| 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 | 580 | 2014 |
| Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions AL Couzens, JDR Knight, MJ Kean, G Teo, A Weiss, WH Dunham, ZY Lin, ... Science signaling 6 (302), rs15-rs15, 2013 | 471 | 2013 |
| 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 | 439 | 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 | 321 | 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 | 213 | 2021 |
| Integrated proteogenomic characterization across major histological types of pediatric brain cancer F Petralia, N Tignor, B Reva, M Koptyra, S Chowdhury, D Rykunov, A Krek, ... Cell 183 (7), 1962-1985. e31, 2020 | 200 | 2020 |
| 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 | 167 | 2020 |
| Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco DA Polasky, F Yu, GC Teo, AI Nesvizhskii Nature Methods 17 (11), 1125-1132, 2020 | 158 | 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 | 152 | 2020 |
| dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts V Demichev, L Szyrwiel, F Yu, GC Teo, G Rosenberger, A Niewienda, ... Nature communications 13 (1), 3944, 2022 | 130 | 2022 |
| Fast deisotoping algorithm and its implementation in the MSFragger search engine GC Teo, DA Polasky, F Yu, AI Nesvizhskii Journal of proteome research 20 (1), 498-505, 2020 | 96 | 2020 |
| Untargeted, spectral library‐free analysis of data‐independent acquisition proteomics data generated using Orbitrap mass spectrometers CC Tsou, CF Tsai, GC Teo, YJ Chen, AI Nesvizhskii Proteomics 16 (15-16), 2257-2271, 2016 | 73 | 2016 |
| MassIVE. quant: a community resource of quantitative mass spectrometry–based proteomics datasets M Choi, J Carver, C Chiva, M Tzouros, T Huang, TH Tsai, B Pullman, ... Nature methods 17 (10), 981-984, 2020 | 65 | 2020 |
| Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness Y Li, TSM Lih, SM Dhanasekaran, R Mannan, L Chen, M Cieslik, Y Wu, ... Cancer Cell 41 (1), 139-163. e17, 2023 | 53 | 2023 |
| 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 | 52 | 2020 |
| SAINTq: Scoring protein‐protein interactions in affinity purification–mass spectrometry experiments with fragment or peptide intensity data G Teo, H Koh, D Fermin, JP Lambert, JDR Knight, AC Gingras, H Choi Proteomics 16 (15-16), 2238-2245, 2016 | 51 | 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 | 36 | 2019 |
| Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors A Kacen, A Javitt, MP Kramer, D Morgenstern, T Tsaban, MD Shmueli, ... Nature biotechnology 41 (2), 239-251, 2023 | 35 | 2023 |
| High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe V Demichev, F Yu, GC Teo, L Szyrwiel, GA Rosenberger, J Decker, ... Biorxiv, 2021.03. 08.434385, 2021 | 34 | 2021 |
| MSBooster: improving peptide identification rates using deep learning-based features KL Yang, F Yu, GC Teo, K Li, V Demichev, M Ralser, AI Nesvizhskii Nature Communications 14 (1), 4539, 2023 | 28 | 2023 |
Alexey NesvizhskiiGodfrey D. Stobbe Professor of Bioinformatics @ University of MichiganVerified email at umich.edu
