Alexey Nesvizhskii
Alexey Nesvizhskii
Godfrey D. Stobbe Professor of Bioinformatics @ University of Michigan
Verified email at - Homepage
Cited by
Cited by
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
A Keller, AI Nesvizhskii, E Kolker, R Aebersold
Analytical chemistry 74 (20), 5383-5392, 2002
A statistical model for identifying proteins by tandem mass spectrometry
AI Nesvizhskii, A Keller, E Kolker, R Aebersold
Analytical chemistry 75 (17), 4646-4658, 2003
The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
D Mellacheruvu, Z Wright, AL Couzens, JP Lambert, NA St-Denis, T Li, ...
Nature methods 10 (8), 730–736, 2013
Interpretation of shotgun proteomic data: the protein inference problem
AI Nesvizhskii, R Aebersold
Molecular & cellular proteomics 4 (10), 1419-1440, 2005
Analysis and validation of proteomic data generated by tandem mass spectrometry
AI Nesvizhskii, O Vitek, R Aebersold
Nature methods 4 (10), 787-797, 2007
The peptideatlas project
F Desiere, EW Deutsch, NL King, AI Nesvizhskii, P Mallick, J Eng, S Chen, ...
Nucleic acids research 34 (suppl_1), D655-D658, 2006
A guided tour of the Trans‐Proteomic Pipeline
EW Deutsch, L Mendoza, D Shteynberg, T Farrah, H Lam, N Tasman, ...
Proteomics 10 (6), 1150-1159, 2010
A global protein kinase and phosphatase interaction network in yeast
A Breitkreutz, H Choi, JR Sharom, L Boucher, V Neduva, B Larsen, ZY Lin, ...
Science 328 (5981), 1043, 2010
The landscape of circular RNA in cancer
JN Vo, M Cieslik, Y Zhang, S Shukla, L Xiao, Y Zhang, YM Wu, ...
Cell 176 (4), 869-881. e13, 2019
SAINT: probabilistic scoring of affinity purification–mass spectrometry data
H Choi, B Larsen, ZY Lin, A Breitkreutz, D Mellacheruvu, D Fermin, ZS Qin, ...
Nature methods 8 (1), 70-73, 2011
Proteogenomics: concepts, applications and computational strategies
AI Nesvizhskii
Nature methods 11 (11), 1114-1125, 2014
An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency
L Ho, JL Ronan, J Wu, BT Staahl, L Chen, A Kuo, J Lessard, ...
Proceedings of the National Academy of Sciences 106 (13), 5181-5186, 2009
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data
S Carr, R Aebersold, M Baldwin, AL Burlingame, K Clauser, A Nesvizhskii
Molecular & Cellular Proteomics 3 (6), 531-533, 2004
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
AI Nesvizhskii
Journal of proteomics 73 (11), 2092-2123, 2010
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
D Shteynberg, EW Deutsch, H Lam, JK Eng, Z Sun, N Tasman, ...
Molecular & cellular proteomics 10 (12), 2011
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics
CC Tsou, D Avtonomov, B Larsen, M Tucholska, H Choi, AC Gingras, ...
Nature methods 12 (3), 258-264, 2015
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
AT Kong, FV Leprevost, DM Avtonomov, D Mellacheruvu, AI Nesvizhskii
Nature methods 14 (5), 513-520, 2017
Significance analysis of spectral count data in label-free shotgun proteomics
H Choi, D Fermin, AI Nesvizhskii
Molecular & cellular proteomics 7 (12), 2373-2385, 2008
A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification
D Mueller, C Bach, D Zeisig, MP Garcia-Cuellar, S Monroe, A Sreekumar, ...
Blood, The Journal of the American Society of Hematology 110 (13), 4445-4454, 2007
SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software
G Teo, G Liu, J Zhang, AI Nesvizhskii, AC Gingras, H Choi
Journal of proteomics 100, 37-43, 2014
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