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Fengchao Yu
Fengchao Yu
Research Investigator, University of Michigan
Adresse e-mail validée de umich.edu - Page d'accueil
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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
2952021
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
2742021
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
2502020
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
2302022
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
2202020
Fast and Comprehensive N-and O-glycoproteomics analysis with MSFragger-Glyco
DA Polasky, F Yu, GC Teo, AI Nesvizhskii
Nature Methods, 2020
2132020
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
1572020
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
1082021
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
1032023
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
982023
Profiling the proteome-wide selectivity of diverse electrophiles
PRA Zanon, F Yu, P Musacchio, L Lewald, M Zollo, K Krauskopf, ...
732021
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
672023
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
372021
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
362018
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
322022
PIPI: PTM-invariant peptide identification using coding method
F Yu, N Li, W Yu
Journal of proteome research 15 (12), 4423-4435, 2016
322016
Multiattribute Glycan Identification and FDR Control for Glycoproteomics
DA Polasky, DJ Geiszler, F Yu, AI Nesvizhskii
Molecular & Cellular Proteomics 21 (3), 2022
312022
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
282017
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
262016
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics
DA Polasky, DJ Geiszler, F Yu, K Li, GC Teo, AI Nesvizhskii
Molecular & Cellular Proteomics 22 (5), 2023
252023
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