Articles with public access mandates - Alexey NesvizhskiiLearn more
Not available anywhere: 4
Review
Proteogenomics: opportunities and caveats
L Dimitrakopoulos, I Prassas, EP Diamandis, A Nesvizhskii, T Kislinger, ...
Clinical chemistry 62 (4), 551-557, 2016
Mandates: Prostate Cancer Canada
Review
Comparative evaluation of proteome discoverer and FragPipe for the TMT-based proteome quantification
T He, Y Liu, Y Zhou, L Li, H Wang, S Chen, J Gao, W Jiang, Y Yu, W Ge, ...
Journal of proteome research 21 (12), 3007-3015, 2022
Mandates: National Natural Science Foundation of China
Review
Integrated proteogenomic characterization of glioblastoma evolution
KH Kim, S Migliozzi, H Koo, JH Hong, SM Park, S Kim, HJ Kwon, S Ha, ...
Cancer Cell 42 (3), 358-377. e8, 2024
Mandates: National Institute of Health and Medical Research, France
Review
Implementing the MSFragger search engine as a node in proteome discoverer
HY Chang, SE Haynes, F Yu, AI Nesvizhskii
Journal of Proteome Research 22 (2), 520-525, 2022
Mandates: US National Institutes of Health
Available somewhere: 193
Review
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
Mandates: US National Institutes of Health, Austrian Science Fund, Canadian Institutes …
Review
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
Mandates: US National Institutes of Health
Review
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
Mandates: US Department of Defense, US National Institutes of Health, Howard Hughes …
Review
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
Mandates: US National Institutes of Health
Review
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
Mandates: US National Institutes of Health, Canadian Institutes of Health Research
Review
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
Mandates: US National Institutes of Health, Canadian Institutes of Health Research
Review
Proteogenomics: concepts, applications and computational strategies
AI Nesvizhskii
Nature methods 11 (11), 1114-1125, 2014
Mandates: US National Institutes of Health
Review
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
Mandates: US National Institutes of Health, Howard Hughes Medical Institute
Review
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
Mandates: US National Institutes of Health, Canadian Institutes of Health Research …
Review
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
Mandates: US National Institutes of Health
Review
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
Mandates: US National Institutes of Health
Review
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
Mandates: US National Institutes of Health
Review
Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma
MA Gillette, S Satpathy, S Cao, SM Dhanasekaran, SV Vasaikar, K Krug, ...
Cell 182 (1), 200-225. e35, 2020
Mandates: US National Institutes of Health
Review
Integrated proteogenomic characterization of clear cell renal cell carcinoma
DJ Clark, SM Dhanasekaran, F Petralia, J Pan, X Song, Y Hu, ...
Cell 179 (4), 964-983. e31, 2019
Mandates: US National Institutes of Health
Review
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
Mandates: German Research Foundation
Review
Proteogenomic and metabolomic characterization of human glioblastoma
LB Wang, A Karpova, MA Gritsenko, JE Kyle, S Cao, Y Li, D Rykunov, ...
Cancer cell 39 (4), 509-528. e20, 2021
Mandates: US Department of Energy, US National Institutes of Health
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