., Olsen, Jesper Velgaard, Beningo, K. A., Paschen, W. & Zhang, X., Sep 2014, In : Journal of Proteome Research. 13, 9, p. 3905–3918 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. Published

    Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance

    Kildegaard, K. R., Hallström, B. M., Blicher, T. H., Sonnenschein, N., Jensen, N. B., Sherstyk, S., Harrison, S. J., Maury, J., Herrgård, M. J., Juncker, A. S., Forster, J., Nielsen, J. & Borodina, I., Sep 2014, In : Metabolic Engineering. 26C, p. 57-66 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  71. Published

    Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin

    Xu, Q., Deller, M. C., Nielsen, T. K., Grant, J. C., Lesley, S. A., Elsliger, M., Deacon, A. M. & Wilson, I. A., Sep 2014, In : PLOS ONE. 9, 9, 9 p., e107309.

    Research output: Contribution to journalJournal articleResearchpeer-review

  72. Published

    Immature truncated O-glycophenotype of cancer directly induces oncogenic features

    Radhakrishnan, P., Dabelsteen, Sally, Madsen, F. B., Francavilla, C., Kopp, K. L., Steentoft, Catharina, Vakhrushev, Sergey, Olsen, Jesper Velgaard, Hansen, Lars, Bennett, Eric Paul, Woetmann, A., Yin, G., Chen, L., Song, H., Bak, Mads, Hlady, R. A., Peters, S. L., Opavsky, R., Thode, C., Qvortrup, Klaus, Schjoldager, Katrine Ter-Borch Gram, Clausen, Henrik, Hollingsworth, M. A. & Wandall, Hans H., 12 Aug 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 39, p. e4066-e4077 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  73. Published

    Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells

    Re, A., Workman, C. T., Waldron, L., Quattrone, A. & Brunak, Søren, 4 Aug 2014, In : Stem Cell Research. 13, 2, p. 316-328 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  74. Published

    Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production

    George, K. W., Chen, A., Jain, A., Batth, Tanveer Singh, Baidoo, E. E. K., Wang, G., Adams, P. D., Petzold, C. J., Keasling, J. D. & Lee, T. S., Aug 2014, In : Biotechnology and Bioengineering. 111, 8, p. 1648-58 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. Published

    The NBS1-Treacle complex controls ribosomal RNA transcription in response to DNA damage

    Larsen, D. H., Hari, F., Clapperton, J. A., Gwerder, M., Gutsche, K., Altmeyer, M., Jungmichel, S., Toledo Lazaro, Luis Ignacio, Fink, D., Rask, M., Grøfte, M., Lukas, Claudia, Nielsen, Michael Lund, Smerdon, S. J., Lukas, Jiri & Stucki, M., Aug 2014, In : Nature Cell Biology. 16, 8, p. 792-803 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  76. Published

    Revision of the Classical Dopamine D2 Agonist Pharmacophore Based on an Integrated Medicinal Chemistry, Homology Modelling and Computational Docking Approach

    Krogsgaard-Larsen, N., Harpsøe, Kasper, Kehler, J., Christoffersen, C. T., Brøsen, P. & Balle, T., 24 Jul 2014, In : Neurochemical Research. 39, 10, p. 1997-2007 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  77. Published

    The growing landscape of lysine acetylation links metabolism and cell signalling

    Choudhary, Chuna Ram, Weinert, B. T., Nishida, Y., Verdin, E. & Mann, Matthias, 23 Jul 2014, In : Nature Reviews. Molecular Cell Biology. 15, 8, p. 536-50 15 p.

    Research output: Contribution to journalReviewResearchpeer-review

  78. Published

    Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-β

    J D'Souza, R. C., Knittle, A. M., Nagaraj, N., van Dinther, M., Choudhary, Chuna Ram, Ten Dijke, P., Mann, Matthias & Sharma, K., Jul 2014, In : Science signaling. 7, 335, p. rs5 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. Published

    Comprehensive Identification of SUMO2/3 Targets and Their Dynamics during Mitosis

    Schou, J., Kelstrup, C. D., Hayward, D. G., Olsen, Jesper Velgaard & Nilsson, Jakob, 27 Jun 2014, In : PLOS ONE. 9, 6, p. e100692 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  80. Published

    XIAP Restricts TNF- and RIP3-Dependent Cell Death and Inflammasome Activation

    Yabal, M., Müller, N., Adler, H., Knies, N., Groß, C. J., Damgaard, R. B., Kanegane, H., Ringelhan, M., Kaufmann, T., Heikenwälder, M., Strasser, A., Groß, O., Ruland, J., Peschel, C., Gyrd-Hansen, M. & Jost, P. J., 26 Jun 2014, In : Cell Reports. 7, 6, p. 1796-1808

    Research output: Contribution to journalJournal articleResearchpeer-review

  81. Published

    Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-Treated Yeast Cells

    Iesmantavicius, V., Weinert, B. T. & Choudhary, Chuna Ram, 24 Jun 2014, In : Molecular & Cellular Proteomics. 13, 8, p. 1979-92 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  82. Published

    Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

    Jensen, A. B., Moseley, Pope Lloyd, Oprea, T. I., Ellesøe, S. G., Eriksson, Robert, Schmock, H., Jensen, P. B., Jensen, Lars Juhl & Brunak, Søren, 24 Jun 2014, In : Nature Communications. 5, 10 p., 4022.

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    PRIME-XS, a European infrastructure for proteomics

    Raijmakers, R., Olsen, Jesper Velgaard, Aebersold, R. & Heck, A. J. R., 23 Jun 2014, In : Molecular & Cellular Proteomics. 13, 8, p. 1901-1904 4 p.

    Research output: Contribution to journalEditorialResearchpeer-review

  84. Published

    Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics

    Lundby, Alicia, Rossin, E. J., Steffensen, Annette Buur, Acha, M. R., Newton-Cheh, C., Pfeufer, A., Lynch, S. N., Olesen, Søren-Peter, Brunak, Søren, Ellinor, P. T., Jukema, J. W., Trompet, S., Ford, I., Macfarlane, P. W., Krijthe, B. P., Hofman, A., Uitterlinden, A. G., Stricker, B. H., Nathoe, H. M., Spiering, W., Daly, M. J., Asselbergs, F. W., van der Harst, P., Milan, D. J., de Bakker, P. I. W., Hansen, K. L., Olsen, Jesper Velgaard & The QT Interval International GWAS Consortium (QT-IGC), T. Q. I. I. G. C. (., 22 Jun 2014, In : Nature Methods. 11, 8, p. 868-874 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  85. Published

    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization

    Arking, D. E., Pulit, S. L., Crotti, L., van der Harst, P., Munroe, P. B., Koopmann, T. T., Sotoodehnia, N., Rossin, E. J., Morley, M., Wang, X., Johnson, A. D., Lundby, Alicia, Gudbjartsson, D. F., Noseworthy, P. A., Eijgelsheim, M., Bradford, Y., Tarasov, K. V., Dörr, M., Müller-Nurasyid, M., Lahtinen, A. M., Nolte, I. M., Smith, A. V., Bis, J. C., Isaacs, A., Newhouse, S. J., Evans, D. S., Post, W. S., Waggott, D., Lyytikäinen, L., Hicks, A. A., Eisele, L., Ellinghaus, D., Hayward, C., Navarro, P., Ulivi, S., Tanaka, T., Tester, D. J., Chatel, S., Gustafsson, S., Kumari, M., Morris, R. W., Naluai, A. T., Padmanabhan, S., Kluttig, A., Strohmer, B., Panayiotou, A. G., Torres, M., Knoflach, M., Olsen, Jesper Velgaard, Hansen, K. L. & CARe Consortium, C. C., 22 Jun 2014, In : Nature Genetics. 46, 8, p. 826-838 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  86. Published

    B-lymphoid tyrosine kinase (Blk) is an oncogene and a potential target for therapy with Dasatinib in cutaneous T-cell lymphoma (CTCL)

    Petersen, David Leander, Krejsgaard, Thorbjørn Frej, Berthelsen, J., Fredholm, S., Willerslev-Olsen, Andreas, Sibbesen, N. A., Bonefeld, Charlotte Menne, Andersen, M. H., Francavilla, C., Olsen, Jesper Velgaard, Hu, T., Zhang, M., Wasik, M. A., Geisler, Carsten, Woetmann, Anders & Ødum, Niels, 12 Jun 2014, In : Leukemia. 28, p. 2109-12 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  87. Published

    Biochemical characterization of human gluconokinase and the proposed metabolic impact of gluconic Acid as determined by constraint based metabolic network analysis

    Rohatgi, N., Nielsen, T. K., Bjørn, S. P., Axelsson, I., Paglia, G., Voldborg, B. G., Palsson, B. O. & Rolfsson, O., 4 Jun 2014, In : PloS one. 9, 6, 9 p., e98760.

    Research output: Contribution to journalJournal articleResearchpeer-review

  88. Published

    Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID)

    Kelstrup, C. D., Freese, C., Heck, A. J. R., Olsen, Jesper Velgaard & Nielsen, Michael Lund, 3 Jun 2014, In : Molecular & Cellular Proteomics. 13, 8, p. 1914-1924 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  89. Published

    A complement to the modern crystallographer's toolbox: caged gadolinium complexes with versatile binding modes

    Stelter, M., Molina, Rafael, Jeudy, S., Kahn, R., Abergel, C. & Hermoso, J. A., Jun 2014, In : Acta crystallographica. Section D, Biological crystallography. 70, Pt 6, p. 1506-16 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  90. Published

    KinomeXplorer: an integrated platform for kinome biology studies

    Horn, H., Schoof, E. M., Kim, J., Robin, X., Miller, M. L., Diella, F., Palma, A., Cesareni, G., Jensen, Lars Juhl & Linding, R., 29 May 2014, In : Nature Methods. 11, 6, p. 603-4 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  91. Published

    Functional and Structural Properties of a Novel Protein and Virulence Factor (sHIP) in Streptococcus pyogenes

    Wisniewska, M., Happonen, L., Kahn, F., Varjosalo, M., Malmström, L., Rosenberger, G., Karlsson, C., Cazzamali, G., Pozdnyakova, I., Frick, I., Björck, L., Streicher, W., Malmström, J. & Wikström, M., 13 May 2014, In : The Journal of Biological Chemistry. 289, p. 18175-18188

    Research output: Contribution to journalJournal articleResearchpeer-review

  92. Published

    Glycopeptide enrichment using a combination of ZIC-HILIC and cotton wool for exploring the glycoproteome of wheat flour albumins

    Dedvisitsakul, P., Jacobsen, S., Svensson, B., Bunkenborg, J., Finnie, C. & Hägglund, Per Mårten, 2 May 2014, In : Journal of Proteome Research. 13, 5, p. 2696-2703 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  93. Published

    A substrate-optimized electrophoretic mobility shift assay for ADAM12

    Kotzsch, A., Skovgaard, T., Buus, U., Andersen, S., Devkota, K. & Berthelsen, J., 1 May 2014, In : Analytical Biochemistry. 452, p. 34-42 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  94. Published

    Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination

    Gao, M., Wei, W., Li, M. H., Wu, Y., Ba, Z., Jin, K., Li, M., Liao, Y., Adhikari, S., Chong, Z., Zhang, T., Guo, C., Tang, T., Zhu, B., Xu, X., Mailand, Niels, Yang, Y., Qi, Y. & Danielsen, J. M. R., May 2014, In : Cell Research. 24, 5, p. 532-41 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    Erratum to: Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population

    Eriksson, Robert, Werge, T., Jensen, Lars Juhl & Brunak, Søren, May 2014, In : Drug Safety. 37, 5, p. 379

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    qcML: an exchange format for quality control metrics from mass spectrometry experiments

    Walzer, M., Pernas, L. E., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., van den Toorn, H. W. P., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, R. A., Kelstrup, C. D., Gatto, L., van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., Lilley, K. S., Olsen, Jesper Velgaard, Heck, A. J. R., Mechtler, K., Aebersold, R., Gevaert, K., Vizcaino, J. A., Hermjakob, H., Kohlbacher, O. & Martens, L., 23 Apr 2014, In : Molecular & Cellular Proteomics. 13, 8, p. 1905-1913 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. Published

    The role of extracellular matrix quality in pulmonary fibrosis

    Kristensen, J. H., Karsdal, M. A., Genovese, F., Johnson, S., Svensson, B., Jacobsen, S., Hägglund, Per Mårten & Leeming, D. J., 14 Apr 2014, In : Respiration. 88, 6, p. 487-499 13 p.

    Research output: Contribution to journalReviewResearchpeer-review

  98. Published

    Comprehensive analysis of the specificity of transcription activator-like effector nucleases

    Juillerat, A., Dubois, G., Valton, J., Thomas, S., Stella, Stefano, Maréchal, A., Langevin, S., Benomari, N., Bertonati, C., Silva, G. H., Daboussi, F., Epinat, J., Montoya, Guillermo, Duclert, A. & Duchateau, P., Apr 2014, In : Nucleic Acids Research. 42, 8, p. 5390-402 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  99. Published

    Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population

    Eriksson, Robert, Werge, T., Jensen, Lars Juhl & Brunak, Søren, Apr 2014, In : Drug Safety. 37, 4, p. 237-47 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. Published

    DoReMi: context-based prioritization of linear motif matches

    Horn, H., Haslam, N. & Jensen, Lars Juhl, 20 Mar 2014, In : PeerJ. 2, 10 p., e315.

    Research output: Contribution to journalJournal articleResearchpeer-review

  101. Published

    Uncovering SUMOylation Dynamics during Cell-Cycle Progression Reveals FoxM1 as a Key Mitotic SUMO Target Protein

    Schimmel, J., Eifler, K., Sigurdsson, J. O., Cuijpers, S. A. G., Hendriks, I. A., Verlaan-de Vries, M., Kelstrup, C. D., Francavilla, C., Medema, R. H., Olsen, Jesper Velgaard & Vertegaal, A. C. O., 20 Mar 2014, In : Molecular Cell. 53, 6, p. 1053-1066

    Research output: Contribution to journalJournal articleResearchpeer-review

  102. Published

    Citrullination regulates pluripotency and histone H1 binding to chromatin

    Christophorou, M. A., Castelo-Branco, G., Halley-Stott, R. P., Oliveira, C. S., Loos, R., Radzisheuskaya, A., Mowen, K. A., Bertone, P., Silva, J. C. R., Zernicka-Goetz, M., Nielsen, Michael Lund, Gurdon, J. B. & Kouzarides, T., 6 Mar 2014, In : Nature. 507, p. 104-108

    Research output: Contribution to journalJournal articleResearchpeer-review