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Fengchao Yu
Fengchao Yu
Research Investigator, University of Michigan
Verified email at umich.edu - Homepage
Title
Cited by
Cited by
Year
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
2092021
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
1712021
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, 2020
1622020
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), 1-8, 2022
157*2022
Fast and Comprehensive N-and O-glycoproteomics analysis with MSFragger-Glyco
DA Polasky, F Yu, GC Teo, AI Nesvizhskii
Nature Methods, 2020
1552020
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
1482020
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
912020
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, 100018, 2021
692021
Profiling the proteome-wide selectivity of diverse electrophiles
PRA Zanon, F Yu, P Musacchio, L Lewald, M Zollo, K Krauskopf, ...
512021
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
39*2023
Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis
S Liu, F Yu, Z Yang, T Wang, H Xiong, C Chang, W Yu, N Li
Molecular & Cellular Proteomics 17 (5), 1010-1027, 2018
312018
PIPI: PTM-invariant peptide identification using coding method
F Yu, N Li, W Yu
Journal of proteome research 15 (12), 4423-4435, 2016
302016
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
29*2023
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
252023
Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity
F Yu, N Li, W Yu
Journal of proteome research 16 (10), 3942-3952, 2017
252017
ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database
F Yu, N Li, W Yu
BMC bioinformatics 17, 1-8, 2016
232016
In planta chemical cross‐linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis
X Zhu, F Yu, Z Yang, S Liu, C Dai, X Lu, C Liu, W Yu, N Li
Proteomics 16 (13), 1915-1927, 2016
212016
SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines
HS Desai, T Yan, F Yu, AW Sun, M Villanueva, AI Nesvizhskii, KM Backus
Molecular & Cellular Proteomics 21 (4), 2022
192022
Development of in Planta Chemical Cross-Linking-Based Quantitative Interactomics in Arabidopsis
S Liu, F Yu, Q Hu, T Wang, L Yu, S Du, W Yu, N Li
Journal of proteome research 17 (9), 3195-3213, 2018
192018
Multiattribute Glycan Identification and FDR Control for Glycoproteomics
DA Polasky, DJ Geiszler, F Yu, AI Nesvizhskii
Molecular & Cellular Proteomics 21 (3), 2022
162022
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