The NNF Center for Protein Research

  1. Published

    Antimicrobial resistance: Harmonisation of national antimicrobial resistance monitoring and surveillance programmes in animals and in animal-derived food

    Franklin, A., Acar, J., Anthony, F., Gupta, R., Nicholls, T., Tamura, Y., Thompson, S., Threlfall, E. J., Vose, D., Van Vuuren, M., White, D. G., Wegener, H. C. & Costarrica, M. L., 1 Jan 2001, In : OIE Revue Scientifique et Technique. 20, 3, p. 859-870 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin

    Franz, A., Ackermann, Leena & Hoppe, T., 2016, In : Frontiers in Genetics. 7, p. 73

    Research output: Contribution to journalReviewResearchpeer-review

  3. Published

    Create and preserve: proteostasis in development and aging is governed by Cdc48/p97/VCP

    Franz, A., Ackermann, Leena & Hoppe, T., Jan 2014, In : B B A - Reviews on Cancer. 1843, 1, p. 205-15 11 p.

    Research output: Contribution to journalReviewResearchpeer-review

  4. Published

    Development of a native Escherichia coli induction system for ionic liquid tolerance

    Frederix, M., Hütter, K., Leu, J., Batth, Tanveer Singh, Turner, W. J., Rüegg, T. L., Blanch, H. W., Simmons, B. A., Adams, P. D., Keasling, J. D., Thelen, M. P., Dunlop, M. J., Petzold, C. J. & Mukhopadhyay, A., 2014, In : PLOS ONE. 9, 7, p. e101115

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

    Frenkel-Morgenstern, M., Danon, T., Christian, T., Igarashi, T., Cohen, L., Hou, Y. & Jensen, Lars Juhl, 2012, In : Molecular Systems Biology. 8, p. 572

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. E-pub ahead of print

    JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

    Friedrichs, M., Shoshi, A., Chmura, Piotr Jaroslaw, Ison, J., Schwammle, V., Schreiber, F., Hofestadt, R. & Sommer, B., 2020, In : Journal of integrative bioinformatics. 16, 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Identification of known and novel recurrent viral sequences in data from multiple patients and multiple cancers

    Friis-Nielsen, J., Kjartansdóttir, K. R., Mollerup, S., Asplund, M., Mourier, T., Jensen, R. H., Hansen, T. A., Rey de la Iglesia, Alba, Richter, S. R., Nielsen, Ida Broman, Alquezar Planas, D. E., Olsen, Pernille Vibeke Selmer, Vinner, Lasse, Fridholm, E. M. H., Nielsen, L. P., Willerslev, Eske, Sicheritz-Pontén, T., Lund, O., Hansen, Anders Johannes, Izarzugaza, J. M. G. & Brunak, Søren, 2016, In : Viruses. 8, 2, 16 p., 53.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Model-Based Discovery of Synthetic Agonists for the Zn2+-Sensing G-Protein-Coupled Receptor 39 (GPR39) Reveals Novel Biological Functions.

    Frimurer, Thomas Michael, Mende, F., Graae, A., Engelstoft, M. S., Egerod, Kristoffer Lihme, Nygaard, R., Gerlach, L., Hansen, J. B., Schwartz, Thue W. & Holst, Birgitte, 2017, In : Journal of Medicinal Chemistry. 60, 3, p. 886-898 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Protein-protein interactions: analysis and prediction

    Frishman, D., Albert, M., Blankenburg, H., Bork, P., Harrington, E. D., Hermjakob, H., Jensen, Lars Juhl, Juan, D. A., Pagel, P., Schachter, V. & Valencia, A., 2009, Modern Genome Annotation: The BioSapien Network. Springer Publishing Company, p. 353-410 (Modern Genome Annotation: The BioSapiens network).

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

  10. Published

    Pdx1 is post-translationally modified in vivo and serine 61 is the principal site of phosphorylation

    Frogne, T., Sylvestersen, K. B., Kubicek, S., Nielsen, Michael Lund & Hecksher-Sørensen, J., 2012, In : P L o S One. 7, 4, p. e35233

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    ADAM12 is expressed in the tumour vasculature and mediates ectodomain shedding of several membrane-anchored endothelial proteins

    Frohlich, C., Klitgaard, M., Noer, J. B., Kotzsch, A., Nehammer, C., Kronqvist, P., Berthelsen, J., Blobel, C., Kveiborg, Marie, Albrechtsen, Reidar & Wewer, Ulla M., 15 May 2013, In : Biochemical Journal. 452, 1, p. 97-109 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    FBH1 co-operates with MUS81 in inducing DNA double-strand breaks and cell death following replication stress

    Fugger, K., Chu, W. K., Haahr, P., Kousholt, A. N., Beck, H., Payne, M. J., Hanada, K., Hickson, Ian David & Sørensen, Claus Storgaard, 2013, In : Nature Communications. 4, p. 1423

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    FBH1 Catalyzes Regression of Stalled Replication Forks

    Fugger, K., Mistrik, M., Neelsen, K. J., Yao, Q., Zellweger, R., Kousholt, A. N., Haahr, Peter Thorlund, Chu, W. K., Bartek, J., Lopes, M., Hickson, Ian David & Sørensen, Claus Storgaard, 10 Mar 2015, In : Cell Reports.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability

    Galanos, P., Pappas, G., Polyzos, A., Kotsinas, A., Svolaki, I., Giakoumakis, N. N., Glytsou, C., Pateras, I. S., Swain, U., Souliotis, V. L., Georgakilas, A. G., Geacintov, N., Scorrano, L., Lukas, Claudia, Lukas, Jiri, Livneh, Z., Lygerou, Z., Chowdhury, D., Sørensen, Claus Storgaard, Bartek, J. & Gorgoulis, V. G., 2018, In : Genome Biology (Online Edition). 19, p. 1-18 37.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells

    Galli, G. G., Carrara, M., Francavilla, C., Honnens de Lichtenberg, Kristian, Olsen, Jesper Velgaard, Calogero, R. A. & Lund, Anders H., 16 Sep 2013, In : Molecular and Cellular Biology.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Glucagon Receptor Signaling and Lipid Metabolism

    Galsgaard, Katrine Douglas, Pedersen, J., Knop, Filip Krag, Holst, Jens Juul & Albrechtsen, Nicolai Jacob Wewer, 2019, In : Frontiers in Physiology. 10, 11 p., 413.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Glucose and Amino Acid Metabolism in Mice Depend Mutually on Glucagon and Insulin Receptor Signaling

    Galsgaard, Katrine Douglas, Winther-Sørensen, Marie, Pedersen, J., Kjeldsen, Sasha Alexandra Sampson, Rosenkilde, Mette, Albrechtsen, Nicolai Jacob Wewer & Holst, Jens Juul, 2019, In : American Journal of Physiology: Endocrinology and Metabolism. 316, 4, p. E660-E673

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    A Novel Role of Human Holliday Junction Resolvase GEN1 in the Maintenance of Centrosome Integrity

    Gao, M., Danielsen, J. M. R., Wei, L., Zhou, D., Xu, Q., Li, M., Yang, Y., Wang, Z. & Tong, W., 16 Nov 2012, In : P L o S One. 7, 11, 13 p., e49687.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. 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

  20. Published

    Synergistic inhibition of the APC/C by the removal of APC15 in HCT116 cells lacking UBE2C

    Garvanska, Dimitriya Hristoforova, Larsen, M. S. Y. & Nilsson, Jakob, 2 Sep 2016, In : Biology Open. 5, p. 1441-1448

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

    Gauthier, N. P., Jensen, Lars Juhl, Wernersson, R., Brunak, Søren & Jensen, T. S., 2010, In : Nucleic Acids Research. 38, Database issue, p. D699-702

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds

    Geertz-Hansen, H. M., Blom, N., Feist, A., Brunak, Søren & Petersen, T. N., 13 Feb 2014, In : Proteins: Structure, Function, and Bioinformatics. 82, 9, p. 1819-1828 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Protein features as determinants of wild-type glycoside hydrolase thermostability

    Geertz-Hansen, H. M., Kiemer, L., Nielsen, M., Stanchev, K., Blom, N., Brunak, Søren & Petersen, T. N., Nov 2017, In : Proteins: Structure, Function, and Bioinformatics. 85, 11, p. 2036-2044 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. 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

  25. Published

    Plasma Proteome Profiling to Assess Human Health and Disease

    Geyer, P. E., Kulak, N. A., Pichler, G., Holdt, L. M., Teupser, D. & Mann, Matthias, 23 Mar 2016, In : Cell Systems. 2, 3, p. 185-95 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Revisiting biomarker discovery by plasma proteomics

    Geyer, P. E., Holdt, L. M., Teupser, D. & Mann, Matthias, 26 Sep 2017, In : Molecular Systems Biology. 13, 9, 16 p., 942.

    Research output: Contribution to journalReviewResearchpeer-review

  27. Published

    Proteomics reveals the effects of sustained weight loss on the human plasma proteome

    Geyer, P. E., Albrechtsen, Nicolai Jacob Wewer, Tyanova, S., Grassl, N., Iepsen, E. P. W., Lundgren, Julie Rehné, Madsbad, Sten, Holst, Jens Juul, Torekov, Signe Sørensen & Mann, Matthias, 22 Dec 2016, In : Molecular Systems Biology. 12, 16 p., 901.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Plasma Proteome Profiling to detect and avoid sample-related biases in biomarker studies

    Geyer, P. E., Voytik, E., Treit, P. V., Doll, S., Kleinhempel, A., Niu, Lili, Müller, J. B., Buchholtz, M., Bader, J. M., Teupser, D., Holdt, L. M. & Mann, Matthias, 2019, In : EMBO Molecular Medicine. 11, 11, e10427.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Quantifying environmental adaptation of metabolic pathways in metagenomics

    Gianoulis, T. A., Raes, J., Patel, P. V., Bjornson, R., Korbel, J. O., Letunic, I., Yamada, T., Paccanaro, A., Snyder, M., Bork, P., Gerstein, M. B. & Jensen, Lars Juhl, 2009, In : Proceedings of the National Academy of Science of the United States of America. 106, 5, p. 1374-9 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. 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

  31. Published

    Lamin A/C-dependent interaction with 53BP1 promotes cellular responses to DNA damage

    Gibbs-Seymour, I., Markiewicz, E., Bekker-Jensen, Simon Holst, Mailand, Niels & Hutchison, C. J., Apr 2015, In : Aging Cell. 14, 2, p. 162-9 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. 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

  33. Published

    Mammary alveolar epithelial cells convert to brown adipocytes in post-lactating mice

    Giordano, A., Perugini, J., Kristensen, D. M., Sartini, L., Frontini, A., Kajimura, S., Kristiansen, Karsten & Cinti, S., 2017, In : Journal of Cellular Physiology. 232, 11, p. 2923-2928 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Lysine 58-cleaved beta2-microglobulin is not detectable by 2D electrophoresis in ex vivo amyloid fibrils of two patients affected by dialysis-related amyloidosis

    Giorgetti, S., Stoppini, M., Tennent, G. A., Relini, A., Marchese, L., Raimondi, S., Monti, M., Marini, S., Østergaard, Ole, Heegaard, N. H. H., Pucci, P., Esposito, G., Merlini, G. & Bellotti, V., Feb 2007, In : Protein Science. 16, 2, p. 343-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Published

    Predicting post-translational lysine acetylation using support vector machines

    Gnad, F., Ren, S., Choudhary, Chuna Ram, Cox, J. & Mann, M., 1 Jul 2010, In : Bioinformatics. 26, 13, p. 1666-8 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Published

    High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast

    Gnad, F., de Godoy, L. M. F., Cox, J., Neuhauser, N., Ren, S., Olsen, Jesper Velgaard & Mann, Matthias, 2009, In : Proteomics. 9, 20, p. 4642-4652 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. E-pub ahead of print

    Azo dying of alpha-keratin material improves microbial keratinase screening and standardization

    Gonzalo, M., Espersen, R., Al-Soud, W. A., Cristiano Falco, F., Hägglund, Per Mårten, Sørensen, Søren Johannes, Svensson, B. & Jacquiod, S., 2020, In : Microbial Biotechnology.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing

    Schjoldager, Katrine Ter-Borch Gram, Vester-Christensen, M. B., Goth, Christoffer Knak, Petersen, T. N., Brunak, Søren, Bennett, Eric Paul, Levery, S. B. & Clausen, Henrik, 18 Nov 2011, In : Journal of Biological Chemistry. 286, 46, p. 40122-32 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. E-pub ahead of print

    Heterogeneity of treatment effect of prophylactic pantoprazole in adult ICU patients: a post hoc analysis of the SUP-ICU trial

    Granholm, A., Marker, S., Krag, M., Zampieri, F. G., Thorsen-Meyer, Hans-Christian, Kaas-Hansen, Benjamin Skov, van der Horst, I. C. C., Lange, Theis, Wetterslev, J., Perner, Anders & Møller, Morten Hylander, Jan 2020, In : Intensive Care Medicine.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    High-resolution transcription atlas of the mitotic cell cycle in budding yeast

    Granovskaia, M. V., Jensen, Lars Juhl, Ritchie, M. E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L. M., 1 Jan 2010, In : Genome Biology (Online Edition). 11, 3, p. R24

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Published

    Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

    Grassl, N., Kulak, N. A., Pichler, G., Geyer, P. E., Jung, J., Schubert, S., Sinitcyn, P., Cox, J. & Mann, Matthias, 21 Apr 2016, In : Genome Medicine. 8, 13 p., 44.

    Research output: Contribution to journalJournal articleResearchpeer-review

  42. Published

    Novel selective thiazoleacetic acids as CRTH2 antagonists developed from in silico derived hits. Part 2

    Grimstrup, M., Rist, Ø., Receveur, J., Frimurer, Thomas Michael, Ulven, Trond, Mathiesen, Jesper M., Kostenis, E. & Högberg, T., 1 Feb 2010, In : Bioorganic & Medicinal Chemistry Letters. 20, 3, p. 1181-1185 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Exploration of SAR features by modifications of thiazoleacetic acids as CRTH2 antagonists

    Grimstrup, M., Receveur, J. M., Rist, Ø., Frimurer, Thomas Michael, Nielsen, P. A., Mathiesen, Jesper M. & Högberg, T., 1 Mar 2010, In : Bioorganic and Medicinal Chemistry Letters. 20, 5, p. 1638-1641 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Toxicogenomics directory of rat hepatotoxicants in vivo and in cultivated hepatocytes

    Grinberg, M., Stöber, R. M., Albrecht, W., Edlund, K., Schug, M., Godoy, P., Cadenas, C., Marchan, R., Lampen, A., Braeuning, A., Buhrke, T., Leist, M., Oberemm, A., Hellwig, B., Kamp, H., Gardner, I., Escher, S., Taboureau, Olivier Thierry, Aguayo Orozco, Alejandro, Sachinidis, A., Ellinger-Ziegelbauer, H., Rahnenführer, J. & Hengstler, J. G., 2018, In : Archives of Toxicology. 92, 12, p. 3517-3533 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Effect of DNA on the conformational dynamics of the endonucleases I-DmoI as provided by molecular dynamics simulations

    Grottesi, A., Cecconi, S., Molina, Rafael & D'abramo, M., Dec 2016, In : Biopolymers. 105, 12, p. 898-904 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    TRIP12 and UBR5 Suppress Spreading of Chromatin Ubiquitylation at Damaged Chromosomes

    Gudjónsson, T., Altmeyer, M. F., Savic, V., Toledo Lazaro, Luis Ignacio, Dinant, C., Grøfte, M., Bartkova, J., Poulsen, M., Oka, Y., Bekker-Jensen, Simon Holst, Mailand, Niels, Neumann, B., Heriche, J., Shearer, R., Saunders, D., Bartek, J., Lukas, Jiri & Lukas, Claudia, 17 Aug 2012, In : Cell. 150, 4, p. 697-709 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. 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

  48. Accepted/In press

    Two new polymorphic structures of human full-length alpha-synuclein fibrils solved by cryo-electron microscopy

    Guerrero-Ferreira, R., Taylor, Nicholas M I, Arteni, A., Kumari, P., Mona, D., Ringler, P., Britschgi, M., Lauer, M. E., Makky, A., Verasdonck, J., Riek, R., Melki, R., Meier, B. H., Böckmann, A., Bousset, L. & Stahlberg, H., 2020, (Accepted/In press) In : eLife.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Published

    Heat shock protein 70 regulates cellular redox status by modulating glutathione-related enzyme activities

    Guo, S., Wharton, W., Moseley, Pope Lloyd & Shi, H., 2007, In : Cell Stress & Chaperones. 12, 3, p. 245-54 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. 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

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