| 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 |
| Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475-476, 2018 | 842 | 2018 |
| 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 | 510 | 2020 |
| Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma MA Gillette, S Satpathy, S Cao, SM Dhanasekaran, SV Vasaikar, K Krug, ... Cell 182 (1), 200-225. e35, 2020 | 478 | 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 |
| Proteogenomic characterization of pancreatic ductal adenocarcinoma L Cao, C Huang, DC Zhou, Y Hu, TM Lih, SR Savage, K Krug, DJ Clark, ... Cell 184 (19), 5031-5052. e26, 2021 | 286 | 2021 |
| Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0 PC Carvalho, DB Lima, FV Leprevost, MDM Santos, JSG Fischer, ... Nature protocols 11 (1), 102-117, 2016 | 267 | 2016 |
| BioContainers: an open-source and community-driven framework for software standardization F da Veiga Leprevost, BA Grüning, S Alves Aflitos, HL Röst, J Uszkoreit, ... Bioinformatics 33 (16), 2580-2582, 2017 | 266 | 2017 |
| 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 | 223 | 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 | 213 | 2020 |
| A proteogenomic portrait of lung squamous cell carcinoma S Satpathy, K Krug, PMJ Beltran, SR Savage, F Petralia, C Kumar-Sinha, ... Cell 184 (16), 4348-4371. e40, 2021 | 203 | 2021 |
| Discovering and linking public omics data sets using the Omics Discovery Index Y Perez-Riverol, M Bai, F da Veiga Leprevost, S Squizzato, YM Park, ... Nature biotechnology 35 (5), 406-409, 2017 | 176 | 2017 |
| Ten simple rules for taking advantage of Git and GitHub Y Perez-Riverol, L Gatto, R Wang, T Sachsenberg, J Uszkoreit, ... PLoS computational biology 12 (7), e1004947, 2016 | 157 | 2016 |
| 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 |
| Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors SI Djomehri, ME Gonzalez, F da Veiga Leprevost, SR Tekula, HY Chang, ... Nature communications 11 (1), 1723, 2020 | 82 | 2020 |
| On best practices in the development of bioinformatics software FV Leprevost, VC Barbosa, EL Francisco, Y Perez-Riverol, PC Carvalho Frontiers in genetics 5, 97575, 2014 | 74 | 2014 |
| 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 | 63 | 2023 |
| Reevaluating the Trypanosoma cruzi proteomic map: The shotgun description of bloodstream trypomastigotes GVF Brunoro, MA Caminha, AT da Silva Ferreira, F da Veiga Leprevost, ... Journal of proteomics 115, 58-65, 2015 | 56 | 2015 |
| 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 | 49* | 2023 |
| Recommendations for the packaging and containerizing of bioinformatics software G Bjorn, S Olivier, P Moreno, M Hervé, D Søndergaard, R Hannes, S Timo, ... F1000Research 7, 2019 | 45* | 2019 |
Alexey NesvizhskiiGodfrey D. Stobbe Professor of Bioinformatics @ University of Michigan在 umich.edu 的电子邮件经过验证
