| 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 | 1559 | 2017 |
| 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 | 687 | 2015 |
| 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 | 523 | 2019 |
| Proteogenomic characterization of endometrial carcinoma Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ... Cell 180 (4), 729-748. e26, 2020 | 372 | 2020 |
| 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 | 370 | 2020 |
| 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 | 257 | 2021 |
| 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 | 224 | 2020 |
| 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 | 208 | 2020 |
| 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 | 99 | 2021 |
| 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 | 59 | 2020 |
| 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 | 42 | 2016 |
| 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 | 41 | 2019 |
| 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 | 36 | 2020 |
| 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 | 31 | 2015 |
| 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 | 25 | 2018 |
| 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 | 25 | 2010 |
| 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 | 17 | 2018 |
| 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 | 4 | 2011 |
| 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 | 4 | 2011 |
| Targeted proteomics data interpretation with DeepMRM J Park, C Wilkins, D Avtonomov, J Hong, S Back, H Kim, N Shulman, ... Cell Reports Methods 3 (7), 2023 | 3 | 2023 |
Alexey NesvizhskiiGodfrey D. Stobbe Professor of Bioinformatics @ University of MichiganVerified email at umich.edu
