The NNF Center for Protein Research

  1. 2018
  2. Published

    Alternative translation initiation generates a functionally distinct isoform of the stress-activated kinase MK2

    Trulley, P., Snieckute, Goda, Bekker-Jensen, D. B., Menon, M. B., Freund, R., Kotlyarov, A., Olsen, Jesper Velgaard, Diaz-Muñoz, M. D., Turner, M., Bekker-Jensen, Simon Holst, Gaestel, M. & Tiedje, C., 2018, In : bioRxiv. 46 p.

    Research output: Contribution to journalJournal articleResearch

  3. Published

    An Integrative Approach to Virus-Host Protein-Protein Interactions

    Cook, H. V. & Jensen, Lars Juhl, 2018, Computational Cell Biology. von Stechow, L. & Delgado, A. S. (eds.). Humana Press, p. 175-196 22 p. (Methods in Molecular Biology, Vol. 1819).

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

  4. Published

    Analysis of Time-Series Gene Expression Data to Explore Mechanisms of Chemical-Induced Hepatic Steatosis Toxicity

    Aguayo Orozco, Alejandro, Bois, F. Y., Brunak, Søren & Taboureau, Olivier Thierry, 2018, In : Frontiers in Genetics. 9, p. 1-15 396.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Analysis of a gene panel for targeted sequencing of colorectal cancer samples

    Jensen, K. H., Izarzugaza, J. M. G., Juncker, A. S., Hansen, R. B., Hansen, T. F., Timshel, P., Blondal, T., Jensen, T. S., Rygaard-Hjalsted, E., Mouritzen, P., Thorsen, M., Wernersson, R., Nielsen, H. B., Jakobsen, A., Brunak, Søren & Sørensen, F. B., 2018, In : OncoTarget. 9, 10, p. 9043-9060 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Arginine Methylation by PRMT2 Controls the Functions of the Actin Nucleator Cobl

    Hou, W., Nemitz, S., Schopper, S., Nielsen, Michael Lund, Kessels, M. M. & Qualmann, B., 2018, In : Developmental Cell. 45, 2, p. 262-275.E8

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Benchmarking common quantification strategies for large-scale phosphoproteomics

    Hogrebe, A., von Stechow, L., Bekker-Jensen, D. B., Weinert, B. T., Kelstrup, C. D. & Olsen, Jesper Velgaard, 2018, In : Nature Communications. 9, 1, p. 1-13 1045.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

    Matey-Hernandez, M. L., Danish Pan Genome Consortium, D. P. G. C., Brunak, Søren, Izarzugaza, J. M. G., Sørensen, L. M., Petersen, Bent, Sibbesen, J. A., Liu, S., Belling, Kirstine G, Have, C. T., Bork-Jensen, J., Sun, J., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, Jun, Eiberg, Hans Rudolf Lytchoff & Kristiansen, Karsten, 2018, In : BMC Bioinformatics. 19, p. 1-12 239.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Blood parameters in a population of blood donors are not affected by hidradenitis suppurativa

    Theut Riis, P., Sigsgaard, V., Pedersen, O. B., Olsen, J., Rigas, A. S., Dinh, K. M., Brodersen, T., Ullum, Henrik, Erikstrup, C., Paarup, H. M., Nielsen, K. R., Petersen, M. S., Burgdorf, K. S., Hjalgrim, H., Rostgaard, K., Banasik, Karina & Jemec, Gregor, 2018, In : European Journal of Dermatology. 28, 3, p. 424-425 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

    Meier, F., Geyer, P. E., Virreira Winter, S., Cox, J. & Mann, Matthias, 2018, In : Nature Methods. 15, 6, p. 440-448 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Comorbidity landscape of the Danish patient population affected by chromosomal abnormalities

    Russo, Francesco, Jørgensen, Isabella Friis, Westergaard, David, Jensen, A. B., Hjaltelin, Jessica Xin, Belling, Kirstine G & Brunak, Søren, 2018, In : European Journal of Human Genetics. 26, p. 697-698

    Research output: Contribution to journalConference abstract in journalResearch

  12. Published

    Comorbidity of migraine with ADHD in adults

    Hansen, Thomas Folkmann, Hoeffding, L. K., Kogelman, L., Haspang, T. M., Ullum, Henrik, Sørensen, E., Erikstrup, C., Pedersen, O. B., Nielsen, K. R., Hjalgrim, H., Paarup, H. M., Werge, Thomas & Burgdorf, K., 2018, In : BMC Neurology. 18, 1, p. 1-9 147.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Computational Structural Biology of S-nitrosylation of Cancer Targets

    Bignon, E., Allega, M. F., Lucchetta, M., Tiberti, M. & Papaleo, Elena, 2018, In : Frontiers in Oncology. 8, p. 1-23 272.

    Research output: Contribution to journalReviewResearchpeer-review

  14. Published

    Constructing a cell-type resolved human liver proteome atlas: THU-034

    Niu, Lili, Geyer, P. & Mann, Matthias, 2018, In : Journal of Hepatology. 68, p. S138-S139

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  15. Published

    Contractile injection systems of bacteriophages and related systems

    Taylor, Nicholas M I, van Raaij, M. J. & Leiman, P. G., 2018, In : Molecular Microbiology. 108, 1, p. 6-15 10 p.

    Research output: Contribution to journalReviewResearchpeer-review

  16. Published

    Control of endothelial cell tube formation by Notch ligand intracellular domain interactions with activator protein 1 (AP-1)

    Forghany, Z., Robertson, F., Lundby, Alicia, Olsen, Jesper Velgaard & Baker, D. A., 2018, In : Journal of Biological Chemistry. 293, 4, p. 1229-1242 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states

    Manolaridis, I., Jackson, S. M., Taylor, Nicholas M I, Kowal, J., Stahlberg, H. & Locher, K. P., 2018, In : Nature. 563, 7731, p. 426-430 5 p.

    Research output: Contribution to journalLetterResearchpeer-review

  18. Published

    DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity

    Gupta, R., Somyajit, Kumar, Narita, Takeo, Maskey, E., Stanlie, A., Kremer, M., Typas, Dimitris, Lammers, M., Mailand, Niels, Nussenzweig, A., Lukas, Jiri & Choudhary, Chuna Ram, 2018, In : Cell. 173, 4, p. 972-988

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy

    Bennetzen, M. V., Kosar, M., Bunkenborg, J., Payne, M. R., Bartkova, J., Lindström, M. S., Lukas, Jiri, Andersen, J. S., Bartek, J. & Larsen, D. H., 2018, In : Cell Cycle. 17, 17, p. 2146-2163

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

    Sinha, S., Eisenhaber, B., Jensen, Lars Juhl, Kalbuaji, B. & Eisenhaber, F., 2018, In : Proteomics. 18, 21-22, p. 1-13 e1800093.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Deletion of APC7 or APC16 Allows Proliferation of Human Cells without the Spindle Assembly Checkpoint

    Wild, T., Budzowska, Magdalena, Hellmuth, S., Eibes, S., Karemore, Gopal, Barisic, Marin, Stemmann, O. & Choudhary, Chuna Ram, 2018, In : Cell Reports. 25, 9, 18 p., 2317-2328.e5.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)

    Hastings, J. F., Han, J. Z. R., Shearer, Robert Francis, Kennedy, S. P., Iconomou, M., Saunders, D. N. & Croucher, D. R., 2018, In : Journal of Visualized Experiments. 136, e57109.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification

    Virreira Winter, S., Meier, F., Wichmann, C., Cox, J., Mann, Matthias & Meissner, F., 2018, In : Nature Methods. 15, 7, p. 527-530 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    ENABLE 2017, the First EUROPEAN PhD and Post-Doc Symposium. Session 3: In Vitro to In Vivo: Modeling Life in 3D

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Cortada, H. X. & Zivanovic, S., 2018, In : Journal of Personalized Medicine. 8, 2, p. 1-5 20.

    Research output: Contribution to journalConference articleResearch

  25. Published

    ENABLE 2017, the First EUROPEAN PhD and Post-Doc Symposium. Session 4: From Discovery to Cure: The Future of Therapeutics

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Xicoy Cortada, H. & Zivanovic, S., 2018, In : Medical Sciences. 6, 2, p. 1-6 6 p., 42.

    Research output: Contribution to journalConference articleResearch

  26. Published

    ENABLE 2017, the First European PhD and Post-Doc Symposium. Session 1: Building the Foundations of Biology: Synthetic and Cellular Research

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Xicoy Cortada, H. & Zivanovic, S., 2018, In : Biomolecules. 8, 3, p. 1-6 46.

    Research output: Contribution to journalConference articleResearch

  27. Published

    ENABLE 2017, the First European PhD and Post-Doc Symposium. Session 2: The OMICS Revolution

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Xicoy Cortada, H. & Zivanovic, S., 2018, In : Biomolecules. 8, 4, p. 1-6 116.

    Research output: Contribution to journalConference articleResearch

  28. Published

    Exploring ECD on a Benchtop Q Exactive Orbitrap Mass Spectrometer

    Fort, K. L., Cramer, C. N., Voinov, V. G., Vasil'ev, Y. V., Lopez, N. I., Beckman, J. S. & Heck, A. J. R., 2018, In : Journal of Proteome Research. 17, 2, p. 926-933 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Extreme disorder in an ultrahigh-affinity protein complex

    Borgia, A., Borgia, M. B., Bugge, Katrine, Kissling, V. M., Heidarsson, P. O., Fernandes, Catarina, Sottini, A., Soranno, A., Buholzer, K. J., Nettels, D., Kragelund, Birthe Brandt, Best, R. B. & Schuler, B., 2018, In : Nature. 555, p. 61-66 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Future Perspectives on GLP-1 Receptor Agonists and GLP-1/glucagon Receptor Co-agonists in the Treatment of NAFLD

    Seghieri, M., Christensen, A. S., Andersen, A., Solini, A., Knop, Filip Krag & Vilsbøll, Tina, 2018, In : Frontiers in Endocrinology. 9, p. 1-10 649.

    Research output: Contribution to journalReviewResearchpeer-review

  31. Published

    Generic Workflow for Mapping of Complex Disulfide Bonds Using In-Source Reduction and Extracted Ion Chromatograms from Data-Dependent Mass Spectrometry

    Cramer, C. N., Kelstrup, C., Olsen, Jesper Velgaard, Haselmann, K. F. & Nielsen, P. K., 2018, In : Analytical Chemistry. 90, 13, p. 8202-8210

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

    Pan, X., Wenzel, Anne, Jensen, Lars Juhl & Gorodkin, Jan, 2018, In : PLoS ONE. 13, 8, 15 p., e0202369.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Glucagon receptor signaling in metabolic diseases

    Albrechtsen, Nicolai Jacob Wewer, 2018, In : Peptides. 100, p. 42-47

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

    Humphrey, S. J., Karayel, O., James, D. E. & Mann, Matthias, 2018, In : Nature Protocols (Print). 13, p. 1897-1916 20 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    How do CRISPR-Cas RNA-guided endonucleases cut specific DNA regions for Genome Editing?

    Montoya, Guillermo, 2018, In : Acta Crystallographica Section A: Foundations and Advances. 74, p. E3 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  36. Published

    How well do force fields capture the strength of salt bridges in proteins?

    Ahmed, Mustapha Carab Hussein, Papaleo, Elena & Lindorff-Larsen, Kresten, 2018, In : PeerJ. 6, 17 p., 4967.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Ibuprofen alters human testicular physiology to produce a state of compensated hypogonadism

    Kristensen, D. M., Desdoits-Lethimonier, C., Mackey, Abigail, Dalgaard, M. D., De Masi, F., Munkbøl, C. H., Styrishave, Bjarne, Antignac, J., Le Bizec, B., Platel, C., Hay-Schmidt, Anders, Jensen, T. K., Lesné, L., Mazaud-Guittot, S., Kristiansen, Karsten, Brunak, Søren, Kjær, Michael, Juul, Anders & Jégou, B., 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 4, p. e715-e724 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    Ibuprofen is deleterious for the development of first trimester human fetal ovary ex vivo

    Leverrier-Penna, S., Mitchell, R. T., Becker, E., Lecante, L., Ben Maamar, M., Homer, N., Lavoue, V., Kristensen, D. M., Dejucq-Rainsford, N., Jegou, B. & Mazaud-Guittot, S., 2018, In : Human Reproduction. 33, 3, p. 482-493

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers

    Tsafou, K., Katschnig, A. M., Radic-Sarikas, B., Mutz, C. N., Iljin, K., Schwentner, R., Kauer, M. O., Mühlbacher, K., Aryee, D. N. T., Westergaard, David, Haapa-Paananen, S., Fey, V., Superti-Furga, G., Toretsky, J., Brunak, Søren & Kovar, H., 2018, In : OncoTarget. 9, 57, p. 31018-31031 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    In vivo brain GPCR signaling elucidated by phosphoproteomics

    Liu, J. J., Sharma, K., Zangrandi, L., Chen, C., Humphrey, S. J., Chiu, Y., Spetea, M., Liu-Chen, L., Schwarzer, C. & Mann, Matthias, 2018, In : Science (New York, N.Y.). 360, 6395, p. 1-11

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Increase in clinically recorded type 2 diabetes after colectomy

    Jensen, A. B., Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Jess, T., Brunak, Søren & Allin, Kristine Højgaard, 2018, In : eLife. 7, e37420.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published
  43. Published

    Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study

    Gudmundsdottir, V., Pedersen, H. K., Allebrandt, K. V., Brorsson, C. A., van Leeuwen, N., Banasik, Karina, Mahajan, A., Groves, C. J., van de Bunt, M., Dawed, A. Y., Fritsche, A., Staiger, H., Simonis-Bik, A. M. C., Deelen, J., Kramer, M. H. H., Dietrich, A., Hübschle, T., Willemsen, G., Häring, H., de Geus, E. J. C., Boomsma, D. I., Eekhoff, E. M. W., Ferrer, J., McCarthy, M. I., Pearson, E. R., Gupta, R., Brunak, Søren & 't Hart, L. M., 2018, In : P L o S One. 13, 1, p. 1-19 e0189886.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer

    Russo, Francesco, Fiscon, G., Conte, F., Rizzo, M., Paci, P. & Pellegrini, M., 2018, Computational Cell Biology. von Stechow, L. & Delgado, A. S. (eds.). Humana Press, p. 75-92 18 p. (Methods in Molecular Biology, Vol. 1819).

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

  45. Published

    Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling

    Batth, Tanveer Singh, Papetti, M., Pfeiffer, Anamarija, Tollenaere, M. A. X., Francavilla, C. & Olsen, Jesper Velgaard, 2018, In : Cell Reports. 22, 10, p. 2784-2796 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Ligand-selective small molecule modulators of the constitutively active vGPCR US28

    Amarandi, R., Lückmann, Michael, Melynis, M., Jakobsen, M. H., Fallah, Z., Spiess, Katja, Hjortø, Gertrud Malene, Pui, A., Frimurer, Thomas Michael & Rosenkilde, Mette, 2018, In : European Journal of Medicinal Chemistry. 155, p. 244-254

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    Limits for resolving isobaric tandem mass tag reporter ions using phase constrained spectrum deconvolution

    Kelstrup, C. D., Aizikov, K., Batth, Tanveer Singh, Kreutzman, A., Grinfeld, D., Lange, O., Mourad, D., Makarov, A. A. & Olsen, Jesper Velgaard, 2018, In : Journal of Proteome Research. 17, 11, p. 4008-4016 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. Published

    MCM2 promotes symmetric inheritance of modified histones during DNA replication

    Petryk, N., Dalby, M., Wenger, Alice, Stromme, C. B., Strandsby, A., Andersson, Robin & Groth, Anja, 2018, In : Science. 361, 6409, p. 1389-1392 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

    Théry, C., Witwer, K. W., Aikawa, E., Alcaraz, M. J., Anderson, J. D., Andriantsitohaina, R., Antoniou, A., Arab, T., Archer, F., Atkin-Smith, G. K., Ayre, D. C., Bach, J., Bachurski, D., Baharvand, H., Balaj, L., Baldacchino, S., Bauer, N. N., Baxter, A. A., Bebawy, M., Beckham, C., Bedina Zavec, A., Benmoussa, A., Berardi, A. C., Bergese, P., Bielska, E., Blenkiron, C., Bobis-Wozowicz, S., Boilard, E., Boireau, W., Bongiovanni, A., Borràs, F. E., Bosch, S., Boulanger, C. M., Breakefield, X., Breglio, A. M., Brennan, M. Á., Brigstock, D. R., Brisson, A., Broekman, M. L., Bromberg, J. F., Bryl-Górecka, P., Buch, S., Buck, A. H., Burger, D., Busatto, S., Buschmann, D., Jørgensen, M. M., Jacobsen, Søren, Nejsum, P., Østergaard, Ole & Xu, J., 2018, In : Journal of Extracellular Vesicles. 7, 1, p. 1-47 1535750.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    Molecular basis of Tousled-Like Kinase 2 activation

    Mortuza, G. B., Hermida, D., Pedersen, A., Segura-Bayona, S., López-Méndez, B., Redondo, P., Rüther, Patrick, Pozdnyakova, I., Garrote, A. M., Muñoz, I. G., Villamor-Payà, M., Jauset, C., Olsen, Jesper Velgaard, Stracker, T. H. & Montoya, Guillermo, 2018, In : Nature Communications. 9, 1, p. 2535 2535.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Published

    Molecular genetic overlap between migraine and major depressive disorder

    Yang, Y., Zhao, H., Boomsma, D. I., Ligthart, L., Belin, A. C., Smith, G. D., Esko, T., Freilinger, T. M., Hansen, Thomas Folkmann, Ikram, M. A., Kallela, M., Kubisch, C., Paraskevi, C., Strachan, D. P., Wessman, M., Gormley, P., Anttila, V., Winsvold, B. S., Palta, P., Esko, T., Pers, Tune H, Farh, K. H., Cuenca-Leon, E., Muona, M., Furlotte, N. A., Kurth, T., Ingason, A., McMahon, G., Ligthart, L., Terwindt, G. M., Kallela, M., Freilinger, T. M., Ran, C., Gordon, S. G., Stam, A. H., Steinberg, S., Borck, G., Koiranen, M., Quaye, L., Adams, H. H. H., Lehtimäki, T., Sarin, A. P., Wedenoja, J., Hinds, D. A., Buring, J. E., Schürks, M., Christensen, A. F., Hansen, Thomas Folkmann, Werge, Thomas & Olesen, Jes, 2018, In : European Journal of Human Genetics. 26, 8, p. 1202-1216 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

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