The NNF Center for Protein Research

  1. 2018
  2. Published

    Assessment of the analgesic dipyrone as a possible (anti) androgenic endocrine disruptor

    Passoni, M. T., Kristensen, Maja Nørgaard, Morais, R. N., Woitkowiak, C., Boareto, A. C., da Silva Amaral, B. A., Grechi, N., Dalsenter, P. R., Munkboel, C. H., Styrishave, Bjarne, Kristensen, D. M., Gomes, C., van Ravenzwaay, B. & Martino-Andrade, A. J., 15 Mar 2018, In : Toxicology Letters. 285, p. 139-147

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Familial co-occurrence of congenital heart defects follows distinct patterns

    Ellesøe, S. G., Workman, C. T., Bouvagnet, P., Loffredo, C. A., McBride, K. L., Hinton, R. B., van Engelen, K., Gertsen, E. C., Mulder, B. J. M., Postma, A. V., Anderson, R. H., Hjortdal, V. E., Brunak, Søren & Larsen, Lars Allan, Mar 2018, In : European Heart Journal. 39, 12, p. 1015–1022

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30

    Kruse, Thomas, Biedenkopf, N., Hertz, Emil Peter Thrane, Dietzel, E., Stalmann, G., López-Méndez, B., Davey, N. E., Nilsson, Jakob & Becker, S., 4 Jan 2018, In : Molecular Cell. 69, 1, p. 136-145 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    miRandola 2017: a curated knowledge base of non-invasive biomarkers

    Russo, Francesco, Di Bella, S., Vannini, F., Berti, G., Scoyni, F., Cook, H. V., Santos, A., Nigita, G., Bonnici, V., Laganà, A., Geraci, F., Pulvirenti, A., Giugno, R., De Masi, F., Belling, Kirstine G, Jensen, Lars Juhl, Brunak, Søren, Pellegrini, M. & Ferro, A., 4 Jan 2018, In : Nucleic Acids Research. 46, D1, p. D354-D359 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Performance evaluation of the Q Exactive HF-X for shotgun proteomics

    Kelstrup, C. D., Bekker-Jensen, D. B., Arrey, T. N., Hogrebe, A., Harder, A. & Olsen, Jesper Velgaard, Jan 2018, In : Journal of Proteome Research. 17, 1, p. 727-738 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    LocText: relation extraction of protein localizations to assist database curation

    Cejuela, J. M., Vinchurkar, S., Goldberg, T., Prabhu Shankar, M. S., Baghudana, A., Bojchevski, A., Uhlig, C., Ofner, A., Raharja-Liu, P., Jensen, Lars Juhl & Rost, B., 2018, In : BMC Bioinformatics. 19, p. 1-11 15.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    A Novel Familial Cardiac Arrhythmia Syndrome with Widespread ST-Segment Depression

    Bundgård, Henning, Jøns, C., Lodder, E. M., Izarzugaza, J. M. G., Romero Herrera, Jose Alejandro, Pehrson, S., Tfelt-Hansen, Jacob, Ahlberg, G., Olesen, Morten Steen Salling, Holst, A. G., Wellens, H., de Villiers, C., Hastings, R., Stuart, G., Brunak, Søren, Wilde, A. A. M., Watkins, H. & Christensen, A. H., 2018, In : The New England Journal of Medicine. 379, 18, p. 1780-1781 2 p.

    Research output: Contribution to journalComment/debateResearch

  9. Published

    A Type III-B Cmr effector complex catalyzes the synthesis of cyclic oligoadenylate second messengers by cooperative substrate binding

    Han, W., Stella, Stefano, Zhang, Y., Guo, Tong, Sulek, Karolina, Peng-Lundgren, L., Montoya, Guillermo & She, Q., 2018, In : Nucleic Acids Research. 46, 19, p. 10319-10330 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

    Westergaard, David, Stærfeldt, H., Tønsberg, C., Jensen, Lars Juhl & Brunak, Søren, 2018, In : PLoS Computational Biology. 14, 2, 16 p., e1005962.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    A computational framework to integrate high-throughput "-omics" datasets for the identification of potential mechanistic links

    Pedersen, Helle Krogh, Forslund, S. K., Gudmundsdottir, V., Petersen, A. Ø., Hildebrand, F., Hyötyläinen, T., Nielsen, Trine, Hansen, Torben, Bork, P., Ehrlich, S. D., Brunak, Søren, Oresic, M., Pedersen, Oluf Borbye & Nielsen, H. B., 2018, In : Nature Protocols. 13, 12, p. 2781-2800 20 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics

    Bache, N., Geyer, P. E., Bekker-Jensen, D. B., Hørning, O., Falkenby, L., Treit, P. V., Doll, S., Paron, I., Müller, J. B., Meier, F., Olsen, Jesper Velgaard, Vorm, O. & Mann, Matthias, 2018, In : Molecular and Cellular Proteomics. 17, 11, p. 2284-2296 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    ADAM12-mediated shedding of basigin controls the subcellular localization and lactate transport of MCT4 and enhances collagen degradation in cancer cells: [Meeting Abstract}

    Albrechtsen, Reidar, Albrechtsen, Nicolai Jacob Wewer & Kveiborg, Marie, 2018, In : International Journal of Experimental Pathology. 99, 6, p. A25-A25

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  14. Published

    Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication

    Reveron-Gomez, Nazaret, González-Aguilera, C., Stewart-Morgan, Kathleen, Petryk, N., Flury, V., Graziano, Simona, Johansen, Jens Vilstrup, Jakobsen, J. S., Alabert, C. & Groth, Anja, 2018, In : Molecular Cell. 72, 2, p. 239-249 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Accurate genotyping across variant classes and lengths using variant graphs

    Sibbesen, J. A., Maretty, L., Krogh, Anders, Petersen, Bent, Sibbesen, J. A., Liu, S., Have, C. T., Bork-Jensen, J., Guo, X., Hansen, Torben, Krogh, Anders, Sørensen, Thorkild I.A., Pedersen, Oluf Borbye, Wang, J. & Brunak, Søren, 2018, In : Nature Genetics. 50, p. 1054-1059 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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, J., Eiberg, Hans Rudolf Lytchoff & Kristiansen, Karsten, 2018, In : BMC Bioinformatics. 19, p. 1-12 239.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Binning microbial genomes using deep learning

    Nissen, J. N., Sønderby, C. K., Almagro Armenteros, Jose Juan, Grønbech, Christopher Heje, Nielsen, H. B., Petersen, T. N., Winther, Ole & Rasmussen, Simon, 2018, In : bioRxiv. p. 490078

    Research output: Contribution to journalJournal articleResearch

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. Published

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

    Wild, T., Budzowska, M., 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

  37. 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

  38. 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

  39. 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 articleResearchpeer-review

  40. 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 articleResearchpeer-review

  41. 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 articleResearchpeer-review

  42. 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 articleResearchpeer-review

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

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