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

  51. 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

  52. E-pub ahead of print

    Multi-site SUMOylation restrains DNA polymerase η interactions with DNA damage sites

    Guérillon, C., Smedegaard, S., Hendriks, Ivo Alexander, Nielsen, Michael Lund & Mailand, Niels, 29 Apr 2020, In : The Journal of Biological Chemistry.

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Published

    Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq

    Gådin, J. R., Buil, A., Colantuoni, C., Jaffe, A. E., Nielsen, J., Shin, J., Hyde, T. M., Kleinman, J. E., Plath, N., Eriksson, P., Brunak, Søren, Didriksen, M., Weinberger, D. R., Folkersen, L. & BrainSeq Consortium, B. C., 2019, In : PLoS ONE. 14, 6, 16 p., e0217765.

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. Published

    Mobi-DIK (Ion Mobility DIA Analysis Kit): Targeted analysis software for diaPASEF data improves proteome coverage

    Ha, A., Frank, M., Meier, F., Brunner, A., Kaspar-Schoenefeld, S., Koch, S., Lubeck, M., Raether, O., Collins, B. C., Aebersold, R., Mann, Matthias & Rost, H., 2019, In : Molecular & Cellular Proteomics. 18, 8, p. S17 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  55. Published

    Activation of the ATR kinase by the RPA-binding protein ETAA1

    Haahr, Peter Thorlund, Hoffmann, Saskia, Tollenaere, M. A. X., Ho, T., Toledo Lazaro, Luis Ignacio, Mann, Matthias, Bekker-Jensen, Simon Holst, Räschle, M. & Mailand, Niels, Nov 2016, In : Nature Cell Biology. 18, 11, p. 1196–1207

    Research output: Contribution to journalJournal articleResearchpeer-review

  56. Published

    ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote Genome Stability

    Haahr, Peter Thorlund, Borgermann, N., Guo, X., Typas, Dimitris, Achuthankutty, D., Hoffmann, Saskia, Shearer, Robert Francis, Sixma, T. K. & Mailand, Niels, 2018, In : Molecular Cell. 70, 1, p. 165-174

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    The Glucose-Insulin Control System

    Hallgreen, Christine Erikstrup, Korsgaard, T. V., Hansen, R. N. & Colding-Jørgensen, M., 11 Jul 2008, Biosimulation in Drug Development. Wiley-VCH, p. 141-196 56 p.

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

  58. Published

    Dynamic lineage priming is driven via direct enhancer regulation by ERK

    Hamilton, William, Mosesson, Y., Soares Monteiro, Ana Rita, Emdal, Kristina Bennet, Knudsen, Teresa Emmilie Toudal, Francavilla, C., Barkai, N., Olsen, Jesper Velgaard & Brickman, Joshua Mark, 2019, In : Nature. 575, p. 355-360

    Research output: Contribution to journalJournal articleResearchpeer-review

  59. 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

  60. Published

    Allosteric regulation of Csx1, a type IIIB-associated CARF domain ribonuclease by RNAs carrying a tetraadenylate tail

    Han, W., Pan, S., López-Méndez, B., Montoya, Guillermo & She, Q., 13 Oct 2017, In : Nucleic Acids Research. 45, 18, p. 10740-10750 11 p., gkx726.

    Research output: Contribution to journalJournal articleResearchpeer-review

  61. Published

    Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation

    Hansen, B. K., Gupta, R., Baldus, L., Lyon, D., Narita, Takeo, Lammers, M., Choudhary, Chuna Ram & Weinert, B. T., 2019, In : Nature Communications. 10, 11 p., 1055.

    Research output: Contribution to journalJournal articleResearchpeer-review

  62. Published

    Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development

    Hansen, K. L., Greenway, S. C., Rosenfeld, J. A., Wakimoto, H., Gorham, J. M., Segrè, A. V., Roberts, A. E., Smoot, L. B., Pu, W. T., C Pereira, A., Mesquita, S. M., Tommerup, Niels, Brunak, Søren, Ballif, B. C., Shaffer, L. G., Donahoe, P. K., Daly, M. J., Seidman, J. G., Seidman, C. E. & Larsen, Lars Allan, 2012, In : Proceedings of the National Academy of Sciences USA (PNAS). 109, 35, p. 14035-40 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  63. Published

    A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

    Hansen, K. L., Hansen, N. T., Karlberg, E. O., Eklund, A. C., Roque, F. S., Donahoe, P. K., Szallasi, Z., Jensen, T. S. & Brunak, Søren, 2008, In : Proceedings of the National Academy of Science of the United States of America. 105, 52, p. 20870-5 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  64. Published

    Dissecting spatio-temporal protein networks driving human heart development and related disorders

    Hansen, K. L., Møllgård, Kjeld, Greenway, S., Wakimoto, H., Gorham, J. M., Workman, C. T., Bendsen, E., Hansen, N. T., Rigina, O., Roque, F. S., Wiese, C., Christoffels, V. M., Roberts, A. E., Smoot, L. B., Pu, W. T., Donahoe, P. K., Tommerup, Niels, Brunak, Søren, Seidman, C. E., Seidman, J. G. & Larsen, Lars Allan, 2010, In : Molecular Systems Biology. 6, p. 381

    Research output: Contribution to journalJournal articleResearchpeer-review

  65. Published

    SCAI promotes DNA double-strand break repair in distinct chromosomal contexts

    Hansen, R. K., Mund, Andreas, Poulsen, S. L., Sandoval, M., Klement, K., Tsouroula, K., Tollenaere, M. A. X., Räschle, M., Soria, R., Offermanns, S., Worzfeld, T., Grosse, R., Brandt, D. T., Rozell, B., Mann, Matthias, Cole, F., Soutoglou, E., Goodarzi, A. A., Daniel, J. A., Mailand, Niels & Bekker-Jensen, Simon Holst, 7 Nov 2016, In : Nature Cell Biology. 18, 12, p. 1357–1366

    Research output: Contribution to journalLetterResearchpeer-review

  66. 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, Jun, 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

  67. 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

  68. Published

    Predicting treatment response using pharmacy register in migraine

    Hansen, Thomas Folkmann, Chalmer, M. A., Haspang, T. M., Kogelman, L. & Olesen, Jes, 2019, In : The Journal of Headache and Pain. 20, p. 31 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  69. Published

    DBDS Genomic Cohort, a prospective and comprehensive resource for integrative and temporal analysis of genetic, environmental and lifestyle factors affecting health of blood donors

    Hansen, Thomas Folkmann, Banasik, Karina, Erikstrup, C., Pedersen, Ole Birger Vesterager, Westergaard, David, Chmura, P. J., Nielsen, K., Thørner, L., Hjalgrim, H., Paarup, H., Larsen, M. A. H., Petersen, M., Jennum, Poul, Andersen, S., Nyegaard, M., Jemec, Gregor, Olesen, Jes, Werge, Thomas, Johansson, P. I., Sørensen, E., Brunak, Søren, Ullum, Henrik & Burgdorf, K. S., 9 Jun 2019, In : BMJ Open. 9, 6, p. 1-7 7 p., e028401.

    Research output: Contribution to journalJournal articleResearchpeer-review

  70. 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

  71. Published

    A quantitative Streptococcus pyogenes - human protein - protein interaction map reveals localization of opsonizing antibodies

    Happonen, L., Hauri, S., Svensson Birkedal, G., Karlsson, C., de Neergaard, T., Khakzad, H., Nordenfelt, P., Wikström, M., Wisniewska, M., Björck, L., Malmström, L. & Malmström, J., 2019, In : Nature Communications. 10, 15 p., 2727.

    Research output: Contribution to journalJournal articleResearchpeer-review

  72. Published

    Molecular determinants of subtype-selective efficacies of cytisine and the novel compound NS3861 at heteromeric nicotinic acetylcholine receptors

    Harpsøe, Kasper, Hald, H., Timmermann, D. B., Jensen, M. L., Dyhring, T., Nielsen, E. Ø., Peters, D., Balle, T., Gajhede, Michael, Kastrup, Jette Sandholm Jensen & Ahring, P. K., 25 Jan 2013, In : Journal of Biological Chemistry. 288, 4, p. 2559-2570 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  73. Published

    Predicting biological networks from genomic data

    Harrington, E. D., Jensen, Lars Juhl & Bork, P., 2008, In : F E B S Letters. 582, 8, p. 1251-8 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  74. Published

    Mesothelial Cell HIF1α Expression Is Metabolically Downregulated by Metformin to Prevent Oncogenic Tumor-Stromal Crosstalk

    Hart, P. C., Kenny, H. A., Grassl, N., Watters, K. M., Litchfield, L. M., Coscia, Fabian, Blaženović, I., Ploetzky, L., Fiehn, O., Mann, Matthias, Lengyel, E. & Romero, I. L., 2019, In : Cell Reports. 29, 12, p. 4086-4098.e6

    Research output: Contribution to journalJournal articleResearchpeer-review

  75. 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

  76. 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

  77. Published

    Are graph databases ready for bioinformatics?

    Have, C. T. & Jensen, Lars Juhl, 21 Oct 2013, In : Bioinformatics (Online). 2 p.

    Research output: Contribution to journalEditorialResearch

  78. Published

    Prenatal exposure to paracetamol/acetaminophen and precursor aniline impairs masculinisation of male brain and behaviour

    Hay-Schmidt, Anders, Finkielman, O. T. E., Jensen, Benjamin Anderschou Holbech, Høgsbro, C. F., Holm, J. B., Johansen, K. H., Jensen, T. K., Andrade, A. M., Swan, S. H., Bornehag, C., Brunak, Søren, Jegou, B., Kristiansen, Karsten & Kristensen, D. M., 2017, In : Reproduction. 154, 2, p. 145-152 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  79. 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

  80. Published

    Stable MCC binding to the APC/C is required for a functional spindle assembly checkpoint

    bmk286, bmk286 & Nilsson, Jakob, 25 Jan 2014, In : E M B O Reports. 15, p. 264-272

    Research output: Contribution to journalJournal articleResearchpeer-review

  81. Published

    Distinct kinetics of serine and threonine dephosphorylation are essential for mitosis

    bmk286, bmk286, Hertz, Emil Peter Thrane, Garvanska, Dimitriya Hristoforova, Kruse, Thomas & Nilsson, Jakob, 2017, In : Nature Cell Biology. 19, p. 1433-1440

    Research output: Contribution to journalJournal articleResearchpeer-review

  82. Published

    Interphase APC/C-Cdc20 inhibition by cyclin A2-Cdk2 ensures efficient mitotic entry

    bmk286, bmk286 & Nilsson, Jakob, Mar 2016, In : Nature Communications. 7, 10 p., 10975.

    Research output: Contribution to journalJournal articleResearchpeer-review

  83. Published

    TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells

    Hekmat, O., Munk, S., Fogh, L., Yadav, R., Francavilla, C., Horn, H., Würtz, S. Ø., Schrohl, A., Damsgaard, B., Romer, M. U., Belling, Kirstine G, Jensen, N. F., Gromova, I., Bekker-Jensen, D. B., Moreira, José, Jensen, Lars Juhl, Gupta, R., Lademann, U. A., Brünner, Nils, Olsen, Jesper Velgaard & Stenvang, Jan, 5 Aug 2013, In : Journal of Proteome Research. 12, 9, p. 4136-4151 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  84. Published

    Four weeks one-leg training and high fat diet does not alter PPARα protein or mRNA expression in human skeletal muscle

    Helge, Jørn Wulff, Bentley, D., Schjerling, P., Willer, M., Gibala, M. J., Franch, J., Tapia-Laliena, M. A., Daugaard, J. R. & Andersen, J. L., 1 Sep 2007, In : European Journal of Applied Physiology. 101, 1, p. 105-114 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  85. Published

    Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

    Hendriks, Ivo Alexander, Lyon, D., Young, C., Jensen, Lars Juhl, Vertegaal, A. C. O. & Nielsen, Michael Lund, Mar 2017, In : Nature Structural and Molecular Biology. 24, 3, p. 325-336 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  86. Published

    A comprehensive compilation of SUMO proteomics

    Hendriks, Ivo Alexander & Vertegaal, A. C. O., Sep 2016, In : Nature Reviews. Molecular Cell Biology. 17, 9, p. 581-95 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  87. Published

    Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4)

    Hendriks, I. A., Schimmel, J., Eifler, K., Olsen, Jesper Velgaard & Vertegaal, A. C. O., 19 Jun 2015, In : The Journal of Biological Chemistry. 290, 25, p. 15526-37 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  88. Published

    SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage

    Hendriks, I. A., Treffers, L. W., Verlaan-de Vries, M., Olsen, Jesper Velgaard & Vertegaal, A. C. O., 17 Mar 2015, In : Cell Reports. 10, 10, p. 1778–1791

    Research output: Contribution to journalJournal articleResearchpeer-review

  89. Published

    An advanced strategy for comprehensive profiling of ADP-ribosylation sites using mass spectrometry-based proteomics

    Hendriks, Ivo Alexander, Buch-Larsen, Sara Charlotte & Nielsen, Michael Lund, 2019, In : Molecular and Cellular Proteomics. 18, 5, p. 1010-1026

    Research output: Contribution to journalJournal articleResearchpeer-review

  90. Published

    Site-specific characterization of endogenous SUMOylation across species and organs

    Hendriks, Ivo Alexander, Lyon, D., Su, D., Skotte, Niels Henning, Daniel, J. A., Jensen, Lars Juhl & Nielsen, Michael Lund, 2018, In : Nature Communications. 9, p. 1-17 2456.

    Research output: Contribution to journalJournal articleResearchpeer-review

  91. 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

  92. Published

    Proteomic evidence of dietary sources in ancient dental calculus

    Hendy, J., Warinner, C., Bouwman, A., Collins, Matthew James, Fiddyment, S., Fischer, R., Hagan, R., Hofman, C. A., Holst, M., Chaves, E., Klaus, L., Larson, G., Mackie, Meaghan, McGrath, K., Mundorff, A. Z., Radini, A., Rao, H., Trachsel, C., Velsko, I. M. & Speller, C. F., 2018, In : Proceedings of the Royal Society B: Biological Sciences. 285, 1883, 977.

    Research output: Contribution to journalJournal articleResearchpeer-review

  93. Published

    Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae

    Henriksen, P., Wagner, S. A., Weinert, B. T., Sharma, S., Bacinskaja, G., Rehman, M., Juffer, A. H., Walther, T. C., Lisby, Michael & Choudhary, Chuna Ram, 2012, In : Molecular & Cellular Proteomics. 11, 11, p. 1510-1522 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  94. Published

    Common genomic signaling among initial DNA damage and radiation-induced apoptosis in peripheral blood lymphocytes from locally advanced breast cancer patients

    Henríquez-Hernández, L. A., Pinar, B., Carmona-Vigo, R., Bordón, E., Rodríguez-Gallego, C., Flores Morales, A. & Lara, P. C., 2013, In : Breast (Edinburgh, Scotland). 22, 1, p. 28-33 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  95. Published

    Molecular Basis of the Mechanisms Controlling MASTL

    Hermida, D., Mortuza, G. B., Pedersen, A., Pozdnyakova, I., Nguyen, T. T. T. N., Maroto, M., Williamson, M., Ebersole, T., Cazzamali, G., Rand, Kasper Dyrberg, Olsen, J. V., Malumbres, M. & Montoya, Guillermo, 2020, In : Molecular & Cellular Proteomics. 19, 2, p. 326-343

    Research output: Contribution to journalJournal articleResearchpeer-review

  96. Published

    The crystal structure of feruloyl esterase A from Aspergillus niger suggests evolutive functional convergence in feruloyl esterase family

    Hermoso, J. A., Sanz-Aparicio, J., Molina, Rafael, Juge, N., González, R. & Faulds, C. B., 30 Apr 2004, In : Journal of Molecular Biology. 338, 3, p. 495-506 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  97. Published

    A Conserved Motif Provides Binding Specificity to the PP2A-B56 Phosphatase

    Hertz, Emil Peter Thrane, Kruse, Thomas, Davey, N. E., López-Méndez, B., Sigurdsson, J. O., Montoya, Guillermo, Olsen, Jesper Velgaard & Nilsson, Jakob, 2016, In : Molecular Cell. 63, 4, p. 686-695 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  98. Published

    Localization of PP2A-B56 to centromeres in Drosophila

    Hertz, Emil Peter Thrane & Nilsson, Jakob, 3 Aug 2017, In : Cell Cycle. 16, 15, p. 1385-1386 2 p.

    Research output: Contribution to journalEditorialResearchpeer-review

  99. Published

    A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution

    Hidalgo, A., Schliessmann, A., Molina, Rafael, Hermoso, J. & Bornscheuer, U. T., Sep 2008, In : Protein Engineering Design and Selection (Print). 21, 9, p. 567-76 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  100. Published

    Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types

    Hjaltelin, Jessica Xin, Izarzugaza, J. M. G., Jensen, Lars Juhl, Russo, Francesco, Westergaard, David & Brunak, Søren, 2019, In : npj Systems Biology and Applications. 5, 10 p., 27.

    Research output: Contribution to journalJournal articleResearchpeer-review

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