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Dmitry Avtonomov
Dmitry Avtonomov
Bertis BioScience
Verified email at dmtavt.com - Homepage
Title
Cited by
Cited by
Year
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
11912017
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
6352015
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
4392019
Proteogenomic characterization of endometrial carcinoma
Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ...
Cell 180 (4), 729-748. e26, 2020
3202020
Philosopher: a versatile toolkit for shotgun proteomics data analysis
F da Veiga Leprevost, SE Haynes, DM Avtonomov, HY Chang, ...
Nature methods 17 (9), 869-870, 2020
2792020
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
C Huang, L Chen, SR Savage, RV Eguez, Y Dou, Y Li, ...
Cancer cell 39 (3), 361-379. e16, 2021
2132021
Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant
F Yu, SE Haynes, GC Teo, DM Avtonomov, DA Polasky, AI Nesvizhskii
Molecular & Cellular Proteomics 19 (9), 1575-1585, 2020
1672020
Identification of modified peptides using localization-aware open search
F Yu, GC Teo, AT Kong, SE Haynes, DM Avtonomov, DJ Geiszler, ...
Nature communications 11 (1), 4065, 2020
1522020
PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results
DJ Geiszler, AT Kong, DM Avtonomov, F Yu, F da Veiga Leprevost, ...
Molecular & Cellular Proteomics 20, 2021
712021
Integrated proteogenomic characterization of clear cell renal cell carcinoma
DJ Clark, SM Dhanasekaran, F Petralia, J Pan, X Song, Y Hu, ...
Cell 180 (1), 207, 2020
522020
BatMass: a Java software platform for LC–MS data visualization in proteomics and metabolomics
DM Avtonomov, A Raskind, AI Nesvizhskii
Journal of proteome research 15 (8), 2500-2509, 2016
392016
Clinical proteomic tumor analysis consortium. 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, 2019
362019
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data
D Fermin, D Avtonomov, H Choi, AI Nesvizhskii
Bioinformatics 31 (7), 1141-1143, 2015
292015
Crystal-C: a computational tool for refinement of open search results
HY Chang, AT Kong, F da Veiga Leprevost, DM Avtonomov, SE Haynes, ...
Journal of proteome research 19 (6), 2511-2515, 2020
262020
DeltaMass: Automated detection and visualization of mass shifts in proteomic open-search results
DM Avtonomov, A Kong, AI Nesvizhskii
Journal of proteome research 18 (2), 715-720, 2018
242018
Accurate mass tag retention time database for urine proteome analysis by chromatography-mass spectrometry
IA Agron, DM Avtonomov, AS Kononikhin, IA Popov, SA Moshkovskii, ...
Biochemistry (Moscow) 75, 636-641, 2010
242010
Imtbx and grppr: software for top-down proteomics utilizing ion mobility-mass spectrometry
DM Avtonomov, DA Polasky, BT Ruotolo, AI Nesvizhskii
Analytical chemistry 90 (3), 2369-2375, 2018
152018
A new method for normalization of the peptide retention times in chromatographic/mass-spectrometric experiments
DM Avtonomov, IA Agron, AS Kononikhin, IA Popov, EN Nikolaev
Russian Journal of Bioorganic Chemistry 37 (2), 146, 2011
42011
Data filtration for more robust alignment of chromatograms of complex peptide mixtures
DM Avtonomov, IA Agron, AS Kononikhin, IA Popov, EN Nikolaev
Bioorganicheskaia Khimiia 37 (2), 165-170, 2011
42011
Database of accurate mass-timestamp for gas chromatography-mass spectrometry analysis of urine proteome
IA Agron, DM Avtonomov, AS Kononikhin, IA Popov, SA Moshkovsky, ...
Biochemistry 25 (4), 598-605, 2010
22010
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