Dmitry Avtonomov
Dmitry Avtonomov
Protein Metrics inc
Verified email at dmtavt.com - Homepage
Title
Cited by
Cited by
Year
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
3522015
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
2342017
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
592019
Proteogenomic characterization of endometrial carcinoma
Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ...
Cell 180 (4), 729-748. e26, 2020
362020
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
272016
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 (5), 636-641, 2010
202010
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
182015
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
112018
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
92018
Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant
F Yu, SE Haynes, GC Teo, DM Avtonomov, DA Polasky, AI Nesvizhskii
BioRxiv, 2020
82020
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
72020
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), 1-9, 2020
72020
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
52020
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
52010
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
32011
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
22020
PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results
DJ Geiszler, AT Kong, DM Avtonomov, F Yu, FV Leprevost, AI Nesvizhski
Molecular & Cellular Proteomics, 100018, 2020
12020
Tear fluid proteome variability in healthy donors
AE Bugrova, AS Kononikhin, DM Avtonomov, IA Popov, DN Galetskiĭ, ...
Rossiiskii fiziologicheskii zhurnal imeni IM Sechenova 99 (4), 527-536, 2013
2013
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, 0
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Articles 1–20