Chuna Ram Choudhary

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• 2024

  Acetylation of histones and non-histone proteins is not a mere consequence of ongoing transcription

  Liebner, T., Kilic, S., Walter, J., Aibara, H., Narita, T. & Choudhary, C., 2024, In: Nature Communications. 15, 12 p., 4962.

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  2 Citations (Scopus)

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• Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties

  Prus, G., Satpathy, S., Weinert, B. T., Narita, T. & Choudhary, C., 2024, In: Cell. 187, 11, p. 2875-2892.e21

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  2 Citations (Scopus)

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• 2023

  Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes

  Narita, T., Higashijima, Y., Kilic, S., Liebner, T., Walter, J. & Choudhary, C., 2023, In: Nature Genetics. 55, p. 679-692

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  18 Citations (Scopus)

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• K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution

  Suryo Rahmanto, A., Blum, C. J., Scalera, C., Heidelberger, J. B., Mesitov, M., Horn-Ghetko, D., Gräf, J. F., Mikicic, I., Hobrecht, R., Orekhova, A., Ostermaier, M., Ebersberger, S., Möckel, M. M., Krapoth, N., Da Silva Fernandes, N., Mizi, A., Zhu, Y., Chen, J. X., Choudhary, C., Papantonis, A. & 4 others, Ulrich, H. D., Schulman, B. A., König, J. & Beli, P., 2023, In: Molecular Cell. 83, 23, p. 4272-4289.e10 29 p.

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  12 Citations (Scopus)

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• TOBF1 modulates mouse embryonic stem cell fate through regulating alternative splicing of pluripotency genes

  Aich, M., Ansari, A. H., Ding, L., Iesmantavicius, V., Paul, D., Choudhary, C., Maiti, S., Buchholz, F. & Chakraborty, D., 2023, In: Cell Reports. 42, 10, 22 p., 113177.

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• 2022

  HDAC6 modulates myofibril stiffness and diastolic function of the heart

  Lin, Y-H., Major, J. L., Liebner, T., Hourani, Z., Travers, J. G., Wennersten, S. A., Haefner, K. R., Cavasin, M. A., Wilson, C. E., Jeong, M. Y., Han, Y., Gotthardt, M., Ferguson, S. K., Ambardekar, A. V., Lam, M. P., Choudhary, C., Granzier, H. L., Woulfe, K. C. & McKinsey, T. A., 2022, In: Journal of Clinical Investigation. 132, 10, 14 p., e148333.

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  25 Citations (Scopus)

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• 2021

  Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release

  Narita, T., Ito, S., Higashijima, Y., Chu, W. K., Neumann, K., Walter, J., Satpathy, S., Liebner, T., Hamilton, W. B., Maskey, E., Prus, G., Shibata, M., Iesmantavicius, V., Brickman, J. M., Anastassiadis, K., Koseki, H. & Choudhary, C., 2021, In: Molecular Cell. 81, 10, p. 2166-2182.e6

  Research output: Contribution to journal › Journal article › Research › peer-review
  99 Citations (Scopus)

• Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination

  Nakamura, K., Kustatscher, G., Alabert, C., Hödl, M., Forne, I., Völker-Albert, M., Satpathy, S., Beyer, T. E., Mailand, N., Choudhary, C., Imhof, A., Rappsilber, J. & Groth, A., 2021, In: Molecular Cell. 81, 3, 23 p.

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  59 Citations (Scopus)

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• SIK2 orchestrates actin-dependent host response upon Salmonella infection

  Hahn, M., Covarrubias-Pinto, A., Herhaus, L., Satpathy, S., Klann, K., Boyle, K. B., Münch, C., Rajalingam, K., Randow, F., Choudhary, C. & Dikic, I., 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 19, 10 p., e2024144118.

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  9 Citations (Scopus)

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• 2020

  Equilibrium between nascent and parental MCM proteins protects replicating genomes

  Sedlackova, H., Rask, M-B., Gupta, R., Choudhary, C., Somyajit, K. & Lukas, J., 2020, In: Nature. 587, p. 297-302 34 p.

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  65 Citations (Scopus)

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• HBO1 is required for the maintenance of leukaemia stem cells

  MacPherson, L., Anokye, J., Yeung, M. M., Lam, E. Y. N., Chan, Y-C., Weng, C-F., Yeh, P., Knezevic, K., Butler, M. S., Hoegl, A., Chan, K-L., Burr, M. L., Gearing, L. J., Willson, T., Liu, J., Choi, J., Yang, Y., Bilardi, R. A., Falk, H., Nghi Nguyen & 28 others, Stupple, P. A., Peat, T. S., Zhang, M., De Silva, M., Carrasco-Pozo, C., Avery, V. M., Khoo, S., Dolezal, O., Dennis, M. L., Nuttall, S., Surjadi, R., Newman, J., Ren, B., Leaver, D. J., Sun, Y., Baell, J. B., Dovey, O., Vassiliou, G. S., Grebien, F., Dawson, S-J., Street, I. P., Monahan, B. J., Burns, C. J., Choudhary, C., Blewitt, M. E., Voss, A. K., Thomas, T. & Dawson, M. A., 2020, In: Nature. 577, 7789, p. 266-270

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  116 Citations (Scopus)

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• Histone Acetyltransferase MOF Blocks Acquisition of Quiescence in Ground-State ESCs through Activating Fatty Acid Oxidation

  Khoa, L. T. P., Tsan, Y-C., Mao, F., Kremer, D. M., Sajjakulnukit, P., Zhang, L., Zhou, B., Tong, X., Bhanu, N. V., Choudhary, C., Garcia, B. A., Yin, L., Smith, G. D., Saunders, T. L., Bielas, S. L., Lyssiotis, C. A. & Dou, Y., 2020, In: Cell Stem Cell. 27, 3, p. 441-458.e10 29 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  39 Citations (Scopus)

• Sequencing of the First Draft of the Human Acetylome

  Choudhary, C. & Mann, M., 2020, In: Clinical Chemistry. 66, 6, p. 852-853 2 p.

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  1 Citation (Scopus)

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• 2019

  Acetylation of intrinsically disordered regions regulates phase separation

  Saito, M., Hess, D., Eglinger, J., Fritsch, A. W., Kreysing, M., Weinert, B. T., Choudhary, C. & Matthias, P., Jan 2019, In: Nature Chemical Biology. 15, 1, p. 51-61

  Research output: Contribution to journal › Journal article › Research › peer-review
  195 Citations (Scopus)

• Analysis and Interpretation of Protein Post-Translational Modification Site Stoichiometry

  Prus, G., Hoegl, A., Weinert, B. T. & Choudhary, C., 2019, In: Trends in Biochemical Sciences. 44, 11, p. 943-960

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  55 Citations (Scopus)

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• Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation

  Hansen, B. K., Gupta, R., Baldus, L., Lyon, D., Narita, T., Lammers, M., Choudhary, C. & Weinert, B. T., 2019, In: Nature Communications. 10, 11 p., 1055.

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  120 Citations (Scopus)

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• Functions and mechanisms of non-histone protein acetylation

  Narita, T., Weinert, B. T. & Choudhary, C., 2019, In: Nature Reviews. Molecular Cell Biology. 20, p. 156-174 19 p.

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  760 Citations (Scopus)

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• Proteomic exploration of lysine acetylation signaling

  Choudhary, C., 2019, In: Molecular & Cellular Proteomics. 18, 8, p. S25 1 p.

  Research output: Contribution to journal › Conference abstract in journal › Research
• 2018

  Deletion of APC7 or APC16 Allows Proliferation of Human Cells without the Spindle Assembly Checkpoint

  Wild, T., Budzowska, M., Hellmuth, S., Eibes, S., Karemore, G., Barisic, M., Stemmann, O. & Choudhary, C., 2018, In: Cell Reports. 25, 9, 18 p., 2317-2328.e5.

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  8 Citations (Scopus)

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• DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity

  Gupta, R., Somyajit, K., Narita, T., Maskey, E., Stanlie, A., Kremer, M., Typas, D., Lammers, M., Mailand, N., Nussenzweig, A., Lukas, J. & Choudhary, C., 2018, In: Cell. 173, 4, p. 972-988

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  316 Citations (Scopus)

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• p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage

  Borisova, M. E., Voigt, A., Tollenaere, M. A. X., Sahu, S. K., Juretschke, T., Kreim, N., Mailand, N., Choudhary, C., Bekker-Jensen, S., Akutsu, M., Wagner, S. A. & Beli, P., 1 Dec 2018, In: Nature Communications. 9, p. 1-16 16 p., 1017.

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  59 Citations (Scopus)

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• STK3 is a therapeutic target for a subset of acute myeloid leukemias

  Camgoz, A., Paszkowski-Rogacz, M., Satpathy, S., Wermke, M., Hamann, M. V., von Bonin, M., Choudhary, C., Knapp, S. & Buchholz, F., 2018, In: OncoTarget. 9, 39, p. 25458-25473 16 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  9 Citations (Scopus)

• Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome

  Weinert, B. T., Narita, T., Satpathy, S., Srinivasan, B., Hansen, B. K., Schölz, C., Hamilton, W. B., Zucconi, B. E., Wang, W. W., Liu, W. R., Brickman, J. M., Kesicki, E. A., Lai, A., Bromberg, K. D., Cole, P. A. & Choudhary, C., 2018, In: Cell. 174, 1, p. 231-244.e12 27 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  293 Citations (Scopus)
• 2017

  Accurate quantification of site-specific acetylation stoichiometry reveals the impact of sirtuin deacetylase CobB on the E. coli acetylome

  Weinert, B. T., Satpathy, S., Hansen, B. K., Lyon, D., Jensen, L. J. & Choudhary, C. R., May 2017, In: Molecular and Cellular Proteomics. 16, p. 759-769

  Research output: Contribution to journal › Journal article › Research › peer-review

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  76 Citations (Scopus)

• Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours

  Lasko, L. M., Jakob, C. G., Edalji, R. P., Qiu, W., Montgomery, D., Digiammarino, E. L., Hansen, T. M., Risi, R. M., Frey, R., Manaves, V., Shaw, B., Algire, M., Hessler, P., Lam, L. T., Uziel, T., Faivre, E., Ferguson, D., Buchanan, F. G., Martin, R. L., Torrent, M. & 16 others, Chiang, G. G., Karukurichi, K., Langston, J. W., Weinert, B. T., Choudhary, C., de Vries, P., Van Drie, J. H., McElligott, D., Kesicki, E., Marmorstein, R., Sun, C., Cole, P. A., Rosenberg, S. H., Michaelides, M. R., Lai, A. & Bromberg, K. D., 5 Oct 2017, In: Nature. 550, 7674, p. 128-132 5 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  499 Citations (Scopus)

• 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, C., Anastassiadis, K., Stewart, A. F. & Buchholz, F., 12 Dec 2017, In: Cell Reports. 21, 11, p. 3012-3021 10 p.

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  25 Citations (Scopus)

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• Redox-sensitive alteration of replisome architecture safeguards genome integrity

  Somyajit, K., Gupta, R., Sedlackova, H., Neelsen, K. J., Ochs, F., Rask, M-B., Choudhary, C. & Lukas, J., 10 Nov 2017, In: Science. 358, 6364, p. 797-802 6 p.

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  124 Citations (Scopus)

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• 2016

  A PTIP-PA1 subcomplex promotes transcription for IgH class switching independently from the associated MLL3/MLL4 methyltransferase complex

  Starnes, L. M., Su, D., Pikkupeura, L. M., Weinert, B. T., Santos, M. A., Mund, A., Soria, R., Cho, Y-W., Pozdnyakova, I., Kubec Højfeldt, M., Lages Lino Vala, A., Yang, W., López-Méndez, B., Lee, J-E., Peng, W., Yuan, J., Ge, K., Montoya, G., Nussenzweig, A., Choudhary, C. R. & 1 others, Daniel, J. A., 15 Jan 2016, In: Genes & Development. 30, 2, p. 149-163 15 p.

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  25 Citations (Scopus)

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• Deubiquitylating enzyme USP9x regulates hippo pathway activity by controlling angiomotin protein turnover

  Nguyen, T. H., Andrejeva, D., Gupta, R., Choudhary, C. R., Hong, X., Eichhorn, P. JA., Loya, A. C. & Cohen, S. M., 29 Mar 2016, In: Cell Discovery. 2, 13 p., 16001.

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  36 Citations (Scopus)

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• Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance

  Pinela da Silva, S. C., Altmannova, V., Luke-Glaser, S., Henriksen, P., Gallina, I., Yang, X., Choudhary, C. R., Luke, B., Krejci, L. & Lisby, M., 2016, In: Genes & Development. 30, 6, p. 700-717 18 p.

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  22 Citations (Scopus)

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• SPATA2 links CYLD to the TNF-α receptor signaling complex and modulates the receptor signaling outcomes

  Wagner, S. A., Satpathy, S., Beli, P. & Choudhary, C. R., 1 Sep 2016, In: E M B O Journal. 35, 17, p. 1868-1884

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  116 Citations (Scopus)

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• The Spindle Assembly Checkpoint Is Not Essential for Viability of Human Cells with Genetically Lowered APC/C Activity

  Wild, T., Larsen, M. S. Y., Narita, T., Schou, J., Nilsson, J. & Choudhary, C. R., 1 Mar 2016, In: Cell Reports. 14, 8, p. 1829-40 12 p.

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  37 Citations (Scopus)

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• 2015

  Acetylation site specificities of lysine deacetylase inhibitors in human cells

  Schölz, C., Weinert, B. T., Wagner, S. A., Beli, P., Miyake, Y., Qi, J., Jensen, L. J., Streicher, W., McCarthy, A. R., Westwood, N. J., Lain, S., Cox, J., Matthias, P., Mann, M., Bradner, J. E. & Choudhary, C. R., 2015, In: Nature Biotechnology. 33, p. 415–423

  Research output: Contribution to journal › Journal article › Research › peer-review
  221 Citations (Scopus)

• Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions

  Weinert, B. T., Moustafa, T., Iesmantavicius, V., Zechner, R. & Choudhary, C. R., 3 Nov 2015, In: E M B O Journal. 34, 21, p. 2620-2632 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  123 Citations (Scopus)

• Avoiding abundance bias in the functional annotation of posttranslationally modified proteins

  Schölz, C., Lyon, D., Refsgaard, J. C., Jensen, L. J., Choudhary, C. R. & Weinert, B. T., Nov 2015, In: Nature Methods. 12, p. 1003-4 2 p.

  Research output: Contribution to journal › Comment/debate › Research › peer-review
  55 Citations (Scopus)

• Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage

  Thorslund, T., Ripplinger, A., Hoffmann, S., Wild, T., Uckelmann, M., Villumsen, B., Narita, T., Sixma, T. K., Choudhary, C. R., Bekker-Jensen, S. & Mailand, N., 19 Nov 2015, In: Nature. 527, 7578, p. 389-93 5 p.

  Research output: Contribution to journal › Letter › Research › peer-review

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  307 Citations (Scopus)

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• Paradoxical resistance of multiple myeloma to proteasome inhibitors by decreased levels of 19S proteasomal subunits

  Acosta-Alvear, D., Cho, M. Y., Wild, T., Buchholz, T. J., Lerner, A. G., Simakova, O., Hahn, J., Korde, N., Landgren, O., Maric, I., Choudhary, C. R., Walter, P., Weissman, J. S. & Kampmann, M., 1 Sep 2015, In: eLife. 4, p. 1-19 e08153.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  74 Citations (Scopus)

• Proteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells

  Bursomanno, S., Beli, P., Khan, A. M., Minocherhomji, S., Wagner, S. A., Bekker-Jensen, S., Mailand, N., Choudhary, C. R., Hickson, I. D. & Liu, Y., Jan 2015, In: DNA Repair. 25, p. 84-96 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  32 Citations (Scopus)

• 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, C. R., Mann, M., Stewart, A. F., Krogan, N. & Buchholz, F., 26 Aug 2015, In: Cell Systems. 1, 2, p. 141-151 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  13 Citations (Scopus)

• Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation

  Satpathy, S., Wagner, S. A., Beli, P., Gupta, R., Kristiansen, T. A., Malinova, D., Francavilla, C., Tolar, P., Bishop, G. A., Hostager, B. S. & Choudhary, C. R., 2015, In: Molecular Systems Biology. 11, 6, 810.

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  96 Citations (Scopus)

• Ubiquitin-SUMO Circuitry Controls Activated Fanconi Anemia ID Complex Dosage in Response to DNA Damage

  Gibbs-Seymour, I., Oka, Y., Rajendra, E., Weinert, B. T., Passmore, L. A., Patel, K. J., Olsen, J. V., Choudhary, C. R., Bekker-Jensen, S. & Mailand, N., Jan 2015, In: Molecular Cell. 57, 1, p. 150-64 15 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  106 Citations (Scopus)
• 2014

  Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

  Weinert, B. T., Iesmantavicius, V., Moustafa, T., Schölz, C., Wagner, S. A., Magnes, C., Zechner, R. & Choudhary, C. R., 31 Jan 2014, In: Molecular Systems Biology. 10, 1, p. 716 12 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  205 Citations (Scopus)

• A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response

  Blasius, M., Wagner, S. A., Choudhary, C. R., Bartek, J. & Jackson, S. P., 4 Sep 2014, In: Genes & Development. 28, 18, p. 1977-1982 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  42 Citations (Scopus)

• Convergence of Ubiquitylation and Phosphorylation Signaling in Rapamycin-Treated Yeast Cells

  Iesmantavicius, V., Weinert, B. T. & Choudhary, C. R., 24 Jun 2014, In: Molecular & Cellular Proteomics. 13, 8, p. 1979-92 14 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  48 Citations (Scopus)

• Specificity and commonality of the phosphoinositide-binding proteome analyzed by quantitative mass spectrometry

  Jungmichel, S., Sylvestersen, K. B., Choudhary, C. R., Nguyen, S., Mann, M. & Nielsen, M. L., 13 Feb 2014, In: Cell Reports. 6, 3, p. 578-91 14 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  65 Citations (Scopus)

• The growing landscape of lysine acetylation links metabolism and cell signalling

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

  Research output: Contribution to journal › Review › Research › peer-review
  1047 Citations (Scopus)

• Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-β

  J D'Souza, R. C., Knittle, A. M., Nagaraj, N., van Dinther, M., Choudhary, C. R., Ten Dijke, P., Mann, M. & Sharma, K., Jul 2014, In: Science Signaling. 7, 335, p. rs5 16 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  34 Citations (Scopus)

• UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells

  Oka, Y., Varmark, H., Vitting-Seerup, K., Beli, P., Waage, J. E., Hakobyan, A., Mistrik, M., Choudhary, C. R., Rohde, M., Bekker-Jensen, S. & Mailand, N., 2014, In: E M B O Reports. 15, 9, p. 956-964 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  37 Citations (Scopus)
• 2013

  Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli

  Weinert, B. T., Iesmantavicius, V., Wagner, S. A., Schölz, C., Gummesson, B., Beli, P., Nyström, T. & Choudhary, C. R., 25 Jul 2013, In: Molecular Cell. 51, 2, p. 265-272 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  358 Citations (Scopus)

• A new cellular stress response that triggers centriolar satellite reorganization and ciliogenesis

  Villumsen, B. H., Danielsen, J. R., Povlsen, L., Sylvestersen, K. B., Merdes, A., Beli, P., Yang, Y-G., Choudhary, C. R., Nielsen, M. L., Mailand, N. & Bekker-Jensen, S., 11 Oct 2013, In: E M B O Journal. 32, 23, p. 3029-3040

  Research output: Contribution to journal › Journal article › Research › peer-review
  102 Citations (Scopus)