Fengchao Yu

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 34

Top Topics

Mass Spectrometry

Machine Learning

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Journal of proteome research

Science translational medicine

This page only lists publications with an associated author ORCID identifier.

Publications

Humberto J Ferreira, Brian J Stevenson, HuiSong Pak, Fengchao Yu, Jessica Almeida Oliveira, Florian Huber, Marie Taillandier-Coindard, Justine Michaux, Emma Ricart-Altimiras, Anne I Kraemer, Lana Elias Kandalaft, Daniel E Speiser, Alexey I Nesvizhskii, Markus Müller, Michal Bassani-Sternberg
Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides. Nature communications 15 (1) (2024)
Ludwig Lautenbacher, Kevin L Yang, Tobias Kockmann, Christian Panse, Matthew Chambers, Elias Kahl, Fengchao Yu, Wassim Gabriel, Dulguun Bold, Tobias Schmidt, Kai Li, Brendan X MacLean, Alexey I Nesvizhskii, Mathias Wilhelm
Koina: Democratizing machine learning for proteomics research. bioRxiv : the preprint server for biology (2024)
Ludwig Lautenbacher, Kevin L Yang, Tobias Kockmann, Christian Panse, Matthew Chambers, Elias Kahl, Fengchao Yu, Wassim Gabriel, Dulguun Bold, Tobias Schmidt, Kai Li, Brendan X MacLean, Alexey I Nesvizhskii, Mathias Wilhelm
Koina: Democratizing machine learning for proteomics research. bioRxiv : the preprint server for biology (2024)
Ludwig Lautenbacher, Kevin L Yang, Tobias Kockmann, Christian Panse, Matthew Chambers, Elias Kahl, Fengchao Yu, Wassim Gabriel, Dulguun Bold, Tobias Schmidt, Kai Li, Brendan X MacLean, Alexey I Nesvizhskii, Mathias Wilhelm
Koina: Democratizing machine learning for proteomics research. bioRxiv : the preprint server for biology (2024)
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M Williams, Lye Meng Markillie, Ronald J Moore, Ernesto S Nakayasu, Jing Chen, Martha L Campbell-Thompson, Clayton E Mathews, Alexey I Nesvizhskii, Wei-Jun Qian, Ying Zhu
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. bioRxiv : the preprint server for biology (2024)
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M Williams, Lye Meng Markillie, Ronald J Moore, Ernesto S Nakayasu, Jing Chen, Martha L Campbell-Thompson, Clayton E Mathews, Alexey I Nesvizhskii, Wei-Jun Qian, Ying Zhu
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. bioRxiv : the preprint server for biology (2024)
Devon Kohler, Mateusz Staniak, Fengchao Yu, Alexey I Nesvizhskii, Olga Vitek
An MSstats workflow for detecting differentially abundant proteins in large-scale data-independent acquisition mass spectrometry experiments with FragPipe processing. Nature protocols (2024)
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M Williams, Lye Meng Markillie, Ronald J Moore, Ernesto S Nakayasu, Jing Chen, Martha L Campbell-Thompson, Clayton E Mathews, Alexey I Nesvizhskii, Wei-Jun Qian, Ying Zhu
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. bioRxiv : the preprint server for biology (2024)
Yuxin Mi, Katie L Burnham, Philip D Charles, Raphael Heilig, Iolanda Vendrell, Justin P Whalley, Hew D Torrance, David Benjamin Antcliffe, Shaun M May, Matthew J Neville, Georgina Berridge, Paula Hutton, Cyndi G Geoghegan, Jayachandran Radhakrishnan, Alexey I Nesvizhskii, Fengchao Yu, null null, Emma E Davenport, Stuart McKechnie, Roger Davies, David J P O'Callaghan, Parind Patel, Ana Gutierrez Del Arroyo, Fredrik Karpe, Anthony C Gordon, Gareth L Ackland, Charles J Hinds, Roman Fischer, Julian C Knight
High-throughput mass spectrometry maps the sepsis plasma proteome and differences in patient response. Science translational medicine 16 (750) (2024)
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M Williams, Lye Meng Markillie, Ronald J Moore, Ernesto S Nakayasu, Jing Chen, Martha L Campbell-Thompson, Clayton E Mathews, Alexey I Nesvizhskii, Wei-Jun Qian, Ying Zhu
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. bioRxiv : the preprint server for biology (2024)
Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel Ricky Steele, Ralf B Schittenhelm, Alexey I Nesvizhskii
Analysis and visualization of quantitative proteomics data using FragPipe-Analyst. bioRxiv : the preprint server for biology (2024)
Humberto J Ferreira, Brian J Stevenson, HuiSong Pak, Fengchao Yu, Jessica Almeida Oliveira, Florian Huber, Marie Taillandier-Coindard, Justine Michaux, Emma Ricart-Altimiras, Anne I Kraemer, Lana Elias Kandalaft, Daniel E Speiser, Alexey I Nesvizhskii, Markus Müller, Michal Bassani-Sternberg
Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides. Nature communications 15 (1) (2024)
Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel Ricky Steele, Ralf B Schittenhelm, Alexey I Nesvizhskii
Analysis and visualization of quantitative proteomics data using FragPipe-Analyst. bioRxiv : the preprint server for biology (2024)
Kai Li, Guo Ci Teo, Kevin L Yang, Fengchao Yu, Alexey I Nesvizhskii
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. bioRxiv : the preprint server for biology (2024)
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M Williams, Lye Meng Markillie, Ronald J Moore, Ernesto S Nakayasu, Jing Chen, Martha L Campbell-Thompson, Clayton E Mathews, Alexey I Nesvizhskii, Wei-Jun Qian, Ying Zhu
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. bioRxiv : the preprint server for biology (2024)
Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel Ricky Steele, Ralf Bernd Schittenhelm, Alexey I Nesvizhskii
Analysis and visualization of quantitative proteomics data using FragPipe-Analyst. bioRxiv : the preprint server for biology (2024)
Kai Li, Guo Ci Teo, Kevin L Yang, Fengchao Yu, Alexey I Nesvizhskii
diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. bioRxiv : the preprint server for biology (2024)
Yuxin Mi, Katie L Burnham, Philip D Charles, Raphael Heilig, Iolanda Vendrell, Justin P Whalley, Hew D Torrance, David Benjamin Antcliffe, Shaun M May, Matthew J Neville, Georgina Berridge, Paula Hutton, Cyndi G Geoghegan, Jayachandran Radhakrishnan, Alexey I Nesvizhskii, Fengchao Yu, null null, Emma E Davenport, Stuart McKechnie, Roger Davies, David J P O'Callaghan, Parind Patel, Ana Gutierrez Del Arroyo, Fredrik Karpe, Anthony C Gordon, Gareth L Ackland, Charles J Hinds, Roman Fischer, Julian C Knight
High-throughput mass spectrometry maps the sepsis plasma proteome and differences in patient response. Science translational medicine 16 (750) (2024)
Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel Ricky Steele, Ralf Bernd Schittenhelm, Alexey I Nesvizhskii
Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst. Journal of proteome research (2024)
Heta Desai, Samuel Ofori, Lisa Boatner, Fengchao Yu, Miranda Villanueva, Nicholas Ung, Alexey I Nesvizhskii, Keriann Backus
Multi-omic stratification of the missense variant cysteinome. bioRxiv : the preprint server for biology (2023)
Joonho Park, Fengchao Yu, James M Fulcher, Sarah M Williams, Kristin Engbrecht, Ronald J Moore, Geremy C Clair, Vladislav A Petyuk, Alexey I Nesvizhskii, Ying Zhu
Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics. Analytical chemistry (2023)
Kevin L Yang, Fengchao Yu, Guo Ci Teo, Kai Li, Vadim Demichev, Markus Ralser, Alexey I Nesvizhskii
MSBooster: improving peptide identification rates using deep learning-based features. Nature communications 14 (1) (2023)
Georges Bedran, Daniel A Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier Antonio Alfaro, Marcin Cieslik, Alexey I Nesvizhskii
Unraveling the glycosylated immunopeptidome with HLA-Glyco. Nature communications 14 (1) (2023)
Daniel J Geiszler, Daniel A Polasky, Fengchao Yu, Alexey I Nesvizhskii
Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides. Nature communications 14 (1) (2023)
Fengchao Yu, Guo Ci Teo, Andy T Kong, Klemens Fröhlich, Ginny Xiaohe Li, Vadim Demichev, Alexey I Nesvizhskii
Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform. Nature communications 14 (1) (2023)
Vadim Demichev, Lukasz Szyrwiel, Fengchao Yu, Guo Ci Teo, George A Rosenberger, Agathe Niewienda, Daniela Ludwig, Jens Decker, Stephanie Kaspar-Schoenefeld, Kathryn S Lilley, Michael Mülleder, Alexey I Nesvizhskii, Markus Ralser
dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nature communications 13 (1) (2022)
Assaf Kacen, Aaron Javitt, Matthias P Kramer, David Morgenstern, Tomer Tsaban, Merav D Shmueli, Guo Ci Teo, Felipe da Veiga Leprevost, Eilon Barnea, Fengchao Yu, Arie Admon, Lea Eisenbach, Yardena Samuels, Ora Schueler-Furman, Yishai Levin, Alexey I Nesvizhskii, Yifat Merbl
Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nature biotechnology (2022)
Hui-Yin Chang, Sarah E Haynes, Fengchao Yu, Alexey I Nesvizhskii
Implementing the MSFragger Search Engine as a Node in Proteome Discoverer. Journal of proteome research (2022)
Daniel A Polasky, Fengchao Yu, Guo Ci Teo, Alexey I Nesvizhskii
Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nature methods 17 (11) (2020)
Daniel J Geiszler, Andy T Kong, Dmitry M Avtonomov, Fengchao Yu, Felipe da Veiga Leprevost, Alexey I Nesvizhskii
PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. Molecular & cellular proteomics : MCP (2020)
Guo Ci Teo, Daniel A Polasky, Fengchao Yu, Alexey I Nesvizhskii
Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine. Journal of proteome research 20 (1) (2020)
Fengchao Yu, Guo Ci Teo, Andy T Kong, Sarah E Haynes, Dmitry M Avtonomov, Daniel J Geiszler, Alexey I Nesvizhskii
Identification of modified peptides using localization-aware open search. Nature communications 11 (1) (2020)
Shichang Liu, Fengchao Yu, Qin Hu, Tingliang Wang, Lujia Yu, Shengwang Du, Weichuan Yu, Ning Li
Development of in Planta Chemical Cross-Linking-Based Quantitative Interactomics in Arabidopsis. Journal of proteome research 17 (9) (2018)
Fengchao Yu, Ning Li, Weichuan Yu
Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity. Journal of proteome research 16 (10) (2017)