Proteomics – University of Copenhagen

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CPR > Staff > Proteomics

Chuna Ram Choudhary

Chuna Ram Choudhary

group leader


  1. 2017
  2. Published
  3. 2016
  4. Published
  5. Published

    Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance. / Pinela da Silva, Sonia Cristina; Altmannova, Veronika; Luke-Glaser, Sarah; Henriksen, Peter; Gallina, Irene; Yang, Xuejiao; Choudhary, Chuna Ram; Luke, Brian; Krejci, Lumir; Lisby, Michael.

    In: Genes & Development, Vol. 30, No. 6, 2016, p. 700-717.

    Publication: Research - peer-reviewJournal article

  6. Published

    A PTIP-PA1 subcomplex promotes transcription for IgH class switching independently from the associated MLL3/MLL4 methyltransferase complex. / Starnes, Linda M; Su, Dan; Pikkupeura, Laura M; Weinert, Brian T; Santos, Margarida A; Mund, Andreas; Soria, Rebeca; Cho, Young-Wook; Pozdnyakova, Irina; Kubec Højfeldt, Martina; Lages Lino Vala, Andrea; Yang, Wenjing; López-Méndez, Blanca; Lee, Ji-Eun; Peng, Weiqun; Yuan, Joan; Ge, Kai; Montoya, Guillermo; Nussenzweig, André; Choudhary, Chuna Ram; Daniel, Jeremy A.

    In: Genes & Development, Vol. 30, No. 2, 15.01.2016, p. 149-163.

    Publication: Research - peer-reviewJournal article

  7. Published

    SPATA2 links CYLD to the TNF-α receptor signaling complex and modulates the receptor signaling outcomes. / Wagner, Sebastian A; Satpathy, Shankha; Beli, Petra; Choudhary, Chuna Ram.

    In: E M B O Journal, Vol. 35, No. 17, 01.09.2016, p. 1868-1884.

    Publication: Research - peer-reviewJournal article

  8. Published
  9. 2015
  10. Published

    Paradoxical resistance of multiple myeloma to proteasome inhibitors by decreased levels of 19S proteasomal subunits. / Acosta-Alvear, Diego; Cho, Min Y; Wild, Thomas; Buchholz, Tonia J; Lerner, Alana G; Simakova, Olga; Hahn, Jamie; Korde, Neha; Landgren, Ola; Maric, Irina; Choudhary, Chuna Ram; Walter, Peter; Weissman, Jonathan S; Kampmann, Martin.

    In: eLife, Vol. 4, e08153, 01.09.2015, p. 1-19.

    Publication: Research - peer-reviewJournal article

  11. Published

    Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells. / Bursomanno, Sara; Beli, Petra; Khan, Asif M; Minocherhomji, Sheroy; Wagner, Sebastian Alexander; Bekker-Jensen, Simon; Mailand, Niels; Choudhary, Chuna Ram; Hickson, Ian D.; Liu, Ying.

    In: DNA Repair, Vol. 25, 01.2015, p. 84-96.

    Publication: Research - peer-reviewJournal article

  12. Published

    Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells. / Ding, Li; Paszkowski-Rogacz, Maciej; Winzi, Maria; Chakraborty, Debojyoti; Theis, Mirko; Singh, Sukhdeep; Ciotta, Giovanni; Poser, Ina; Roguev, Assen; Chu, Wai Kit; Choudhary, Chuna Ram; Mann, Matthias; Stewart, A Francis; Krogan, Nevan; Buchholz, Frank.

    In: Cell systems, Vol. 1, No. 2, 26.08.2015, p. 141-151.

    Publication: Research - peer-reviewJournal article

  13. Published

    Ubiquitin-SUMO Circuitry Controls Activated Fanconi Anemia ID Complex Dosage in Response to DNA Damage. / Gibbs-Seymour, Ian; Oka, Yasuyoshi; Rajendra, Eeson; Weinert, Brian Tate; Passmore, Lori A; Patel, Ketan J; Olsen, Jesper V; Choudhary, Chuna Ram; Bekker-Jensen, Simon; Mailand, Niels.

    In: Molecular Cell, Vol. 57, No. 1, 01.2015, p. 150-64.

    Publication: Research - peer-reviewJournal article

  14. Published

    Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation. / Satpathy, Shankha; Wagner, Sebastian A; Beli, Petra; Gupta, Rajat; Kristiansen, Trine A; Malinova, Dessislava; Francavilla, Chiara; Tolar, Pavel; Bishop, Gail A; Hostager, Bruce S; Choudhary, Chuna Ram.

    In: Molecular Systems Biology, Vol. 11, No. 6, 810, 2015.

    Publication: Research - peer-reviewJournal article

  15. Published

    Acetylation site specificities of lysine deacetylase inhibitors in human cells. / Schölz, Christian; Weinert, Brian Tate; Wagner, Sebastian A; Beli, Petra; Miyake, Yasuyuki; Qi, Jun; Jensen, Lars J; Streicher, Werner; McCarthy, Anna R; Westwood, Nicholas J; Lain, Sonia; Cox, Jürgen; Matthias, Patrick; Mann, Matthias; Bradner, James E; Choudhary, Chuna Ram.

    In: Nature Biotechnology, Vol. 33, 2015, p. 415–423.

    Publication: Research - peer-reviewJournal article

  16. Published

    Avoiding abundance bias in the functional annotation of posttranslationally modified proteins. / Schölz, Christian; Lyon, David; Refsgaard, Jan C; Jensen, Lars Juhl; Choudhary, Chuna Ram; Weinert, Brian T.

    In: Nature Methods, Vol. 12, 11.2015, p. 1003-4.

    Publication: Research - peer-reviewComment/debate

  17. Published

    Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage. / Thorslund, Tina; Ripplinger, Anita; Hoffmann, Saskia; Wild, Thomas; Uckelmann, Michael; Villumsen, Bine; Narita, Takeo; Sixma, Titia K; Choudhary, Chuna Ram; Bekker-Jensen, Simon; Mailand, Niels.

    In: Nature, Vol. 527, No. 7578, 19.11.2015, p. 389-93.

    Publication: Research - peer-reviewLetter

  18. Published

    Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions. / Weinert, Brian T; Moustafa, Tarek; Iesmantavicius, Vytautas; Zechner, Rudolf; Choudhary, Chuna Ram.

    In: E M B O Journal, Vol. 34, No. 21, 03.11.2015, p. 2620-2632.

    Publication: Research - peer-reviewJournal article

  19. 2014
  20. Published

    A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response. / Blasius, Melanie; Wagner, Sebastian A; Choudhary, Chuna Ram; Bartek, Jiri; Jackson, Stephen P.

    In: Genes & Development, Vol. 28, No. 18, 04.09.2014, p. 1977-1982.

    Publication: Research - peer-reviewJournal article

  21. Published

    The growing landscape of lysine acetylation links metabolism and cell signalling. / Choudhary, Chuna Ram; Weinert, Brian Tate; Nishida, Yuya; Verdin, Eric; Mann, Matthias.

    In: Nature Reviews. Molecular Cell Biology, Vol. 15, No. 8, 23.07.2014, p. 536-50.

    Publication: Research - peer-reviewReview

  22. Published

    Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-Treated Yeast Cells. / Iesmantavicius, Vytautas; Weinert, Brian Tate; Choudhary, Chuna Ram.

    In: Molecular & Cellular Proteomics, Vol. 13, No. 8, 24.06.2014, p. 1979-92.

    Publication: Research - peer-reviewJournal article

  23. Published

    Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-β. / J D'Souza, Rochelle C; Knittle, Anna M; Nagaraj, Nagarjuna; van Dinther, Maarten; Choudhary, Chuna Ram; Ten Dijke, Peter; Mann, Matthias; Sharma, Kirti.

    In: Science signaling, Vol. 7, No. 335, 07.2014, p. rs5.

    Publication: Research - peer-reviewJournal article

  24. Published

    Specificity and commonality of the phosphoinositide-binding proteome analyzed by quantitative mass spectrometry. / Jungmichel, Stephanie; Sylvestersen, Kathrine B; Choudhary, Chuna Ram; Nguyen, Steve; Mann, Matthias; Nielsen, Michael L.

    In: Cell Reports, Vol. 6, No. 3, 13.02.2014, p. 578-91.

    Publication: Research - peer-reviewJournal article

  25. Published

    UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells. / Oka, Yasuyoshi; Varmark, Hanne; Vitting-Seerup, Kristoffer; Beli, Petra; Waage, Johannes Eichler; Hakobyan, Anna; Mistrik, Martin; Choudhary, Chuna Ram; Rohde, Mikkel; Bekker-Jensen, Simon; Mailand, Niels.

    In: E M B O Reports, Vol. 15, No. 9, 2014, p. 956-964.

    Publication: Research - peer-reviewJournal article

  26. Published

    Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. / Weinert, Brian Tate; Iesmantavicius, Vytautas; Moustafa, Tarek; Schölz, Christian; Wagner, Sebastian A; Magnes, Christoph; Zechner, Rudolf; Choudhary, Chuna Ram.

    In: Molecular Systems Biology, Vol. 10, No. 1, 31.01.2014, p. 716.

    Publication: Research - peer-reviewJournal article

  27. 2013
  28. Published

    OTULIN Restricts Met1-Linked Ubiquitination to Control Innate Immune Signaling. / Fiil, Berthe Katrine; Damgaard, Rune Busk; Wagner, Sebastian Alexander; Keusekotten, Kirstin; Fritsch, Melanie; Bekker-Jensen, Simon; Mailand, Niels; Choudhary, Chuna Ram; Komander, David; Gyrd-Hansen, Mads.

    In: Molecular Cell, Vol. 50, No. 6, 27.06.2013, p. 818-30.

    Publication: Research - peer-reviewJournal article

  29. Published

    RNF111/Arkadia is a SUMO-targeted ubiquitin ligase that facilitates the DNA damage response. / Poulsen, Sara L; Hansen, Rebecca K; Wagner, Sebastian A; van Cuijk, Loes; van Belle, Gijsbert J; Streicher, Werner; Wikström, Mats; Choudhary, Chuna Ram; Houtsmuller, Adriaan B; Marteijn, Jurgen A; Bekker-Jensen, Simon; Mailand, Niels.

    In: Journal of Cell Biology, Vol. 201, No. 6, 10.06.2013, p. 797-807.

    Publication: Research - peer-reviewJournal article

  30. Published

    A new cellular stress response that triggers centriolar satellite reorganization and ciliogenesis. / Villumsen, Bine H; Danielsen, Jannie R; Povlsen, Lou; Sylvestersen, Kathrine B; Merdes, Andreas; Beli, Petra; Yang, Yun-Gui; Choudhary, Chuna Ram; Nielsen, Michael L; Mailand, Niels; Bekker-Jensen, Simon.

    In: E M B O Journal, Vol. 32, No. 23, 11.10.2013, p. 3029-3040.

    Publication: Research - peer-reviewJournal article

  31. Published

    Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli. / Weinert, Brian T; Iesmantavicius, Vytautas; Wagner, Sebastian A; Schölz, Christian; Gummesson, Bertil; Beli, Petra; Nyström, Thomas; Choudhary, Chuna Ram.

    In: Molecular Cell, Vol. 51, No. 2, 25.07.2013, p. 265-272.

    Publication: Research - peer-reviewJournal article

  32. Published

    Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. / Weinert, Brian T; Schölz, Christian; Wagner, Sebastian A; Iesmantavicius, Vytautas; Su, Dan; Daniel, Jeremy A; Choudhary, Chuna Ram.

    In: Cell Reports, Vol. 4, No. 4, 29.08.2013, p. 842-51.

    Publication: Research - peer-reviewJournal article

  33. 2012
  34. Published

    Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response. / Beli, Petra; Lukashchuk, Natalia; Wagner, Sebastian A; Weinert, Brian T; Olsen, Jesper V; Baskcomb, Linda; Mann, Matthias; Jackson, Stephen P; Choudhary, Chuna Ram.

    In: Molecular Cell, Vol. 46, No. 2, 2012, p. 212-25.

    Publication: Research - peer-reviewJournal article

  35. Published

    Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. / Henriksen, Peter; Wagner, Sebastian Alexander; Weinert, Brian Tate; Sharma, Satyan; Bacinskaja, Giedré; Rehman, Michael; Juffer, André H.; Walther, Tobias C.; Lisby, Michael; Choudhary, Chuna Ram.

    In: Molecular & Cellular Proteomics, Vol. 11, No. 11, 2012, p. 1510-1522.

    Publication: Research - peer-reviewJournal article

  36. Published

    Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. / Lundby, Alicia; Hansen, Kasper Lage; Weinert, Brian Tate; Breinholt Bekker-Jensen, Dorte; Secher, Anna; Skovgaard, Tine; Kelstrup, Christian; Dmytriyev, Anatoliy; Choudhary, Chuna Ram; Lundby, Carsten; Olsen, Jesper Velgaard.

    In: Cell Reports, Vol. 2, No. 2, 30.08.2012, p. 419-431.

    Publication: Research - peer-reviewJournal article

  37. Published

    DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks. / Mosbech, Anna; Gibbs-Seymour, Ian; Kagias, Konstantinos; Thorslund, Tina; Beli, Petra; Povlsen, Lou; Nielsen, Sofie Vincents; Smedegaard, Stine; Sedgwick, Garry; Lukas, Claudia; Hartmann-Petersen, Rasmus; Lukas, Jiri; Choudhary, Chuna Ram; Pocock, Roger David John; Bekker-Jensen, Simon; Mailand, Niels.

    In: Nature Structural and Molecular Biology, Vol. 19, No. 11, 2012, p. 1084-92.

    Publication: Research - peer-reviewJournal article

  38. Published

    Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. / Povlsen, Lou K; Beli, Petra; Wagner, Sebastian A; Poulsen, Sara L; Sylvestersen, Kathrine B; Poulsen, Jon Wriedt; Nielsen, Michael L; Bekker-Jensen, Simon; Mailand, Niels; Choudhary, Chuna Ram.

    In: Nature Cell Biology, Vol. 14, No. 10, 10.2012, p. 1089-98.

    Publication: Research - peer-reviewJournal article

  39. Published

    SOCS1 cooperates with FLT3-ITD in the development of myeloproliferative disease by promoting the escape from external cytokine control. / Reddy, P.N.G.; Serve, H.; Brandts, C.H.; Sargin, B.; Choudhary, C.; Müller-Tidow, C.; Berdel, W.E.; Stein, S.; Grez, M.

    In: Blood, Vol. 120, No. 8, 23.08.2012, p. 1691-1702.

    Publication: Research - peer-reviewJournal article

  40. Published

    Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3. / Sol, E-ri Maria; Wagner, Sebastian A; Weinert, Brian T; Kumar, Amit; Kim, Hyun-Seok; Deng, Chu-Xia; Choudhary, Chuna Ram.

    In: PloS one, Vol. 7, No. 12, 07.12.2012, p. e50545.

    Publication: Research - peer-reviewJournal article

  41. Published

    Proteomic analyses reveal divergent ubiquitylation site patterns in murinetissues. / Wagner, Sebastian A; Beli, Petra; Weinert, Brian T; Schölz, Christian Friedhold; Kelstrup, Christian D; Young, Clifford; Nielsen, Michael Lund; Olsen, Jesper V; Brakebusch, Cord; Choudhary, Chuna Ram.

    In: Molecular & Cellular Proteomics, 2012.

    Publication: Research - peer-reviewJournal article

  42. 2011
  43. Published

    A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1. / Blasius, Melanie; Forment, Josep V; Thakkar, Neha; Wagner, Sebastian A; Choudhary, Chuna Ram; Jackson, Stephen P.

    In: Genome Biology (Online Edition), Vol. 12, No. 8, 2011, p. R78.

    Publication: Research - peer-reviewJournal article

  44. Published

    A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles. / Wagner, Sebastian Alexander; Beli, Petra; Weinert, Brian Tate; Nielsen, Michael Lund; Cox, Jürgen; Mann, Matthias; Choudhary, Chuna Ram.

    In: Molecular and Cellular Proteomics, Vol. 10, No. 10, 01.10.2011, p. M111.013284.

    Publication: Research - peer-reviewJournal article

  45. Published

    Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. / Weinert, Brian T; Wagner, Sebastian A; Horn, Heiko; Henriksen, Peter; Liu, Wenshe R; Olsen, Jesper V; Jensen, Lars J; Choudhary, Chuna Ram.

    In: Science Signaling, Vol. 4, No. 183, 2011, p. ra48.

    Publication: Research - peer-reviewJournal article

  46. Published

    Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. / Wild, Philipp; Farhan, Hesso; McEwan, David G; Wagner, Sebastian; Rogov, Vladimir V; Brady, Nathan R; Richter, Benjamin; Korac, Jelena; Waidmann, Oliver; Choudhary, Chunaram; Dötsch, Volker; Bumann, Dirk; Dikic, Ivan.

    In: Science, Vol. 333, No. 6039, 08.07.2011, p. 228-33.

    Publication: Research - peer-reviewJournal article

  47. 2010
  48. Published

    Decoding signalling networks by mass spectrometry-based proteomics. / Choudhary, Chuna Ram; Mann, Matthias.

    In: Nature Reviews. Molecular Cell Biology, Vol. 11, No. 6, 01.06.2010, p. 427-39.

    Publication: Research - peer-reviewJournal article

  49. Published

    Predicting post-translational lysine acetylation using support vector machines. / Gnad, Florian; Ren, Shubin; Choudhary, Chunaram; Cox, Jürgen; Mann, Matthias.

    In: Bioinformatics, Vol. 26, No. 13, 01.07.2010, p. 1666-8.

    Publication: Research - peer-reviewJournal article

  50. Published

    Human SIRT6 promotes DNA end resection through CtIP deacetylation. / Kaidi, Abderrahmane; Weinert, Brian T; Choudhary, Chunaram; Jackson, Stephen P.

    In: Science, Vol. 329, No. 5997, 10.09.2010, p. 1348-53.

    Publication: Research - peer-reviewJournal article

  51. 2009
  52. Published

    Lysine acetylation targets protein complexes and co-regulates major cellular functions. / Choudhary, Chuna Ram; Kumar, Chanchal; Gnad, Florian; Nielsen, Michael L; Rehman, Michael; Walther, Tobias C; Olsen, Jesper V; Mann, Matthias.

    In: Science, Vol. 325, No. 5942, 2009, p. 834-40.

    Publication: Research - peer-reviewJournal article

  53. Published

    Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes. / Choudhary, Chuna Ram; Olsen, Jesper V; Brandts, Christian; Cox, Jürgen; Reddy, Pavankumar N G; Böhmer, Frank D; Gerke, Volker; Schmidt-Arras, Dirk-E; Berdel, Wolfgang E; Müller-Tidow, Carsten; Mann, Matthias; Serve, Hubert.

    In: Molecular Cell, Vol. 36, No. 2, 2009, p. 326-39.

    Publication: Research - peer-reviewJournal article

  54. 2005
  55. Identification of a novel activating mutation (Y842C) within the activation loop of FLT3 in patients with acute myeloid leukemia (AML). / Kindler, Thomas; Breitenbuecher, Frank; Kasper, Stefan; Estey, Eli; Giles, Francis; Feldman, Eric; Ehninger, Gerhard; Schiller, Gary; Klimek, Virginia; Nimer, Stephen D; Gratwohl, Alois; Choudhary, Chuna Ram; Mueller-Tidow, Constan; Serve, Hubert; Gschaidmeier, Harald; Cohen, Pamela S; Huber, Christoph; Fischer, Thomas.

    In: Blood, Vol. 105, No. 1, 2005, p. 335-40.

    Publication: Research - peer-reviewJournal article

ID: 13781159