Fengchao Yu

University of Michigan, Ann Arbor, Michigan, USA

I am a research investigator from Alexey Nesvizhskii's lab at University of Michigan. I got my PhD degree from Weichuan Yu's lab at The Hong Kong University of Science and Technology. My research interests include Proteomics, Bioinformatics, computational biology, machine learning, and statistics.

Research Experience

Department of Pathology, University of Michigan

Research Investigator
May 2021 - present

Department of Pathology, University of Michigan

Research Fellow
January 2019 - April 2021

Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology

Research Associate
June 2017 - December 2018

Division of Biomedical Engineering, The Hong Kong University of Science and Technology

Doctor of Philosophy
September 2012 - June 2017

Department of Optical Engineering, Zhejiang University

Master of Engineering
September 2009 - March 2012

Journal Publications

  1. Petyuk, V.A., Yu, L., Olson, H.M., Yu, F., Clair, G., Qian, W.J., Shulman, J.M. & Bennett, D.A. (2021). Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss. Journal of Proteome Research, 20(5), 2266-2282.
  2. Yu, F.*, Haynes, S., & Nesvizhskii, A. (2021). IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs. Molecular & Cellular Proteomics, 20, 100077.
  3. Huang, C., Chen, L., Savage, S. R., Eguez, R. V., Dou, Y., Li, Y., ... & Piehowski, P. D. (2021). Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell, 39(3), 361-379.
  4. Teo, G. C., Polasky, D., Yu, F., & Nesvizhskii, A. (2020). Fast deisotoping algorithm and its implementation in the MSFragger search engine. Journal of Proteome Research, 20(1), 498-505.
  5. Geiszler, D., Kong, A., Avtonomov, D., Yu, F., Leprevost, F., & Nesvizhskii, A. (2020). PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. Molecular & Cellular Proteomics, 20, 100018.
  6. Polasky, D., Yu, F., Teo, G. C., & Nesvizhskii, A. (2020). Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nature Methods, 17(11), 1125–1132.
  7. Yu, F., Teo, G. C., Kong, A., Avtonomov, D., Geiszler, D., & Nesvizhskii, A. (2020). Identification of modified peptides using localization-aware open search. Nature Communications, 11(1), 4065.
  8. Yu, F.*, Haynes, S.*, Teo, G. C., Avtonomov, D., Polasky, D., & Nesvizhskii, A. (2020). Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Molecular & Cellular Proteomics, 19(9), 1575-1585. (* co-first author)
  9. Dai, J.*, Yu, F.*, Chen Zhou, & Yu, W. (2020). Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study. IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi: 10.1109/TCBB.2020.2991207. (* co-first author)
  10. Liu, S.*, Yu, F.*, Hu, Q., Wang, T., Yu, L., Du, S., Yu, W., & Li, N. (2018). Development of in planta chemical cross-linking-based quantitative interactomics in Arabidopsis. Journal of Proteome Research, 17(9), 3195-3213. (* co-first author)
  11. Dai, J.*, Jiang, W.*, Yu, F.*, & Yu, W. (2018). Xolik: finding cross-linked peptides with maximum paired scores in linear time. Bioinformatics, 35(2), 251-257. (* co-first author)
  12. Liu, S.*, Yu, F.*, Yang, Z., Wang, T., Xiong, H., Chang, C., Yu, W., & Li, N. (2018). Establishment of dimethyl labeling-based quantitative acetylproteomics in Arabidopsis. Molecular & Cellular Proteomics, 17(5), 1010-1027. (* co-first author)
  13. Yu, F., Li, N., & Yu, W. (2017). Exhaustively identifying cross-linked peptides with a linear computational complexity. Journal of Proteome Research, 16(10), 3942-3952.
  14. Yu, F., Li, N., & Yu, W. (2016). PIPI: PTM-invariant peptide identification using coding method. Journal of Proteome Research, 15(12), 4423-4435.
  15. Yu, F., Li, N., & Yu, W. (2016). ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database. BMC Boinformatics, 17(1), 217.
  16. Zhu, X.*, Yu, F.*, Yang, Z., Liu, S., Dai, C., Lu, X., Liu, C., Yu, W., & Li, N. (2016). In planta chemical cross‐linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis. Proteomics, 16(13), 1915-1927. (* co-first author)
  17. Yu, F., Liu, H., Hu, Z., & Shi, P. (2012). Graphics processing unit (GPU)-accelerated particle filter framework for positron emission tomography image reconstruction. JOSA A, 29(4), 637-643.

Presentations

  1. Yu, F., Haynes, S., & Nesvizhskii, A. (2021, March). False discovery rate-controlled match-between-runs enables accurate and sensitive label free quantification. 17th Annual US HUPO Conference (US HUPO 2021). (poster presentation), virtual conference.
  2. Yu, F., Teo, G. C., Kong, A., Haynes, S., Avtonomov, D., Geiszler, D., & Nesvizhskii, A. (2020, June). Improved identification of modified peptides using localization-aware open search. 28th Conference on Intelligent Systems for Molecular Biology (ISMB 2020). (poster presentation), virtual conference.
  3. Yu, F., Haynes, S., Avtonomov, D., Kong, A., Leprevost, F., & Nesvizhskii, A. (2020, June). Breaking the logjam: fast peptide identification and quantification in timsTOF PASEF data. 68th ASMS Conference on Mass Spectrometry and Allied Topics (ASMS 2020). (poster presentation), virtual conference.
  4. Yu, F., Haynes, S., Teo, G. C., Kong, A., Avtonomov, D., Leprevost, F., Chang, H.-Y., Geiszler, D., Polasky, D., & Nesvizhskii, A. (2020, March). Fast and quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. 16th Annual US HUPO Conference (US HUPO 2020). (poster presentation), virtual conference.
  5. Yu, F., Teo, G. C., Kong, A., Leprevost, F., Avtonomov, D., Chang, H., Geiszler, D., Haynes, S., Polasky, D., & Nesvizhskii, A. (2019, October). MSFragger: fast and sensitive peptide identification in diverse proteomic datasets. 18th Human Proteome Organization World Congress (HUPO 2019). (poster presentation), Adelaide, Australia.
  6. Yu, F., Teo, G. C., Kong, A., Leprevost, F., Chang, H., & Nesvizhskii, A. (2019, June). Comparison of open search tools. 67th ASMS Conference on Mass Spectrometry and Allied Topics (ASMS 2019). (poster presentation), Atlanta, Georgia.
  7. Yu, F., Li, N., & Yu, W. (2018, August). PTM-invariant peptide identification. 5th China Workshop on Computational Proteomics (CNCP 2018). (oral presentation), Beijing, China.
  8. Yu, F., Li, N., & Yu, W. (2017, August). PIPI: PTM-invariant peptide identification using coding method. Post-translational Modification Networks, Gordon Research Conference. (poster presentation), Hong Kong, China.
  9. Yu, F., Li, N., & Yu, W. (2017, August). PIPI: PTM-invariant peptide identification using coding method. 11th International Conference on Computational Systems Biology (ISB 2017). (oral presentation), Shenzhen, China.
  10. Yu, F., Li, N., & Yu, W. (2017, May). Exhaustively identifying cross-linked peptides with a linear complexity. 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017). (poster presentation), Hong Kong, China.
  11. Yu, F., Liu, H., & Shi, P. (2012, January). PET image reconstruction based on particle filter framework. In Biomedical and Health Informatics (BHI), 2012 IEEE-EMBS International Conference on (pp. 851-853). IEEE.
  12. Yu, F., Liu, H., & Shi, P. (2011, September). PET image reconstruction: GPU-accelerated particle filter framework. In Image Processing (ICIP), 2011 18th IEEE International Conference on (pp. 417-420). IEEE.

Awards

  • US HUPO (United States Human Proteome Organization) Travel Stipend Award (2020)
  • UGC Research Travel Grant Award (2018-19)
  • UGC Research Travel Grant Award (2018-19)
  • UGC Research Travel Grant Award (2017-18)
  • UGC Research Travel Grant Award (2016-17)
  • Graduate Student Research Award Program of HKMHDIA (Hong Kong Medical & Healthcare Device Industries Association Limited) (2015-16)

Professional Activities

Journal reviewer

Journal Reviewed
Nature Communications 1
Nature Computational Science 3
Briefings in Bioinformatics 12
Bioinformatics 10
Journal of Proteome Research 5
Proteomics 5
Journal of Proteomics 1
Analytical Chemistry 5
ACS Omega 1
BMC Bioinformatics 8
BMC Genomics 1
Rapid Communications in Mass Spectrometry 1
Bioinformatics Advances 3
total: 56