Fengchao Yu

University of Michigan, Ann Arbor, Michigan, USA

I am a research fellow 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 Fellow
January 2019 - Present

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

Research Associate
July 2017 - December 2018

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

Doctor of Philosophy in Bioengineering
September 2012 - May 2017

Department of Optical Engineering, Zhejiang University

Master in Optical Engineering
September 2009 - March 2012



  1. Dai, J.*, Yu, F.*, & Yu, W. (2018). Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study. Bioinformatics, under review. (* co-first author) (bioRxiv pre-print)
  2. 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) (JCR Ranking: Q1)
  3. 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) (Project page: http://bioinformatics.ust.hk/Xolik.html) (JCR Ranking: Q1)
  4. 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) (JCR Ranking: Q1)
  5. 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. (Project page: https://github.com/fcyu/ECL2, https://github.com/fcyu/ECLViewer2) (JCR Ranking: Q1)
  6. Yu, F., Li, N., & Yu, W. (2016). PIPI: PTM-Invariant Peptide Identification Using Coding Method. Journal of Proteome Research, 15(12), 4423-4435.
  7. (Project page: https://github.com/fcyu/PIPI) (JCR Ranking: Q1)
  8. 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. (Project page: https://github.com/fcyu/ECL) (JCR Ranking: Q1)
  9. 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), pp.1915-1927. (* co-first author) (JCR Ranking: Q2)

PET Image Reconstruction

  1. 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. (JCR Ranking: Q3)
  2. 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.
  3. 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.

Patents (Chinese)

  1. 刘华峰,余风潮。“一种基于粒子滤波的静态PET图像重建方法。” 中国专利:102184559A,公开日期:2011年9月14日。
  2. 刘华峰,余风潮。“一种基于GPU多核并行处理的PET图像重建方法。” 中国专利:102831627A,公开日期:2012年12月19日。


  • 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)
  • Graduate Student Second-Class Honor (2011)
  • Excellent Bachelor Thesis(2009)
  • Third-Class Scholarship (2008)
  • Third-Class Scholarship (2007)
  • Third-Class Scholarship (2006)


Programming Languages