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Namrata D. Udeshi, Ph.D. - Publications

Affiliations: 
2009 University of Virginia, Charlottesville, VA 
Area:
Analytical Biochemistry
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Phulphagar KM, Ctortecka C, Jacome ASV, Klaeger S, Verzani EK, Hernandez GM, Udeshi ND, Clauser KR, Abelin JG, Carr SA. Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry. Molecular & Cellular Proteomics : McP. 100563. PMID 37142057 DOI: 10.1016/j.mcpro.2023.100563  0.712
2023 Abelin JG, Bergstrom EJ, Rivera KD, Taylor HB, Klaeger S, Xu C, Verzani EK, Jackson White C, Woldemichael HB, Virshup M, Olive ME, Maynard M, Vartany SA, Allen JD, Phulphagar K, ... ... Udeshi ND, et al. Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues. Nature Communications. 14: 1851. PMID 37012232 DOI: 10.1038/s41467-023-37547-0  0.7
2023 Phulphagar KM, Ctortecka C, Vaca Jacome AS, Klaeger S, Verzani EK, Hernandez GM, Udeshi N, Clauser K, Abelin J, Carr SA. Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry. Biorxiv : the Preprint Server For Biology. PMID 36993564 DOI: 10.1101/2023.03.10.532106  0.709
2022 Yang R, Meyer AS, Droujinine IA, Udeshi ND, Hu Y, Guo J, McMahon JA, Carey DK, Xu C, Fang Q, Sha J, Qin S, Rocco D, Wohlschlegel J, Ting AY, et al. A genetic model for proximity labelling of the mammalian secretome. Open Biology. 12: 220149. PMID 35946312 DOI: 10.1098/rsob.220149  0.331
2020 Cho KF, Branon TC, Rajeev S, Svinkina T, Udeshi ND, Thoudam T, Kwak C, Rhee HW, Lee IK, Carr SA, Ting AY. Split-TurboID enables contact-dependent proximity labeling in cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 32424107 DOI: 10.1073/Pnas.1919528117  0.365
2020 Li J, Han S, Li H, Udeshi ND, Svinkina T, Mani DR, Xu C, Guajardo R, Xie Q, Li T, Luginbuhl DJ, Wu B, McLaughlin CN, Xie A, Kaewsapsak P, et al. Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. Cell. PMID 31955847 DOI: 10.1016/J.Cell.2019.12.029  0.327
2020 Udeshi ND, Mani DC, Satpathy S, Fereshetian S, Gasser JA, Svinkina T, Olive ME, Ebert BL, Mertins P, Carr SA. Rapid and deep-scale ubiquitylation profiling for biology and translational research. Nature Communications. 11: 359. PMID 31953384 DOI: 10.1038/S41467-019-14175-1  0.424
2019 Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, et al. Multi-Omics analysis identifies MGA as a negative regulator of the MYC pathway in lung adenocarcinoma. Molecular Cancer Research : McR. PMID 31862696 DOI: 10.1158/1541-7786.Mcr-19-0657  0.316
2019 Sperling AS, Burgess M, Keshishian H, Gasser JA, Bhatt S, Jan M, Słabicki M, Sellar RS, Fink EC, Miller PG, Liddicoat BJ, Sievers QL, Sharma R, Adams DN, Olesinski EA, ... ... Udeshi ND, et al. Patterns of substrate affinity, competition and degradation kinetics underlie biological activity of thalidomide analogs. Blood. PMID 31043423 DOI: 10.1182/Blood.2019000789  0.332
2019 Sanz R, Ovando-Roche P, Udeshi ND, Carr SA, Chung CY, Khurana V. In Situ Peroxidase Labeling and Mass Spectrometry of Alpha-Synuclein in Rat Cortical Neurons. Methods in Molecular Biology (Clifton, N.J.). 1948: 235-246. PMID 30771182 DOI: 10.1007/978-1-4939-9124-2_18  0.371
2019 Belizaire R, Koochaki S, Udeshi N, Vedder A, Sun L, Schenone M, Carr S, Padron E, Ebert BL. Oncogenic Mechanisms of CBL E3 Ubiquitin Ligase Mutations in Myeloid Malignancies Blood. 134: 563-563. DOI: 10.1182/Blood-2019-122503  0.324
2018 Myers SA, Klaeger S, Satpathy S, Viner R, Choi J, Rogers J, Clauser K, Udeshi ND, Carr SA. Evaluation of advanced precursor determination for tandem mass tag (TMT)-based quantitative proteomics across instrument platforms. Journal of Proteome Research. PMID 30351145 DOI: 10.1021/Acs.Jproteome.8B00611  0.41
2018 Wang YJ, Vaidyanathan PP, Rojas-Duran MF, Udeshi ND, Bartoli KM, Carr SA, Gilbert WV. Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast. Plos Biology. 16: e2005903. PMID 30208026 DOI: 10.1371/Journal.Pbio.2005903  0.374
2018 Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY. Efficient proximity labeling in living cells and organisms with TurboID. Nature Biotechnology. PMID 30125270 DOI: 10.1038/Nbt.4201  0.357
2018 Steinebach C, Lindner S, Udeshi ND, Mani DC, Kehm H, Köpff S, Carr SA, Gütschow M, Kronke J. Homo-PROTACs for the Chemical Knockdown of Cereblon. Acs Chemical Biology. PMID 30118587 DOI: 10.1021/Acschembio.8B00693  0.334
2018 Fink EC, McConkey M, Adams DN, Haldar SD, Kennedy JA, Guirguis AA, Udeshi ND, Mani DR, Chen M, Liddicoat B, Svinkina T, Nguyen AT, Carr SA, Ebert BL. Crbn is sufficient to confer sensitivity to thalidomide and its derivatives in mice. Blood. PMID 30064974 DOI: 10.1182/Blood-2018-05-852798  0.309
2018 Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, ... ... Udeshi ND, et al. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry. Nature Protocols. PMID 29988108 DOI: 10.1038/S41596-018-0006-9  0.408
2018 Zhang Y, Burberry A, Wang JY, Sandoe J, Ghosh S, Udeshi ND, Svinkina T, Mordes DA, Mok J, Charlton M, Li QZ, Carr SA, Eggan K. The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis. Genes & Development. PMID 29950492 DOI: 10.1101/Gad.313932.118  0.337
2018 Lindner S, Steinebach C, Udeshi N, Mani D, Kehm H, Köpff S, Carr SA, Gütschow M, Krönke J. Pomalidomide-Based Homo-Protacs for the Chemical Knockdown of Cereblon Blood. 132: 260-260. DOI: 10.1182/Blood-2018-99-116376  0.315
2017 Udeshi ND, Pedram K, Svinkina T, Fereshetian S, Myers SA, Aygun O, Krug K, Clauser K, Ryan D, Ast T, Mootha VK, Ting AY, Carr SA. Antibodies to biotin enable large-scale detection of biotinylation sites on proteins. Nature Methods. PMID 29039416 DOI: 10.1038/Nmeth.4465  0.42
2017 Martínez-Turiño S, Pérez JJ, Hervás M, Navajas R, Ciordia S, Udeshi ND, Shabanowitz J, Hunt DF, García JA. Phosphorylation coexists with O-GlcNAcylation in a plant virus protein and influences viral infection. Molecular Plant Pathology. PMID 29024291 DOI: 10.1111/Mpp.12626  0.549
2017 Sieber J, Wieder N, Ostrosky-Frid M, Dvela-Levitt M, Aygün O, Udeshi ND, Carr SA, Greka A. Lysine trimethylation regulates 78 kDa glucose-regulated protein proteostasis during endoplasmic reticulum stress. The Journal of Biological Chemistry. PMID 28912266 DOI: 10.1074/Jbc.M117.797084  0.307
2017 Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY. Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. Elife. 6. PMID 28441135 DOI: 10.7554/Elife.24463  0.355
2017 Han S, Udeshi ND, Deerinck TJ, Svinkina T, Ellisman MH, Carr SA, Ting AY. Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. Cell Chemical Biology. PMID 28238724 DOI: 10.1016/J.Chembiol.2017.02.002  0.369
2017 Chung CY, Khurana V, Yi S, Sahni N, Loh KH, Auluck PK, Baru V, Udeshi ND, Freyzon Y, Carr SA, Hill DE, Vidal M, Ting AY, Lindquist S. In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Cell Systems. PMID 28131823 DOI: 10.1016/J.Cels.2017.01.002  0.328
2016 Hung V, Udeshi ND, Lam SS, Loh KH, Cox KJ, Pedram K, Carr SA, Ting AY. Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. Nature Protocols. 11: 456-75. PMID 26866790 DOI: 10.1038/Nprot.2016.018  0.396
2015 Chen CL, Hu Y, Udeshi ND, Lau TY, Wirtz-Peitz F, He L, Ting AY, Carr SA, Perrimon N. Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase. Proceedings of the National Academy of Sciences of the United States of America. PMID 26362788 DOI: 10.1073/Pnas.1515623112  0.385
2015 Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA. Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies and an optimized proteomic workflow. Molecular & Cellular Proteomics : McP. PMID 25953088 DOI: 10.1074/Mcp.O114.047555  0.44
2015 Creech AL, Taylor JE, Maier VK, Wu X, Feeney CM, Udeshi ND, Peach SE, Boehm JS, Lee JT, Carr SA, Jaffe JD. Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry. Methods (San Diego, Calif.). 72: 57-64. PMID 25448295 DOI: 10.1016/J.Ymeth.2014.10.033  0.347
2014 Theurillat JP, Udeshi ND, Errington WJ, Svinkina T, Baca SC, Pop M, Wild PJ, Blattner M, Groner AC, Rubin MA, Moch H, Prive GG, Carr SA, Garraway LA. Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer. Science (New York, N.Y.). 346: 85-89. PMID 25278611 DOI: 10.1126/Science.1250255  0.312
2014 Hung V, Zou P, Rhee HW, Udeshi ND, Cracan V, Svinkina T, Carr SA, Mootha VK, Ting AY. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Molecular Cell. 55: 332-41. PMID 25002142 DOI: 10.1016/J.Molcel.2014.06.003  0.363
2014 Krönke J, Udeshi ND, Narla A, Grauman P, Hurst SN, McConkey M, Svinkina T, Heckl D, Comer E, Li X, Ciarlo C, Hartman E, Munshi N, Schenone M, Schreiber SL, et al. Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells. Science (New York, N.Y.). 343: 301-5. PMID 24292625 DOI: 10.1126/Science.1244851  0.321
2014 Fink EC, Krönke J, Hurst SN, Udeshi ND, Svinkina T, Schneider RK, McConkey ME, Järås M, Bullinger L, Carr SA, Ebert BL. Lenalidomide Induces Ubiquitination and Degradation of CSNK1A1 in MDS with Del(5q) Blood. 124: 4-4. DOI: 10.1182/Blood.V124.21.4.4  0.328
2013 Udeshi ND, Mertins P, Svinkina T, Carr SA. Large-scale identification of ubiquitination sites by mass spectrometry. Nature Protocols. 8: 1950-60. PMID 24051958 DOI: 10.1038/Nprot.2013.120  0.449
2013 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA. Integrated proteomic analysis of post-translational modifications by serial enrichment. Nature Methods. 10: 634-7. PMID 23749302 DOI: 10.1038/Nmeth.2518  0.437
2013 Pérez Jde J, Udeshi ND, Shabanowitz J, Ciordia S, Juárez S, Scott CL, Olszewski NE, Hunt DF, García JA. O-GlcNAc modification of the coat protein of the potyvirus Plum pox virus enhances viral infection. Virology. 442: 122-31. PMID 23639873 DOI: 10.1016/J.Virol.2013.03.029  0.519
2013 Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science (New York, N.Y.). 339: 1328-31. PMID 23371551 DOI: 10.1126/Science.1230593  0.426
2013 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA. Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments. Molecular & Cellular Proteomics : McP. 12: 825-31. PMID 23266961 DOI: 10.1074/Mcp.O112.027094  0.333
2013 Kim YC, Jahren N, Stone MD, Udeshi ND, Markowski TW, Witthuhn BA, Shabanowitz J, Hunt DF, Olszewski NE. Identification and origin of N-linked β-D-N-acetylglucosamine monosaccharide modifications on Arabidopsis proteins. Plant Physiology. 161: 455-64. PMID 23144189 DOI: 10.1104/Pp.112.208900  0.504
2013 Krönke J, Udeshi N, Narla A, Grauman P, Hurst S, McConkey M, Svinkina T, Heckl D, Comer E, Li X, Ciarlo C, Hartman E, Schenone M, Schreiber S, Carr SA, et al. Lenalidomide Promotes CRBN-Mediated Ubiquitination and Degradation of IKZF1 and IKZF3 Blood. 122: LBA-5-LBA-5. DOI: 10.1182/Blood.V122.21.Lba-5.Lba-5  0.359
2012 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Molecular & Cellular Proteomics : McP. 11: 148-59. PMID 22505724 DOI: 10.1074/Mcp.M111.016857  0.427
2012 Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Molecular & Cellular Proteomics : McP. 11: 128-37. PMID 22442256 DOI: 10.1074/Mcp.M111.015941  0.319
2012 Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Molecular & Cellular Proteomics : McP. 11: M111.014423. PMID 22210691 DOI: 10.1074/Mcp.M111.014423  0.387
2012 Krönke J, Narla A, Hurst SN, Udeshi N, Schenone M, McConkey M, Grauman P, Heckl D, McAuley R, Ciarlo C, Comer E, Li X, Carr SA, Ebert BL. Inhibition of the CRBN-DDB1-CUL4-ROC1 E3 Ubiquitin Ligase Mediates the Anti-Proliferative and Immunomodulatory Properties of Lenalidomide Blood. 120: 919-919. DOI: 10.1182/Blood.V120.21.919.919  0.381
2011 Kim YC, Udeshi ND, Balsbaugh JL, Shabanowitz J, Hunt DF, Olszewski NE. O-GlcNAcylation of the Plum pox virus capsid protein catalyzed by SECRET AGENT: characterization of O-GlcNAc sites by electron transfer dissociation mass spectrometry. Amino Acids. 40: 869-76. PMID 20676902 DOI: 10.1007/S00726-010-0706-0  0.717
2010 Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW. Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis. Science Signaling. 3: ra2. PMID 20068230 DOI: 10.1126/Scisignal.2000526  0.695
2010 Wang Z, Udeshi ND, O'Malley M, Shabanowitz J, Hunt DF, Hart GW. Enrichment and site mapping of O-linked N-acetylglucosamine by a combination of chemical/enzymatic tagging, photochemical cleavage, and electron transfer dissociation mass spectrometry. Molecular & Cellular Proteomics : McP. 9: 153-60. PMID 19692427 DOI: 10.1074/Mcp.M900268-Mcp200  0.602
2009 Housley MP, Udeshi ND, Rodgers JT, Shabanowitz J, Puigserver P, Hunt DF, Hart GW. A PGC-1alpha-O-GlcNAc transferase complex regulates FoxO transcription factor activity in response to glucose. The Journal of Biological Chemistry. 284: 5148-57. PMID 19103600 DOI: 10.1074/Jbc.M808890200  0.5
2008 Udeshi ND, Compton PD, Shabanowitz J, Hunt DF, Rose KL. Methods for analyzing peptides and proteins on a chromatographic timescale by electron-transfer dissociation mass spectrometry. Nature Protocols. 3: 1709-17. PMID 18927556 DOI: 10.1038/Nprot.2008.159  0.713
2008 Housley MP, Rodgers JT, Udeshi ND, Kelly TJ, Shabanowitz J, Hunt DF, Puigserver P, Hart GW. O-GlcNAc regulates FoxO activation in response to glucose. The Journal of Biological Chemistry. 283: 16283-92. PMID 18420577 DOI: 10.1074/Jbc.M802240200  0.497
2007 Udeshi ND, Shabanowitz J, Hunt DF, Rose KL. Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS. The Febs Journal. 274: 6269-76. PMID 18021239 DOI: 10.1111/J.1742-4658.2007.06148.X  0.559
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