The NNF Center for Protein Research

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  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

    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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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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