| 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 | 332 | 2020 |
| IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs F Yu, SE Haynes, AI Nesvizhskii Molecular & Cellular Proteomics 20, 2021 | 226 | 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 | 197 | 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 | 193 | 2020 |
| Variable-velocity traveling-wave ion mobility separation enhances peak capacity for data-independent acquisition proteomics SE Haynes, DA Polasky, SM Dixit, JD Majmudar, K Neeson, BT Ruotolo, ... Analytical Chemistry, 2017 | 94 | 2017 |
| 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 | 81 | 2023 |
| Oxidase activity of the barnacle adhesive interface involves peroxide-dependent catechol oxidase and lysyl oxidase enzymes CR So, JM Scancella, KP Fears, T Essock-Burns, SE Haynes, DH Leary, ... ACS Applied Materials & Interfaces 9 (13), 11493-11505, 2017 | 59 | 2017 |
| Identification of Pirin as a molecular target of the CCG-1423/CCG-203971 series of antifibrotic and antimetastatic compounds EM Lisabeth, D Kahl, I Gopallawa, SE Haynes, SA Misek, PL Campbell, ... ACS pharmacology & translational science 2 (2), 92-100, 2019 | 40 | 2019 |
| Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite Z Wang, DH Leary, J Liu, RE Settlage, KP Fears, SH North, A Mostaghim, ... BMC genomics 16, 1-14, 2015 | 40 | 2015 |
| HDAC8 substrates identified by genetically encoded active site photocrosslinking JE Lopez, SE Haynes, JD Majmudar, BR Martin, CA Fierke Journal of the American Chemical Society 139 (45), 16222-16227, 2017 | 33 | 2017 |
| 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 | 32 | 2020 |
| Profiling protein S‐sulfination with maleimide‐linked probes YH Kuo, AM Konopko, NB Borotto, JD Majmudar, SE Haynes, BR Martin ChemBioChem 18 (20), 2028-2032, 2017 | 29 | 2017 |
| Parthenolide Destabilizes Microtubules by Covalently Modifying Tubulin T Hotta, S Haynes, TL Blasius, M Gebbie, EL Eberhardt, D Sept, ... Current Biology 31, 1-8, 2021 | 27 | 2021 |
| DIA-SIFT: a precursor and product ion filter for accurate stable isotope data-independent acquisition proteomics SE Haynes, JD Majmudar, BR Martin Analytical chemistry 90 (15), 8722-8726, 2018 | 15 | 2018 |
| Autoinhibited kinesin-1 adopts a hierarchical folding pattern Z Tan, Y Yue, F Leprevost, S Haynes, V Basrur, AI Nesvizhskii, KJ Verhey, ... Elife 12, RP86776, 2023 | 14 | 2023 |
| EML2-S constitutes a new class of proteins that recognizes and regulates the dynamics of tyrosinated microtubules T Hotta, TS McAlear, Y Yue, T Higaki, SE Haynes, AI Nesvizhskii, D Sept, ... Current Biology 32 (18), 3898-3910. e14, 2022 | 11 | 2022 |
| Kinesin-binding protein remodels the kinesin motor to prevent microtubule-binding AL Solon, Z Tan, KL Schutt, L Jepsen, SE Haynes, AI Nesvizhskii, D Sept, ... Science Advances 7 (47), 2021 | 7 | 2021 |
| MS2Prop: A machine learning model that directly predicts chemical properties from mass spectrometry data for novel compounds G Voronov, A Frandsen, B Bargh, D Healey, R Lightheart, T Kind, ... bioRxiv 10 (2022.10), 09.511482, 2022 | 6 | 2022 |
| Teaching Python for Data Science: Collaborative development of a modular & interactive curriculum M Duda, KL Sovacool, N Farzaneh, VK Nguyen, SE Haynes, H Falk, ... Journal of Open Source Education, 2021 | 5 | 2021 |
| Comprehensive proteogenomic characterization of rare kidney tumors GX Li, L Chen, Y Hsiao, R Mannan, Y Zhang, J Luo, F Petralia, H Cho, ... Cell Reports Medicine 5 (5), 2024 | 1 | 2024 |
Alexey NesvizhskiiGodfrey D. Stobbe Professor of Bioinformatics @ University of MichiganVerified email at umich.edu