| 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 | 1278 | 2017 |
| 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 | 465 | 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 | 335 | 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 | 307 | 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 | 168 | 2020 |
| Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae MA Freeberg, T Han, JJ Moresco, A Kong, YC Yang, ZJ Lu, JR Yates, ... Genome biology 14, 1-20, 2013 | 111 | 2013 |
| 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 | 83 | 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 | 53 | 2020 |
| Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform F Yu, GC Teo, AT Kong, K Fröhlich, GX Li, V Demichev, AI Nesvizhskii Nature Communications 14 (1), 4154, 2023 | 40 | 2023 |
| 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 | 37 | 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 | 30 | 2020 |
| 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 | 24 | 2018 |
| One-stop analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform F Yu, GC Teo, AT Kong, GX Li, V Demichev, AI Nesvizhskii bioRxiv, 2022.10. 28.514272, 2022 | 8 | 2022 |
| Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi HK Kweon, AT Kong, KE Hersberger, S Huang, AI Nesvizhskii, Y Wang, ... Journal of Proteome Research 23 (1), 71-83, 2023 | 2 | 2023 |
| Using MSFragger for ultrafast database searching AI Nesvizhskii, AT Kong, FV Leprevost, DM Avtonomov, D Mellacheruvu | | 2017 |
| Computational Strategies for Proteogenomics Analyses A Kong | | 2017 |
