Work Experience

Department of Medicine, Vanderbilt University Medical Center
Research Fellow, Feb. 2024 - Present
Advisor: Dr. Marcela Brissova

Research Interest
  • Using statistical and machine learning models to understand islet biology and diabetes
  • Explore the application of vision-language models in biomedical data, espectially in the context of islet biology and diabetes
  • Develop data integration tools based on knowledge graphs to jointly analyze human genomic/epigenomic/transcriptome/4D genome data
  • Chromatin 3D structural pattern analysis

Education

University of Michigan – Ann Arbor, Depart. of Computational Medicine and Bioinformatics (DCMB)
Ph.D. Bioinformatics, Sep. 2018 - Dec. 2023
Advisor: Dr. Jie Liu

Peking University, College of Chemistry and Molecular Engineering (CCME)
BSc. Chemical Biology, Sep. 2014 - Jul. 2018
Awards for Outstanding Graduates of Peking University and CCME

Peking University, National School of Development (NSD)
Dual Bachelor of Economics, Sep. 2015 - Jul. 2018

Publication

Accepted or published: (*co-first author)
  • Tao., Y., Feng, F., Luo, X., & Liu., J. (2024). CNTools: A computational toolbox for cellular neighborhood analysis from cell images. PLos Computational Biology, 20.8 (2024): e1012344.
  • Zhang, Z., Feng, F., Qiu, Y., & Liu, J. (2023). A generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome. Nucleic Acids Research, 51(12), 5931-5947.
  • IGVF Consortium (2024). Deciphering the impact of genomic variation on function. Nature, 633(8028), 47-57.
  • Feng, F., Tang, F., Gao, Y., Zhu, D., ... & Liu, J. (2023). GenomicKB: a knowledge graph for human genomics. Nucleic Acids Research, 51.D1, D950-D956.
  • Zhang, Z., Feng, F., & Liu, J. (2022). Characterizing collaborative transcription regulation with a graph-based deep learning approach. PLoS Computational Biology, 18(6), e1010162.
  • Feng, F., Yao, Y., Wang, X. Q. D., Zhang, X., & Liu, J. (2022). Connecting high-resolution 3D chromatin organization with epigenomics. Nature Communications, 13(1), 1-10.
  • Li, X., Feng, F., Pu, H., Leung, W. Y., & Liu, J. (2021). scHiCTools: A computational toolbox for analyzing single-cell Hi-C data. PLoS Computational Biology, 17(5), e1008978.
  • Himadewi, P.*, Wang, X. Q. D.*, Feng, F.*, Gore, H., Liu, Y., Yu, L., ... & Zhang, X. (2021). 3'HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression. Elife, 10, e70557.
  • Zhang, X., Wang, X. Q. D., Gore, H., Himadewi, P., Feng, F., & Liu, J. (2020). 3D Genomics of Acute Meyloid Leukemia Reveals the Imbalance between DNA Methylation Canyon Interactions and Leukemic Specific Enhancer Network Interactions. Blood, 136, 45.
  • Feng, F., Lai, L., & Pei, J. (2018). Computational chemical synthesis analysis and pathway design. Frontiers in Chemistry, 6, 199.
Submitted, under review, or preprint:
  • Huang, Y., Han, Z., Luo, X., ..., Feng, F., ... & Liu, J. (2024). Building a literature knowledge base towards transparent biomedical AI. (under review by Nature Machine Intelligence)
  • Hong, C. K., Feng, F.*, Ramanathan, V., Liu, J., & Hansen, A. S. (2025). Genome structure mapping with high-resolution 3D genomics and deep learning. (under review by Science)
  • Luo, X., Huang, Y., Tao, Y.,Feng, F., Hopkirk, A., Bate, T. S., ... & Liu, J. (2024). CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations. (under review by Nucleic Acids Research)
  • Saunders, D. C., Hart, N., Pan, F. C., ..., Feng, F., ... & Brissova, M. (2024). Mapping histological and functional maturation of human endocrine pancreas across early postnatal periods. (under review by Nature Communications)
  • Evans-Molina, C., Pettway, Y. D., Saunders, ..., Feng, F., ... & Brissova, M. (2024). Heterogeneous endocrine cell composition defines human islet functional phenotypes. (under review by Nature Communications)
  • Varshney, A., Manickam, N., Orchard, P., Tovar, ..., Feng, F., ... & Parker, S. C. (2024). Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. bioRxiv.
  • Feng, F., Moran, S. P., & Liu, J. (2024). Quagga: a stripe caller for chromatin contact maps (under review by Genome Research)

Invited Talks

  • "Defining human pancreatic cell composition and spatial distribution with machine learning methods", AI in Precision Medicine of Diabetes and Other Chronic Diseases Workshop, Rockville, USA, October 2024
  • "Application of knowledge graphs in biomedical fields", CCHC Omics Seminar, Nashville, USA, October 2024
  • "GenomicKB: a knowledge graph for human genome", Intellectual Systems of Molecular Biology (ISMB), Lyon, France, July 2023
  • "A generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome", Great Lakes Bioinformatics (GLBIO) conference, Montreal, Canada, May 2023
  • "An overview of Hi-C downstream analysis", Chromatin 3D Folding Workshop, UT Health, Houston, USA, March 2023
  • "GenomicKB: a knowledge graph for human genome", Tools and Technology Seminar, University of Michigan, Ann Arbor, USA, January 2023
  • "Connecting high-resolution 3D chromatin organization with epigenomics", Intellectual Systems of Molecular Biology (ISMB), Madison, USA, July 2022
  • "An accurate and interpretable model for predicting high-resolution 3D chromatin organization", 4DN Consortium Joint Analysis Working Group, September 2019

Teaching

  • Graduate Student Instructor (GSI), BIOINF 593/EECS 598 Machine Learning in Computational Biology, University of Michigan, 2022 Fall

Invited Peer Review Experience

  • Co-reviewer, Nature Metabolism, since 2024
  • Co-reviewer, Nature Communications, since 2023
  • Reviewer, PLoS Computational Biology, since 2022
  • Reviewer, Conference on Neural Information Processing Systems (NeurIPS) AI4Science Workshop, since 2021
  • Reviewer, International Conference on Machine Learning (ICML) AI4Science Workshop, since 2022
  • Reviewer, International Conference on Machine Learning (ICML) Generative AI and Biology (GenBio) Workshop, since 2023

Awards

  • Data Resource Trainee Scholar Award, Integrated Islet Distribution Program (IIDP), 2025
  • AI Workshop Young Scholar Travel Award, National Institute of Diabetes and Digestive and Kidney Disease (NIDDK), 2024
  • Rackham Conference Travel Award, University of Michigan, 2022 and 2023
  • Program in Biomedical Sciences Fellowship, University of Michigan, 2019
  • Outstanding Graduates of Peking University and CCME, 2018
  • Gold Medal in Chinese Chemistry Olympiad (Top 100 in China), 2013