The NNF Center for Protein Research

  1. Published

    Enamel proteome sequences from Dmanisi (Georgia) enable molecular phylogeny beyond the limits of ancient DNA preservation

    Cappellini, Enrico, Welker, Frido, Olsen, Jesper Velgaard, Lordkipanidze, D. & Willerslev, Eske, 2019, In : American Journal of Physical Anthropology. 168, suppl. 68, p. 35 1 p.

    Research output: Contribution to journalConference abstract in journalResearch

  2. Published

    Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)

    Cappellini, Enrico, Gentry, A., Palkopoulou, E., Ishida, Y., Cram, D., Roos, A., Watson, M., Johansson, U. S., Fernholm, B., Agnelli, P., Barbagli, F., Littlewood, D. T. J., Kelstrup, C., Olsen, Jesper Velgaard, Lister, A. M., Roca, A. L., Dalén, L. & Gilbert, M Thomas P, 2014, In : Zoological Journal of the Linnean Society. 170, 1, p. 222-232 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    Systems biology approach identifies the kinase Csnk1a1 as a regulator of the DNA damage response in embryonic stem cells

    Carreras Puigvert, J., von Stechow, L., Siddappa, R., Pines, A., Bahjat, M., Haazen, L. C. J. M., Olsen, Jesper Velgaard, Vrieling, H., Meerman, J. H. N., Mullenders, L. H. F., van de Water, B. & Danen, E. H. J., 2013, In : Science Signaling. 6, 259, p. ra5 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  4. Published

    Mislocalization of the MRN complex prevents ATR signaling during adenovirus infection

    Carson, C. T., Orazio, N. I., Lee, D. V., Suh, J., Bekker-Jensen, Simon Holst, Araujo, F. D., Lakdawala, S. S., Lilley, C. E., Bartek, J., Lukas, Jiri & Weitzman, M. D., 2009, In : EMBO Journal. 28, 6, p. 652-62 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver

    Cavalli, M., Diamanti, K., Pan, G., Spalinskas, R., Kumar, C., Deshmukh, Atul Shahaji, Mann, Matthias, Sahlén, P., Komorowski, J. & Wadelius, C., 16 Mar 2020, In : O M I C S: A Journal of Integrative Biology.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    EphrinB1/EphB3b Coordinate Bidirectional Epithelial-Mesenchymal Interactions Controlling Liver Morphogenesis and Laterality

    Cayuso, J., Dzementsei, A., Fischer, J. C., Karemore, Gopal, Caviglia, Sara, Bartholdson, J., Wright, G. J. & Ober, Elke, 7 Nov 2016, In : Developmental Cell. 39, 3, p. 316-328 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Published

    LocText: relation extraction of protein localizations to assist database curation

    Cejuela, J. M., Vinchurkar, S., Goldberg, T., Prabhu Shankar, M. S., Baghudana, A., Bojchevski, A., Uhlig, C., Ofner, A., Raharja-Liu, P., Jensen, Lars Juhl & Rost, B., 2018, In : BMC Bioinformatics. 19, p. 1-11 15.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Published

    CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer

    Cepeda, D., Ng, H., Sharifi, H. R., Mahmoudi, S., Cerrato, V. S., Fredlund, E., Magnusson, K., Nilsson, H., Malyukova, A., Rantala, J., Klevebring, D., Viñals, F., Bhaskaran, N., Zakaria, S. M., Rahmanto, A. S., Grotegut, S., Nielsen, Michael Lund, Szigyarto, C. A., Sun, D., Lerner, M., Navani, S., Widschwendter, M., Uhlén, M., Jirström, K., Pontén, F., Wohlschlegel, J., Grandér, D., Spruck, C., Larsson, L. & Sangfelt, O., 3 Jul 2013, In : E M B O Molecular Medicine (Online). 5, 7, p. 1067-1086 20 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  9. Published

    lncRNA Panct1 Maintains Mouse Embryonic Stem Cell Identity by Regulating TOBF1 Recruitment to Oct-Sox Sequences in Early G1

    Chakraborty, D., Paszkowski-Rogacz, M., Berger, N., Ding, L., Mircetic, J., Fu, J., Iesmantavicius, V., Choudhary, Chuna Ram, Anastassiadis, K., Stewart, A. F. & Buchholz, F., 12 Dec 2017, In : Cell Reports. 21, 11, p. 3012-3021 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

    Nosographic analysis of osmophobia and field testing of diagnostic criteria including osmophobia

    Chalmer, M. A., Hansen, Thomas Folkmann & Olesen, Jes, 2019, In : Cephalalgia. 39, 1, p. 38-43 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. E-pub ahead of print

    Proposed new diagnostic criteria for chronic migraine

    Chalmer, M. A., Hansen, Thomas Folkmann, Lebedeva, E. R., Dodick, D. W., Lipton, R. B. & Olesen, Jes, 2020, In : Cephalalgia.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Published

    Replication fork stability confers chemoresistance in BRCA-deficient cells

    Chaudhuri, A. R., Callen, E., Ding, X., Gogola, E., Duarte, A. A., Lee, J., Wong, N., Lafarga, V., Calvo, J. A., Panzarino, N. J., John, S., Day, A., Crespo, A. V., Shen, B., Starnes, L. M., de Ruiter, J. R., Daniel, J. A., Konstantinopoulos, P. A., Cortez, D., Cantor, S. B., Fernandez-Capetillo, O., Ge, K., Jonkers, J., Rottenberg, S., Sharan, S. K. & Nussenzweig, A., 2016, In : Nature. 535, 7612, p. 382-7 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

    Chhabra, S. R., Joachimiak, M. P., Petzold, C. J., Zane, G. M., Price, M. N., Reveco, S. A., Fok, V., Johanson, A. R., Batth, Tanveer Singh, Singer, M., Chandonia, J., Joyner, D., Hazen, T. C., Arkin, A. P., Wall, J. D., Singh, A. K. & Keasling, J. D., 2011, In : PLOS ONE. 6, 6, p. e21470

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Published

    MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome

    Chiavacci, E., Daurizio, R., Guzzolino, E., Russo, Francesco, Baumgart, M., Groth, M., Mariani, L., Donofrio, M., Arisi, I., Pellegrini, M., Cellerino, A., Cremisi, F. & Pitto, L., 14 Dec 2015, In : Scientific Reports. 5, 18240.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Published

    Lysine acetylation targets protein complexes and co-regulates major cellular functions

    Choudhary, Chuna Ram, Kumar, C., Gnad, F., Nielsen, Michael Lund, Rehman, M., Walther, T. C., Olsen, Jesper Velgaard & Mann, Matthias, 2009, In : Science. 325, 5942, p. 834-40 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. Published

    Decoding signalling networks by mass spectrometry-based proteomics

    Choudhary, Chuna Ram & Mann, Matthias, 1 Jun 2010, In : Nature Reviews. Molecular Cell Biology. 11, 6, p. 427-39 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  17. Published

    Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes

    Choudhary, Chuna Ram, Olsen, Jesper Velgaard, Brandts, C., Cox, J., Reddy, P. N. G., Böhmer, F. D., Gerke, V., Schmidt-Arras, D., Berdel, W. E., Müller-Tidow, C., Mann, Matthias & Serve, H., 2009, In : Molecular Cell. 36, 2, p. 326-39 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Published

    The growing landscape of lysine acetylation links metabolism and cell signalling

    Choudhary, Chuna Ram, Weinert, B. T., Nishida, Y., Verdin, E. & Mann, Matthias, 23 Jul 2014, In : Nature Reviews. Molecular Cell Biology. 15, 8, p. 536-50 15 p.

    Research output: Contribution to journalReviewResearchpeer-review

  19. Published

    Quantitative phosphoproteomics dissection of 7TM receptor signaling using full and biased agonists

    Christensen, G. L., Kelstrup, C., Lyngsø, C., Sarwar, U., Bøgebo, R., Sheikh, S. P., Gammeltoft, S., Olsen, Jesper Velgaard & Hansen, J. L., Jul 2010, In : Molecular and Cellular Proteomics. 9, 7, p. 1540-53 14 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Bile acids drive colonic secretion of glucagon-like-peptide 1 and peptide-YY in rodents

    Christiansen, Charlotte Bayer, Trammell, Sam, Albrechtsen, Nicolai Jacob Wewer, Schoonjans, K., Albrechtsen, Reidar, Gillum, Matthew Paul, Kuhre, Rune Ehrenreich & Holst, Jens Juul, 2019, In : American Journal of Physiology: Gastrointestinal and Liver Physiology. 316, 5, p. G574-G584 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Published

    Citrullination regulates pluripotency and histone H1 binding to chromatin

    Christophorou, M. A., Castelo-Branco, G., Halley-Stott, R. P., Oliveira, C. S., Loos, R., Radzisheuskaya, A., Mowen, K. A., Bertone, P., Silva, J. C. R., Zernicka-Goetz, M., Nielsen, Michael Lund, Gurdon, J. B. & Kouzarides, T., 6 Mar 2014, In : Nature. 507, p. 104-108

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. Published

    FBH1 influences DNA replication fork stability and homologous recombination through ubiquitylation of RAD51

    Chu, W. K., Payne, M. J., Beli, P., Hanada, K., Choudhary, C. & Hickson, Ian David, 2015, In : Nature Communications. 6, 7 p., 5931.

    Research output: Contribution to journalJournal articleResearchpeer-review

  23. Published

    Ezrin mediates c-Myc actions in prostate cancer cell invasion

    Chuan, Y. C., Iglesias Gato, Diego, Fernandez-Perez, L., Cedazo-Minguez, A., Pang, S., Norstedt, G., Pousette, A. & Flores-Morales, A., 2010, In : Oncogene. 29, 10, p. 1531-42 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. Published

    Molecular Portrait of Breast-Cancer-Derived Cell Lines Reveals Poor Similarity with Tumors

    Cifani, P., Kirik, U., Waldemarson, S. & James, P., 2 Jul 2015, In : Journal of Proteome Research. 14, 7, p. 2819-27 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Published

    GLP-1 Is a Coronary Artery Vasodilator in Humans

    Clarke, S. J., Giblett, J. P., Yang, L. L., Hubsch, A., Zhao, T., Aetesam-ur-Rahman, M., West, N. E. J., O'Sullivan, M., Figg, N., Bennett, M., Albrechtsen, Nicolai Jacob Wewer, Deacon, Carolyn F., Cheriyan, J. & Hoole, S. P., 20 Nov 2018, In : Journal of the American Heart Association. 7, 22, 14 p., e010321.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Published

    Interpreting pathways to discover cancer driver genes with Moonlight

    Colaprico, A., Olsen, C., Bailey, M. H., Odom, G. J., Terkelsen, T., Silva, T. C., Olsen, A. V., Cantini, L., Zinovyev, A., Barillot, E., Noushmehr, H., Bertoli, G., Castiglioni, I., Cava, C., Bontempi, G., Chen, X. S. & Papaleo, Elena, 2020, In : Nature Communications. 11, 17 p., 69.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Published

    Proteomics for blood biomarker exploration of severe mental illness: pitfalls of the past and potential for the future

    Comes, A. L., Papiol, S., Mueller, T., Geyer, P. E., Mann, Matthias & Schulze, T. G., 2018, In : Translational Psychiatry. 8, p. 1-15 15 p., 160.

    Research output: Contribution to journalReviewResearchpeer-review

  28. Published

    Functional and in silico assessment of MAX variants of unknown significance

    Comino-Méndez, I., Leandro-García, L. J., Montoya, Guillermo, Inglada-Pérez, L., de Cubas, A. A., Currás-Freixes, M., Tysoe, C., Izatt, L., Letón, R., Gómez-Graña, Á., Mancikova, V., Apellániz-Ruiz, M., Mannelli, M., Schiavi, F., Favier, J., Gimenez-Roqueplo, A., Timmers, H. J. L. M., Roncador, G., Garcia, J. F., Rodríguez-Antona, C., Robledo, M. & Cascón, A., Nov 2015, In : Journal of Molecular Medicine. 93, 11, p. 1247-55 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Published

    4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement

    Cong, Y., Baker, M. L., Jakana, J., Woolford, D., Miller, E. J., Reissmann, S., Kumar, R. N., Redding-Johanson, A. M., Batth, Tanveer Singh, Mukhopadhyay, A., Ludtke, S. J., Frydman, J. & Chiu, W., 16 Mar 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 11, p. 4967-72 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Published

    An Integrative Approach to Virus-Host Protein-Protein Interactions

    Cook, H. V. & Jensen, Lars Juhl, 2018, Computational Cell Biology. von Stechow, L. & Delgado, A. S. (eds.). Humana Press, p. 175-196 22 p. (Methods in Molecular Biology, Vol. 1819).

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

  31. Published

    A Guide to Dictionary-Based Text Mining

    Cook, H. V. & Jensen, Lars Juhl, 2019, Bioinformatics and Drug Discovery. Larson, R. S. & Oprea, T. I. (eds.). 3 ed. Humana Press, Vol. 1939. p. 73-89 17 p. (Methods in Molecular Biology).

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

  32. Published

    Viruses.STRING: A Virus-Host Protein-Protein Interaction Database

    Cook, H. V., Doncheva, Nadezhda Tsankova, Szklarczyk, D., von Mering, C. & Jensen, Lars Juhl, 2018, In : Viruses. 10, 10, p. 1-11 519.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Published

    Ctk1 function is necessary for full translation initiation activity in Saccharomyces cerevisiae

    Coordes, B., Brünger, K. M., Burger, K., Soufi, B., Horenk, J., Eick, D., Olsen, Jesper Velgaard & Sträßer, K., Jan 2015, In : Eukaryotic Cell (Online Edition). 14, 1, p. 86 95 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Published

    Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer

    Coscia, Fabian, Lengyel, E., Duraiswamy, J., Ashcroft, B., Bassani-Sternberg, M., Wierer, M., Johnson, A., Wroblewski, K., Montag, A., Yamada, S. D., López-Méndez, B., Nilsson, Jakob, Mund, Andreas, Mann, Matthias & Curtis, M., 2018, In : Cell. 175, 1, p. 159-170.e16

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. Accepted/In press

    A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis

    Coscia, Fabian, Doll, S., Bech, Jacob Mathias, Schweizer, L., Mund, Andreas, Lengyel, E., Lindebjerg, J., Madsen, G. I., Moreira, José & Mann, Matthias, 10 Mar 2020, (Accepted/In press) In : Journal of Pathology.

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. Published

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

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

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Published

    Functional and structural characterization of plastidic starch phosphorylase during barley endosperm development

    Cuesta-Seijo, J. A., Ruzanski, C., Krucewicz, K., Meier, S., Hägglund, Per Mårten, Svensson, B. & Palcic, M. M., Apr 2017, In : PLoS ONE. 12, 4, e0175488.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. 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

  47. Published

    Inhibition of coagulation factors by recombinant barley serpin BSZx

    Dahl, S. W., Rasmussen, Søren Kjærsgaard, Petersen, L. C. & Hejgaard, J., 30 Sep 1996, In : FEBS letters. 394, 2, p. 165-168 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  48. 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

  49. 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

  50. 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

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