The NNF Center for Protein Research

  1. Published

    Quantitative, high-resolution proteomics for data-driven systems biology

    Cox, J. & Mann, Matthias, 7 Jul 2011, In : Annual Review of Biochemistry. 80, p. 273-299 27 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    Andromeda - a peptide search engine integrated into the MaxQuant environment

    Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, Jesper Velgaard & Mann, Matthias, 1 Apr 2011, In : Journal of Proteome Research. 10, 4, p. 1794-805 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Complete Mapping of Complex Disulfide Patterns with Closely-Spaced Cysteines by In-Source Reduction and Data-Dependent Mass Spectrometry

    Cramer, C. N., Kelstrup, C. D., Olsen, Jesper Velgaard, Haselmann, K. F. & Nielsen, P. K., 6 Jun 2017, In : Analytical Chemistry. 89, 11, p. 5949-5957 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Disulfide Linkage Characterization of Disulfide Bond-Containing Proteins and Peptides by Reducing Electrochemistry and Mass Spectrometry

    Cramer, C. N., Haselmann, K. F., Olsen, Jesper Velgaard & Nielsen, P. K., 2 Feb 2016, In : Analytical Chemistry. 88, 3, p. 1585-1592 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    Generic Workflow for Mapping of Complex Disulfide Bonds Using In-Source Reduction and Extracted Ion Chromatograms from Data-Dependent Mass Spectrometry

    Cramer, C. N., Kelstrup, C., Olsen, Jesper Velgaard, Haselmann, K. F. & Nielsen, P. K., 2018, In : Analytical Chemistry. 90, 13, p. 8202-8210

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

    Croft, L. J., Szklarczyk, D., Jensen, Lars Juhl & Gorodkin, Jan, 2012, In : B M C Systems Biology. 6, 1, p. 90

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    Early differences in islets from prediabetic NOD mice: combined microarray and proteomic analysis

    Crèvecoeur, I., Gudmundsdottir, V., Vig, S., Marques Câmara Sodré, F., D'Hertog, W., Fierro, A. C., Van Lommel, L., Gysemans, C., Marchal, K., Waelkens, E., Schuit, F., Brunak, Søren, Overbergh, L. & Mathieu, C., Mar 2017, In : Diabetologia. 60, 3, p. 475-489 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

    Csikász-Nagy, A., Kapuy, O., Tóth, A., Pál, C., Jensen, Lars Juhl, Uhlmann, F., Tyson, J. J. & Novák, B., 2009, In : Molecular Systems Biology. 5, p. 236

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism

    Cuesta-Astroz, Y., Santos, A., Oliveira, G. & Jensen, Lars Juhl, 2019, In : Frontiers in Immunology. 10, 17 p., 212.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Discovering miRNA regulatory networks in holt-oram syndrome using a zebrafish model

    D'Aurizio, R., Russo, Francesco, Chiavacci, E., Baumgart, M., Groth, M., D'Onofrio, M., Arisi, I., Rainaldi, G., Pitto, L. & Pellegrini, M., 14 Jul 2016, In : Frontiers in Bioengineering and Biotechnology. 4, JUL, 60.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Published

    A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation

    Dalgaard, M. D., Weinhold, N., Edsgärd, D., Silver, J. D., Pers, T. H., Nielsen, J. E., Jørgensen, N., Juul, Anders, Gerds, Thomas Alexander, Giwercman, A., Giwercman, Y. L., Cohn-Cedermark, G., Virtanen, H. E., Toppari, J., Daugaard, G., Jensen, T. S., Brunak, Søren, Rajpert-De Meyts, E., Skakkebæk, N. E., Leffers, H. & Gupta, R., 2012, In : Journal of Medical Genetics. 49, 1, p. 58-65 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Ten simple rules for getting help from online scientific communities

    Dall'olio, G. M., Marino, J., Schubert, M., Keys, K. L., Stefan, M. I., Gillespie, C. S., Poulain, P., Shameer, K., Sugar, R., Invergo, B. M., Jensen, Lars Juhl, Bertranpetit, J. & Laayouni, H., 1 Sep 2011, In : P L o S Computational Biology. 7, 9, p. e1002202

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Clinical association to FKBP5 rs1360780 in patients with depression

    Dam, Henrik, Buch, J. O. D., Nielsen, Annelaura Bach, Weikop, P., Werge, Thomas & Jørgensen, M. B., 2019, In : Psychiatric Genetics. 29, 6, p. 220-225 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

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