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Huihui Fan, MD, PhD

Research Assistant Professor

Huihui Fan, MD, PhD joined SBMI in March 2021 after concluding five years of post-doctoral training with the focus on cancer epigenetics from the Van Andel Research Institute in Grand Rapids, Michigan. Fan earned her PhD in Biophysics (Field of Study: Bioinformatics) from Harbin Medical University, China in 2014. Prior to her PhD program, she studied Basic Medicine as a medical undergraduate student.

Fan’s research has been mainly focused on Applied Bioinformatics over the past decade, from computational systems biology in human complex disorders to cancer epigenetics. She is also interested in developing mathematical methodologies or pipelines to process large-scale genomic and epigenomic data. For the first three years of her post-doctoral training, she was honored to lead the cancer epigenetic analysis for multiple PanCancer working groups in TCGA consortia, where Fan developed gene silencing calling and between-platform normalization pipeline for DNA methylation profiling data. Currently, Fan is working on artificial intelligence and single-cell transcriptomics to gain a much better understanding of disorders in human brain, for example brain tumors and Alzheimer’s diseases.

Fan is a member of the American Association for Cancer Research (AACR), and has been served as both reviewer and guest editor for several high-impact scientific journals. Fan has published 30 peer-reviewed papers, with more than 9,500 citations.

Phone: 713-500-3900

Staff Support

 Leticia Flores
Phone: 713-500-3912


  • PhD, Biophysics, Harbin Medical University, 2014
  • MD, Basic Medicine, Harbin Medical University, 2011

Areas of Expertise

  • Computational Systems Biology
  • Cancer Epigenetics
  • Integration of Multi-OMICs Data
  • Development of Mathematical Methodologies or Pipelines

Selected Publications

  1. Fan H*, Atiya H*, Wang Y, Pisanic TR, Wang T, Shih L, Foy KK, Frisbie L, Chandler C, Shen H, Coffman L. Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis. Cell Reports (2020) (*Authors contributed equally to the work)
  2. Brown JR, Chan DK, Shank JJ, Griffith KA, Fan H, Szulawski R, Yang K, Reynolds RK, Johnston C, McLean K, Uppal S, Liu JR, Cabrera L, Taylor SE, Orr BC, Modugno F, Mehta P, Bregenzer M, Mehta G, Shen H, Coffman LG, Buckanovich RJ. Phase II clinical trial of metformin as a cancer stem cell-targeting agent in ovarian cancer. JCI Insight (2020)
  3. George JW*, Fan H*, Johnson B, Carpenter TJ, Foy KK, Chatterjee A, Patterson AL, Koeman J, Adams M, Madaj ZB, Chesla D, Marsh EE, Triche TJ, Shen H, Teixeira JM. Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids. Cell Reports (2019) (*Authors contributed equally to the work)
  4. Corces et al. (Fan H is one of the authors in The Cancer Genome Atlas Network) The Immune Landscape of Cancer. Immunity. (2019)
  5. Liu et al. (Fan H is one of the authors in The Cancer Genome Atlas Network) Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell (2018)
  6. Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell (2018)
  7. Hoadley et al. (Fan H is one of the authors in The Cancer Genome Atlas Network) Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell (2018)
  8. Malta et al. (Fan H is one of the authors in The Cancer Genome Atlas Network) Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell (2018)
  9. Sanchez-Vega et al. (Fan H is one of the authors in The Cancer Genome Atlas Network) Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell (2018)
  10. Campbell JD*, Yau C*, Bowlby R*, Liu Y*, Brennan K*, Fan H*, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Reports (2018) (*Authors contributed equally to the work)