The NNF Center for Protein Research

  1. Published

    Inhibitor of apoptosis (IAP) proteins in regulation of inflammation and innate immunity

    Damgaard, R. B. & Gyrd-Hansen, M., 2011, In : Discovery Medicine. 11, 58, p. 221-31 11 p.

    Research output: Contribution to journalReviewResearchpeer-review

  2. Published

    The Ubiquitin Ligase XIAP Recruits LUBAC for NOD2 Signaling in Inflammation and Innate Immunity

    Damgaard, R. B., Nachbur, U., Yabal, M., Wong, W. W., Fiil, B. K., Kastirr, M., Rieser, E., Rickard, J. A., Bankovacki, A., Peschel, C., Ruland, J., Bekker-Jensen, Simon Holst, Mailand, Niels, Kaufmann, T., Strasser, A., Walczak, H., Silke, J., Jost, P. J. & Gyrd-Hansen, M., 2012, In : Molecular Cell. 46, 6, p. 746-58 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Disease-causing mutations in the XIAP BIR2 domain impair NOD2-dependent immune signalling

    Damgaard, R. B., Fiil, B. K., Speckmann, C., Yabal, M., Stadt, U. Z., Bekker-Jensen, Simon Holst, Jost, P. J., Ehl, S., Mailand, Niels & Gyrd-Hansen, M., 1 Jul 2013, In : E M B O Journal. 5, p. 1278-1295 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Loss of ATM kinase activity leads to embryonic lethality in mice

    Daniel, J. A., Pellegrini, M., Filsuf, D., Nussenzweig, A., Belkina, N. V., Feigenbaum, L., Lee, B., Sleckman, B. P., You, Z., Guo, Z. & Paull, T. T., 6 Aug 2012, In : Journal of Cell Biology. 198, 3, p. 295-304 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    The AID-induced DNA damage response in chromatin

    Daniel, J. A. & Nussenzweig, A., 9 May 2013, In : Molecular Cell. 50, 3, p. 309-21 13 p.

    Research output: Contribution to journalReviewResearchpeer-review

  6. Published

    Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level

    Danielsen, J. M. R., Sylvestersen, K. B., Bekker-Jensen, Simon Holst, Szklarczyk, D., Poulsen, J. W., Horn, H., Jensen, Lars Juhl, Mailand, Niels & Nielsen, Michael Lund, 1 Mar 2011, In : Molecular and Cellular Proteomics. 10, 3, p. M110.003590

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger

    Danielsen, J. M. R., Povlsen, L. K., Villumsen, B. H., Streicher, W., Nilsson, Jakob, Wikström, M., Bekker-Jensen, Simon Holst & Mailand, Niels, 2012, In : Journal of Cell Biology. 197, 2, p. 179-87 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    LEDGF (p75) promotes DNA-end resection and homologous recombination

    Daugaard, M., Baude, A., Fugger, K., Povlsen, L. K., Beck, H., Sørensen, Claus Storgaard, Petersen, N. H. T., Sorensen, P. H. B., Lukas, Claudia, Bartek, J., Lukas, Jiri, Rohde, M. & Jaattela, Marja, Aug 2012, In : Nature Structural & Molecular Biology. 19, 8, p. 803-810 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Structure of p15PAF-PCNA complex and implications for clamp sliding during DNA replication and repair

    De Biasio, A., de Opakua, A. I., Mortuza, G. B., Molina, Rafael, Cordeiro, T. N., Castillo, F., Villate, M., Merino, N., Delgado, S., Gil-Cartón, D., Luque, I., Diercks, T., Bernadó, P., Montoya, Guillermo & Blanco, F. J., 12 Mar 2015, In : Nature Communications. 6, p. 1-12 6439.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Glycopeptide enrichment using a combination of ZIC-HILIC and cotton wool for exploring the glycoproteome of wheat flour albumins

    Dedvisitsakul, P., Jacobsen, S., Svensson, B., Bunkenborg, J., Finnie, C. & Hägglund, Per Mårten, 2 May 2014, In : Journal of Proteome Research. 13, 5, p. 2696-2703 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    Protein sequences bound to mineral surfaces persist into deep time

    Demarchi, B., Hall, S., Roncal-Herrero, T., Freeman, C. L., Woolley, J., Crisp, M. K., Wilson, J., Fotaki, Anna Katerina, Fischer, R., Kessler, B. M., Jersie-Christensen, R. R., Olsen, Jesper Velgaard, Haile, J., Thomas, J., Marean, C. W., Parkington, J., Presslee, S., Lee-Thorp, J., Ditchfield, P., Hamilton, J. F., Ward, M. W., Wang, C. M., Shaw, M. D., Harrison, T., Domínguez-Rodrigo, M., MacPhee, R. D. E., Kwekason, A., Ecker, M., Kolska Horwitz, L., Chazan, M., Kröger, R., Thomas-Oates, J., Harding, J. H., Cappellini, Enrico, Penkman, K. & Collins, Matthew James, 2016, In : eLife. 5, 50 p., e17092.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Immunologic manifestations of autophagy

    Deretic, V., Kimura, T., Timmins, G., Moseley, Pope Lloyd, Chauhan, S. & Mandell, M., 2015, In : Journal of Clinical Investigation. 125, 1, p. 75-84 10 p.

    Research output: Contribution to journalReviewResearchpeer-review

  13. Published

    Exercise-induced phospho-proteins in skeletal muscle

    Deshmukh, Atul Shahaji, Hawley, J. A. & Zierath, Juleen R, Sep 2008, In : International journal of obesity (2005). 32 Suppl 4, p. S18-23

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    Nitric oxide increases cyclic GMP levels, AMP-activated protein kinase (AMPK)alpha1-specific activity and glucose transport in human skeletal muscle

    Deshmukh, Atul Shahaji, Long, Y. C., de Castro Barbosa, T., Karlsson, H. K. R., Glund, S., Zavadoski, W. J., Gibbs, E. M., Koistinen, H. A., Wallberg-Henriksson, H. & Zierath, Juleen R, Jun 2010, In : Diabetologia. 53, 6, p. 1142-50 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Proteomics of Skeletal Muscle: Focus on Insulin Resistance and Exercise Biology

    Deshmukh, A., 2016, In : Proteomes. 4, 1, 19 p., 6.

    Research output: Contribution to journalReviewResearchpeer-review

  16. Published

    Proteomics-Based Comparative Mapping of the Secretomes of Human Brown and White Adipocytes Reveals EPDR1 as a Novel Batokine

    Deshmukh, Atul Shahaji, Peijs, Lone, Beaudry, J. L., Jespersen, N. Z., Nielsen, Carsten Haagen, Ma, T., Brunner, A. D., Larsen, T. J., Bayarri-Olmos, R., Prabhakar, B. S., Helgstrand, C., Severinsen, M. C. K., Holst, Birgitte, Kjær, Andreas, Tang-Christensen, M., Sanfridson, A., Garred, Peter, Privé, G. G., Pedersen, Bente Klarlund, Gerhart-Hines, Z., Nielsen, S., Drucker, D. J., Mann, Matthias & Schéele, Camilla Charlotte, 2019, In : Cell Metabolism. 30, 5, p. 963-975.e7 21 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Role of the AMPKgamma3 isoform in hypoxia-stimulated glucose transport in glycolytic skeletal muscle

    Deshmukh, Atul Shahaji, Glund, S., Tom, R. Z. & Zierath, Juleen R, Dec 2009, In : American Journal of Physiology: Endocrinology and Metabolism. 297, 6, p. E1388-94

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways and transcription factors

    Deshmukh, Atul Shahaji, Murgia, M., Nagaraja, N., Treebak, Jonas Thue, Cox, J. & Mann, Matthias, Apr 2015, In : Molecular and Cellular Proteomics. 14, 4, p. 841-853

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Published

    Insulin-stimulated glucose uptake in healthy and insulin-resistant skeletal muscle

    Deshmukh, Atul Shahaji, 1 Apr 2016, In : Hormone Molecular Biology and Clinical Investigation. 26, 1, p. 13-24 12 p.

    Research output: Contribution to journalReviewResearchpeer-review

  20. Published

    Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

    Deshmukh, Atul Shahaji, Cox, J., Jensen, Lars Juhl, Meissner, F. & Mann, Matthias, 6 Nov 2015, In : Journal of Proteome Research. 14, 11, p. 4885-95 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Analogues of the natural product Sinefungin as inhibitors of EHMT1 and EHMT2

    Devkota, K., Lohse, Brian, Liu, Q., Wang, M., Stærk, Dan, Berthelsen, J. & Clausen, Rasmus Prætorius, 2014, In : A C S Medicinal Chemistry Letters. 5, 4, p. 293-297

    Research output: Contribution to journalLetterResearchpeer-review

  22. Published

    Enhancement of the stability of a prolipase from Rhizopus oryzae toward aldehydes by saturation mutagenesis

    Di Lorenzo, M., Hidalgo, A., Molina, Rafael, Hermoso, J. A., Pirozzi, D. & Bornscheuer, U. T., Nov 2007, In : Applied and Environmental Microbiology. 73, 22, p. 7291-9 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    ENABLE 2017, the First European PhD and Post-Doc Symposium. Session 2: The OMICS Revolution

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Xicoy Cortada, H. & Zivanovic, S., 2018, In : Biomolecules. 8, 4, p. 1-6 116.

    Research output: Contribution to journalConference articleResearch

  24. Published

    ENABLE 2017, the First EUROPEAN PhD and Post-Doc Symposium. Session 3: In Vitro to In Vivo: Modeling Life in 3D

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Cortada, H. X. & Zivanovic, S., 2018, In : Journal of Personalized Medicine. 8, 2, p. 1-5 20.

    Research output: Contribution to journalConference articleResearch

  25. Published

    ENABLE 2017, the First European PhD and Post-Doc Symposium. Session 1: Building the Foundations of Biology: Synthetic and Cellular Research

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Xicoy Cortada, H. & Zivanovic, S., 2018, In : Biomolecules. 8, 3, p. 1-6 46.

    Research output: Contribution to journalConference articleResearch

  26. Published

    ENABLE 2017, the First EUROPEAN PhD and Post-Doc Symposium. Session 4: From Discovery to Cure: The Future of Therapeutics

    Di Mauro, G., Dondi, A., Giangreco, G., Hogrebe, A., Louer, E., Magistrati, E., Mullari, Meeli, Turon, G., Verdurmen, W., Xicoy Cortada, H. & Zivanovic, S., 2018, In : Medical Sciences. 6, 2, p. 1-6 6 p., 42.

    Research output: Contribution to journalConference articleResearch

  27. Published

    Self-reported restless legs syndrome and involuntary leg movements during sleep are associated with symptoms of attention deficit hyperactivity disorder

    Didriksen, M., Thørner, L. W., Erikstrup, C., Pedersen, O. B., Paarup, H. M., Petersen, M., Hansen, T. F., Banasik, Karina, Nielsen, K. R., Hjalgrim, H., Jennum, Poul, Sørensen, E., Burgdorf, K. S. & Ullum, Henrik, 2019, In : Sleep Medicine. 57, p. 115-121 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. Published

    Structural Analysis of a Complex between Small Ubiquitin-like Modifier 1 (SUMO1) and the ZZ Domain of CREB-binding Protein (CBP/p300) Reveals a New Interaction Surface on SUMO

    Diehl, C., Akke, M., Bekker-Jensen, Simon Holst, Mailand, Niels, Streicher, W. & Wikström, M., 10 Jun 2016, In : Journal of Biological Chemistry. 291, 24, p. 12658-12672 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes

    Diehl, C., Wisniewska, M., Frick, I., Streicher, W., Björck, L., Malmström, J. & Wikström, M., 2016, In : Frontiers in Microbiology. 7, 9 p., 95.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    Insight in the multilevel regulation of NER

    Dijk, M., Typas, Dimitris, Mullenders, L. & Pines, A., 15 Nov 2014, In : Experimental Cell Research. 329, 1, p. 116-23 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Published

    NOTCH3 inactivation increases triple negative breast cancer sensitivity to gefitinib by promoting EGFR tyrosine dephosphorylation and its intracellular arrest

    Diluvio, G., Del Gaudio, F., Giuli, M. V., Franciosa, Giulia, Giuliani, E., Palermo, R., Besharat, Z. M., Pignataro, M. G., Vacca, A., d'Amati, G., Maroder, M., Talora, C., Capalbo, C., Bellavia, D. & Checquolo, S., 2018, In : Critical Reviews in Oncogenesis. 7, p. 1-15 42.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Published

    Histone displacement during nucleotide excision repair

    Dinant, C., Bartek, J. & Bekker-Jensen, Simon Holst, 17 Oct 2012, In : International Journal of Molecular Sciences (Online). 13, 10, p. 13322-13337 16 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

    Ding, L., Paszkowski-Rogacz, M., Winzi, M., Chakraborty, D., Theis, M., Singh, S., Ciotta, G., Poser, I., Roguev, A., Chu, W. K., Choudhary, Chuna Ram, Mann, Matthias, Stewart, A. F., Krogan, N. & Buchholz, F., 26 Aug 2015, In : Cell Systems. 1, 2, p. 141-151 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Dairy consumption, systolic blood pressure, and risk of hypertension: Mendelian randomization study

    Ding, M., Huang, T., Bergholdt, H. K. M., Sørensen, Thorkild I.A., Linneberg, Allan René, Sandholt, C. H., Pedersen, Oluf Borbye, Hansen, Torben, Oskari Kilpeläinen, Tuomas, CHARGE Consortium, C. C., Nordestgaard, Børge, Ellervik, Christina, Qi, L. & Mendelian Randomization of Dairy Consumption Working Group, M. R. O. D. C. W. G., 2017, In : The BMJ. 356, 10 p., j1000.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Accepted/In press

    Cross-sectional study identifies lower risk of Staphylococcus aureus nasal colonization in Danish blood donors with hidradenitis suppurativa symptoms

    Dinh, K. M., Erikstrup, L. T., Andersen, R. K., Andersen, P. S., Mikkelsen, S., Kjerulff, B. D., Burgdorf, K. S., Hansen, Thomas Folkmann, Nielsen, K. R., Hjalgrim, H., Jemec, Gregor, Ullum, Henrik, Erikstrup, C. & Pedersen, O. B., 2020, (Accepted/In press) In : British Journal of Dermatology.

    Research output: Contribution to journalLetterResearchpeer-review

  36. Published

    Phospho.ELM: a database of phosphorylation sites--update 2011

    Dinkel, H., Chica, C., Via, A., Gould, C. M., Jensen, Lars Juhl, Gibson, T. J. & Diella, F., 1 Jan 2011, In : Nucleic Acids Symposium Series. 39, Database issue, p. D261-7

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Published

    LPS-induced cytokine levels are repressed by elevated expression of HSP70 in rats: possible role of NF-kappaB

    Dokladny, K., Lobb, R., Wharton, W., Ma, T. Y. & Moseley, Pope Lloyd, Mar 2010, In : Cell Stress & Chaperones. 15, 2, p. 153-63 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. Published

    Lack of cross-tolerance following heat and cadmium exposure in functional MDCK monolayers

    Dokladny, K., Wharton, W., Ma, T. Y. & Moseley, Pope Lloyd, Oct 2008, In : Journal of Applied Toxicology. 28, 7, p. 885-94 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Published

    Intestinal epithelial barrier function and tight junction proteins with heat and exercise

    Dokladny, K., Zuhl, M. N. & Moseley, Pope Lloyd, 15 Mar 2016, In : Journal of Applied Physiology. 120, 6, p. 692-701 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  40. Published

    Heat shock response and autophagy - cooperation and control

    Dokladny, K., Myers, O. B. & Moseley, Pope Lloyd, 2015, In : Autophagy. 11, 2, p. 200-213 14 p.

    Research output: Contribution to journalReviewResearchpeer-review

  41. 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

  42. Published

    Region and cell-type resolved quantitative proteomic map of the human heart

    Doll, S., Dreßen, M., Geyer, P. E., Itzhak, D. N., Braun, C., Doppler, S. A., Meier, F., Deutsch, M., Lahm, H., Lange, R., Krane, M. & Mann, Matthias, 13 Nov 2017, In : Nature Communications. 8, 1, 13 p., 1469.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Published

    Rapid proteomic analysis for solid tumors reveals LSD1 as a drug target in an end-stage cancer patient

    Doll, S., Kriegmair, M. C., Santos Delgado, Alberto, Wierer, M., Coscia, Fabian, Neil, Helen, Porubsky, S., Geyer, P. E., Mund, Andreas, Nuhn, P. & Mann, Matthias, 2018, In : Molecular Oncology. 12, 8, p. 1296-1307 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Published

    Renew or die: The molecular mechanisms of peptidoglycan recycling and antibiotic resistance in Gram-negative pathogens

    Domínguez-Gil, T., Molina, Rafael, Alcorlo, M. & Hermoso, J. A., Sep 2016, In : Drug Resistance Updates. 28, p. 91-104 14 p.

    Research output: Contribution to journalReviewResearchpeer-review

  45. Published

    Cytoscape stringApp: Network analysis and visualization of proteomics data

    Doncheva, Nadezhda Tsankova, Morris, J., Gorodkin, Jan & Jensen, Lars Juhl, 2019, In : Journal of Proteome Research. 18, 2, p. 623-632

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. Published

    Molecular architecture of the Jumonji C family histone demethylase KDM5B

    Dorosz, J., Kristensen, L. H., Aduri, N. G., Mirza, Osman Asghar, Lousen, R., Bucciarelli, S., Mehta, V., Sellés Baiget, Selene, Solbak, Sara Marie Øie, Bach, Anders, Mesa, Pablo, Hernandez, P. A., Montoya, Guillermo, Nguyen, T. T. T. N., Rand, Kasper Dyrberg, Boesen, T. & Gajhede, Michael, 2019, In : Scientific Reports. 9, 13 p., 4019.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. Published

    A spatially resolved proteomic atlas of psoriatic skin

    Dyring-Andersen, Beatrice, Lovendorf, M. B., Santos, A., Coscia, Fabian, Sørensen, L. B. P., Niu, Lili, Andersen, J. L., Teunissen, M. B., Skov, L. & Mann, Matthias, 2019, In : Journal of Investigative Dermatology. 139, 9, suppl., p. S260 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  48. Published

    A spatially resolved proteomic atlas of human skin and its associated immune system

    Dyring-Andersen, Beatrice, Coscia, Fabian, Santos, A., Løvendorf, M. B., Sørensen, L. B. P., Niu, Lili, Andersen, J. L., Clark, R., Skov, L., Teunissen, M. B. & Mann, Matthias, 2019, In : Journal of Investigative Dermatology. 139, 9, suppl., p. S259 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  49. Published

    A Map of General and Specialized Chromatin Readers in Mouse Tissues Generated by Label-free Interaction Proteomics

    Eberl, H. C., Mann, M., Spruijt, C. G., Vermeulen, M. & Kelstrup, C. D., 24 Jan 2013, In : Molecular Cell. 49, 2, p. 368-378 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Published

    Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts

    Eckert, M. A., Coscia, Fabian, Chryplewicz, A., Chang, J. W., Hernandez, K. M., Pan, S., Tienda, S. M., Nahotko, D. A., Li, G., Blaženović, I., Lastra, R. R., Curtis, M., Yamada, S. D., Perets, R., McGregor, S. M., Andrade, J., Fiehn, O., Moellering, R. E., Mann, Matthias & Lengyel, E., 2019, In : Nature. 569, 7758, p. 723-728

    Research output: Contribution to journalLetterResearchpeer-review

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