The NNF Center for Protein Research

  1. 2019
  2. Published

    Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas

    Molina, Rafael, Stella, Stefano, Feng, M., Sofos, Nicholas Heelund, Jauniskis, V., Pozdnyakova, I., López-Méndez, B., She, Q. & Montoya, Guillermo, 2019, In : Nature Communications. 10, 14 p., 4302.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Survival prediction in intensive-care units based on aggregation of long-term disease history and acute physiology: a retrospective study of the Danish National Patient Registry and electronic patient records

    Nielsen, Annelaura Bach, Thorsen-Meyer, Hans-Christian, Belling, Kirstine G, Nielsen, Anna Pors, Thomas, C. E., Chmura, Piotr Jaroslaw, Lademann, M., Moseley, Pope Lloyd, Heimann, M., Dybdahl, L., Spangsege, L., Hulsen, P., Perner, Anders & Brunak, Søren, 2019, In : The Lancet Digital Health. 1, 2, p. e78-e89 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Sweet google O’ mine - The importance of online search engines for MS-facilitated, database-independent identification of peptide-encoded book prefaces: A EUPA YPIC challenge entry

    Hogrebe, A. & Jersie-Christensen, R. R., 2019, In : EuPA Open Proteomics. 22-23, p. 14-18 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    TH2BS11ph histone mark is enriched in the unsynapsed axes of the XY body and predominantly associates with H3K4me3-containing genomic regions in mammalian spermatocytes

    Mahadevan, I. A., Pentakota, Satya Krishna, Roy, R., Bhaduri, U. & Satyanarayana Rao, M. R., 2019, In : Epigenetics & Chromatin. 12, 1, 23 p., 53.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    TRAIP drives replisome disassembly and mitotic DNA repair synthesis at sites of incomplete DNA replication

    Sonneville, R., Bhowmick, Rahul, Hoffmann, Saskia, Mailand, Niels, Hickson, Ian David & Labib, K., 2019, In : eLife. 8, 19 p., e48686.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Tail Structure and Dynamics

    Bhatt, Shweta, Leiman, P. G. & Taylor, Nicholas M I, 2019, Reference Module in Life Sciences. Elsevier

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

  8. Published

    The bio.tools registry of software tools and data resources for the life sciences

    Ison, J., Ienasescu, H., Chmura, Piotr Jaroslaw, Rydza, E., Ménager, H., Kalaš, M., Schwämmle, V., Grüning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Vařeková, R. S., Raček, T., Vondrášek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R., Nyrönen, T., Valencia, A., Capella, S., Gelpí, J., Zambelli, F., Savakis, B., Leskošek, B., Rapacki, K., Blanchet, C., Jimenez, R., Oliveira, A., Vriend, G., Collin, O., van Helden, J., Løngreen, P. & Brunak, Søren, 2019, In : Genome Biology. 20, 1, 4 p., 164.

    Research output: Contribution to journalLetterResearchpeer-review

  9. Published

    The CMG Helicase Bypasses DNA-Protein Cross-Links to Facilitate Their Repair

    Sparks, J. L., Chistol, G., Gao, A. O., Räschle, M., Larsen, Nicolai Balle, Mann, Matthias, Duxin, Julien & Walter, J. C., 2019, In : Cell. 176, 1-2, p. 167-181.e21 36 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine

    Doll, S., Gnad, F. & Mann, Matthias, 2019, In : Proteomics - Clinical Applications. 13, 2, 10 p., e1800113.

    Research output: Contribution to journalReviewResearchpeer-review

  11. Published

    The RIF1-PP1 Axis Controls Abscission Timing in Human Cells

    Bhowmick, Rahul, Thakur, Roshan Singh, Venegas, A. B., Liu, Ying, Nilsson, Jakob, Barisic, Marin & Hickson, Ian David, 2019, In : Current Biology. 29, 7, p. 1232-1242.e5

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    The Role of TTP Phosphorylation in the Regulation of Inflammatory Cytokine Production by MK2/3

    Ronkina, N., Shushakova, N., Tiedje, C., Yakovleva, T., Tollenaere, M. A. X., Scott, A., Batth, Tanveer Singh, Olsen, Jesper Velgaard, Helmke, A., Bekker-Jensen, Simon Holst, Clark, A. R., Kotlyarov, A. & Gaestel, M., 2019, In : Journal of immunology (Baltimore, Md. : 1950). 203, 8, p. 2291-2300 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    The ever expanding scope of electrospray mass spectrometry-a 30 year journey

    Mann, Matthias, 2019, In : Nature Communications. 10, 3744.

    Research output: Contribution to journalComment/debateResearch

  14. Published

    The first step towards personalized risk prediction for common epilepsies

    Hansen, Thomas Folkmann & Møller, R. S., 2019, In : Brain. 142, p. 3316-3318 3 p.

    Research output: Contribution to journalComment/debateResearch

  15. Published

    The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep

    Noya, S. B., Colameo, D., Brüning, F., Spinnler, A., Mircsof, D., Opitz, L., Mann, Matthias, Tyagarajan, S. K., Robles, M. S. & Brown, S. A., 2019, In : Science. 366, 6462, eaav2642 .

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    The human endogenous metabolome as a pharmacology baseline for drug discovery

    Bofill, A., Jalencas, X., Oprea, T. I. & Mestres, J., 2019, In : Drug Discovery Today. 24, 9-12, p. 1806-1820

    Research output: Contribution to journalReviewResearchpeer-review

  17. Published

    The liver-alpha cell axis and type 2 diabetes

    Albrechtsen, Nicolai Jacob Wewer, Pedersen, J., Galsgaard, Katrine Douglas, Winther-Sørensen, Marie, Suppli, M. P., Janah, L., Gromada, J., Vilstrup, H., Knop, Filip Krag & Holst, Jens Juul, 2019, In : Endocrine Reviews. 40, 5, p. 1353-1366

    Research output: Contribution to journalReviewResearchpeer-review

  18. Published

    The p97-Ataxin 3 complex regulates homeostasis of the DNA damage response E3 ubiquitin ligase RNF8

    Singh, A. N., Oehler, J., Torrecilla, I., Kilgas, S., Li, S., Vaz, B., Guerillon, C., Fielden, J., Esperanza Hernandez-Carralero, Cabrera, E., Tullis, I. D. C., Meerang, M., Barber, P. R., Freire, R., Parsons, J., Vojnovic, B., Kiltie, A. E., Mailand, Niels & Ramadan, K., 2019, In : EMBO Journal. 38, 25 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    The use of systems biology in chemical risk assessment

    Aguayo Orozco, Alejandro, Taboureau, Olivier Thierry & Brunak, Søren, 2019, In : Current Opinion in Toxicology. 15, p. 48-54 7 p.

    Research output: Contribution to journalReviewResearchpeer-review

  20. Published

    Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS

    Lesne, J., Bousquet, M., Marcoux, J. & Locard-Paulet, Marie, 2019, In : Bioinformatics and Biology Insights. 13, 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Transcriptome analysis in patients with temporal lobe epilepsy

    Kjær, C., Barzaghi, G., Bak, Lasse Kristoffer, Goetze, Jens P. , Yde, C. W., Woldbye, David Paul Drucker, Pinborg, Lars Hageman & Jensen, Lars Juhl, 2019, In : Brain. 142, 10, p. 49-64 16 p., e55.

    Research output: Contribution to journalLetterResearchpeer-review

  22. Published

    Transcriptome landscape of protein-coding genes and long noncoding RNAs in the colon and blood of DSS-induced mouse model of Acute ulcerative colitis

    Yarani, R., Palasca, O., Doncheva, Nadezhda Tsankova, Anthon, Christian, Pilecki, B., Litman, Thomas, Holmskov, U., Jensen, Lars Juhl, Gorodkin, Jan & Pociot, Flemming, 2019, In : Journal of Crohn's and Colitis. 13, p. S129-S130

    Research output: Contribution to journalConference abstract in journalResearchpeer-review

  23. Published

    Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave

    Schroeder, Hannes, Margaryan, Ashot, Szmyt, M., Theulot, B., Włodarczak, P., Rasmussen, Simon, Gopalakrishnan, Shyam, Szczepanek, A., Konopka, T., Jensen, Theis Zetner Trolle, Witkowska, B., Wilk, S., Przybyła, M. M., Pospieszny, Ł., Sjögren, K., Belka, Z., Olsen, J., Kristiansen, K., Willerslev, Eske, Frei, K. M., Sikora, Martin, Johannsen, N. N. & Allentoft, Morten Erik, 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 22, p. 10705-10710

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase

    Bignon, E., Rizza, S., Filomeni, G. & Papaleo, Elena, 2019, In : Computational and Structural Biotechnology Journal. 17, p. 415-429 15 p.

    Research output: Contribution to journalReviewResearchpeer-review

  25. Published

    What outcomes are important to patients with mild cognitive impairment or Alzheimer's disease, their caregivers, and health-care professionals? A systematic review

    Tochel, C., Smith, M., Baldwin, H., Gustavsson, A., Ly, A., Bexelius, C., Nelson, M., Bintener, C., Fantoni, E., Garre-Olmo, J., Janssen, O., Jindra, C., Jørgensen, Isabella Friis, McKeown, A., Öztürk, B., Ponjoan, A., Potashman, M. H., Reed, C., Roncancio-Diaz, E., Vos, S., Sudlow, C. & ROADMAP consortium, R. C., 2019, In : Alzheimer's and Dementia: Diagnosis, Assessment and Disease Monitoring. 11, p. 231-247 17 p.

    Research output: Contribution to journalReviewResearchpeer-review

  26. Published

    eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

    Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunic, I., Rattei, T., Jensen, Lars Juhl, von Mering, C. & Bork, P., 2019, In : Nucleic Acids Research. 47, D1, p. D309-D314 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    sAOP: linking chemical stressors to adverse outcomes pathway networks

    Aguayo Orozco, Alejandro, Audouze, K., Siggaard, T., Barouki, R., Brunak, Søren & Taboureau, Olivier Thierry, 2019, In : Bioinformatics. 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. 2018
  29. Published

    Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity

    Stella, Stefano, Mesa, Pablo, Thomsen, J., Paul, Bijoya, Alcón, P., Jensen, Simon Bo, Saligram, B., Moses, M. E., Hatzakis, Nikos & Montoya, Guillermo, 13 Dec 2018, In : Cell. 175, 7, p. 1856-1871.e21 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    GLP-1 Is a Coronary Artery Vasodilator in Humans

    Clarke, S. J., Giblett, J. P., Yang, L. L., Hubsch, A., Zhao, T., Aetesam-ur-Rahman, M., West, N. E. J., O'Sullivan, M., Figg, N., Bennett, M., Albrechtsen, Nicolai Jacob Wewer, Deacon, Carolyn F., Cheriyan, J. & Hoole, S. P., 20 Nov 2018, In : Journal of the American Heart Association. 7, 22, 14 p., e010321.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    Integrated proximal proteomics reveals IRS2 as a determinant of cell survival in ALK-driven neuroblastoma

    Emdal, Kristina Bennet, Pedersen, A., Bekker-Jensen, D. B., Lundby, Alicia, Claeys, S., De Preter, K., Speleman, F., Francavilla, C. & Olsen, Jesper Velgaard, 20 Nov 2018, In : Science signaling. 11, 557, p. 1-17 17 p., eaap9752.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published
  33. Published

    WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

    Pan, X., Xiong, K., Anthon, Christian, Hyttel, Poul, Freude, Kristine, Jensen, Lars Juhl & Gorodkin, Jan, 6 Nov 2018, In : Genes. 9, 11, 11 p., 536.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Recovery of gut microbiota of healthy adults following antibiotic exposure

    Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, Kristine Højgaard, Nielsen, Trine, Hansen, Tue Haldor, Liang, S., Feng, Q., Zhang, C., Pyl, P. T., Coelho, L. P., Yang, H., Wang, J., Typas, A., Nielsen, M. F., Nielsen, H. B., Bork, P., Wang, Jun, Vilsbøll, Tina, Hansen, Torben, Knop, Filip Krag, Arumugam, Mani & Pedersen, Oluf Borbye, Nov 2018, In : Nature Microbiology. 3, 11, p. 1255-1265 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers

    Hendy, J., Colonese, A. C., Franz, I., Fernandes, R., Fischer, R., Orton, D., Lucquin, A., Spindler, L., Anvari, J., Stroud, E., Biehl, P. F., Speller, C., Boivin, N., Mackie, Meaghan, Jersie-Christensen, R. R., Olsen, Jesper Velgaard, Collins, Matthew James, Craig, O. E. & Rosenstock, E., 3 Oct 2018, In : Nature Communications. 9, 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    Præcisionskardiologi

    Haue, Amalie Dahl, Vissing, C. R., Tfelt-Hansen, Jacob, Brunak, Søren, Bundgård, Henning & Weeke, P. E., 1 Oct 2018, In : Ugeskrift for Laeger. 180, 20A, p. 1851-54

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations

    Bastys, T., Gapsys, V., Doncheva, Nadezhda Tsankova, Kaiser, R., De Groot, B. L. & Kalinina, O. V., 10 Jul 2018, In : Journal of Chemical Theory and Computation. 14, 7, p. 3397-3408

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    Effective lock-in strategy for proteomic analysis of corona complexes bound to amino-free ligands of gold nanoparticles

    Zhou, M., Tang, M., Li, S., Peng, L., Huang, H., Fang, Q., Liu, Z., Xie, P., Li, G. & Zhou, J., 9 Jul 2018, In : Nanoscale. 10, 26, p. 12413-12423 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. 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

  40. 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

  41. 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

  42. 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 Delgado, Alberto, 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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, Jun & Brunak, Søren, 2018, In : Nature Genetics. 50, p. 1054-1059 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

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