Huihui Fan, M.D., Ph.D.

Huihui Fan, M.D., Ph.D.
Postdoctoral fellow, Shen Laboratory


Dr. Huihui Fan is a bioinformatics expert with a special interest in pan-cancer analysis. She completed her M.D. and her Ph.D. in bioinformatics at Harbin Medical University, where her work focused on transcriptional and epigenetic regulation in complex diseases. She is the recipient of numerous awards from the National Science Foundation (China), most recently for using diagnostic ultrasound methods for breast cancer based on “-omics” data from biomedical imaging. As a postdoctoral fellow in the laboratory of Dr. Hui Shen at Van Andel Institute, Dr. Fan significantly contributed to The Cancer Genome Atlas PanCancer Atlas, particularly studies in squamous cancers, kidney cancers and gynecological cancers.


Current research focus

I have a particular interest in ovarian cancer. Determining its histological subtypes, such as clear cell, will greatly help the community understand this deadly disease and also pave the way for therapeutic target discovery. I approach it through the lens of DNA methylation, while integrating gene expression, to explore distinct characteristics among different molecular groups, if any, and identify epigenetic silencing targets during the malignant transformation of cancer. I am also interested in computationally identifying human imprinted genes.

Education & Training

Lecturer, Harbin Medical University

Ph.D. in bioinformatics, Harbin Medical University (Advisor:  Prof. Xia Li)
Thesis: Pathogenic dissections of complex diseases based on transcriptional and epigenetic regulations

M.D., Harbin Medical University

Awards & External Funding

Diagnostic ultrasound for breast cancer based on omics data from biomedical imaging, The National Natural Science Foundation, China (2017–2021)

Identification of risk factors driven by dynamic differential DNA methylation and exploration of their mechanisms of action, The National Natural Science Foundation, China (2016–2018)

Identification of risk circulating non-coding RNAs (miRNA/IncRNA) and functional analysis of their synergistically regulation risk pathways in cardiovascular diseases, The National Natural Science Foundation, China (2014–2016)

Dissecting ESC-specific cross-talk between transcription regulation and chromatin state through integrating large-scale “omics” data, The National Natural Science Foundation, China (2012–2014)

Identifying key genes and related pathways during the malignant progression of inflammation-associated cancer, Ph.D. fellowship, Harbin Innovation Foundation (2012–2014)


To view a list of selected publications click below.

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Fan H, Atiya HI, Wang Y, Pisanic TR, Wang TH, Shih IM, Foy KK, Frisbie L, Buckanovich RJ, Chomiak AA, Tiedemann RL, Rothbart SB, Chandler C, Shen H, Coffman LG. 2020. Epigenomic reprogramming toward mesenchymal-epithelial transition in ovarian-cancer-associated mesenchymal stem cells drives metastasis. Cell Rep 33(10):108473.

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. 2019. Integrated epigenome, exome, and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids. Cell Rep.

Ricketts CJ…Fan H…Shen H…Laird PW…Spellman P, Rathmell K, Linehan WM. 2018. Comprehensive molecular characterization of renal cell carcinoma. Cell Rep 23(1):313–326.

Berger AC, Korkut A, Kanchi RS…Fan H, Shen H…Akbani R. 2018. A comprehensive pan-cancer molecular study of gynecological and breast cancers. Can Cell 33(4):690–705.

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…Shen H…Laird PW…Waes CV. 2018. Genomic, pathway network, and immunologic features distinguishing squamous carcinomas. Cell Rep 23(1):194–212.

Knijnenburg T, Wang L, Zimmerman MT, Chambwe N…Fan H, Shen H…Laird PW…Wang C. 2018. Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas. Cell Rep 23(1):239–254.

Liu N, Li C, Huang Y, Yi Y, Bo W, Li C, Li Y, Hu Y, Li K, Wang H, Zhuang L*, Fan H*, Wang D*. 2015. A functional module-based exploration between inflammation and cancer in esophagus. Sci Rep 5:15340.
*Co-corresponding authors

Guan X, Yi Y, Huang Y, Hu Y, Li X, Wang X*, Fan H*, Wang G*, Wang D*. 2015. Revealing potential molecular targets bridging colitis and colorectal cancer based on multidimensional integration strategy. Oncotarget 6(35):37600–37612.

Fan H, Zhao H, Pang L, Liu L, Zhang G, Yu F, Liu T, Xu C, Xiao Y, Li X. 2015. Systematically prioritizing functional differentially methylated regions (fDMRs) by integrating multi-omics data in colorectal cancer. Sci Rep 5:12789.

Ping Y, Deng Y, Wang L, Zhang H, Zhang Y, Xu C, Zhao H, Fan H, Yu F, Xiao Y, Li X. 2015. Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multidimensional genomic data. Nucleic Acids Res.

Zhao H, Liu T, Liu L, Zhang G, Pang L, Yu F, Fan H, Ping Y, Wang L, Xu C, Xiao Y, Li X. 2015. Chromatin states modify network motifs contributing to cell specific functions. Sci Rep 5:11938.

Xiao Y, Yu F, Pang L, Zhao H, Liu L, Zhang G, Liu T, Zhang H, Fan H, Zhang Y, Pang B, Li X. 2015. MeSiC: A model-based method for estimating 5 mC levels at single-CpG resolution from MeDIP-seq. Sci Rep 5:14699.

Zhao H, Xu J, Pang L, Zhang Y, Fan H, Liu L, Liu T, Yu F, Zhang G, Lan Y, Bai J, Li X, Xiao Y. 2015. Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis. BMC Med Genomics 8:62.

Xu C, Ping Y, Li X, Zhao H, Wang L, Fan H, Xiao Y, Li X. 2014. Prioritizing candidate disease miRNAs by integrating phenotype associations of multiple diseases with matched miRNA and mRNA expression profiles. Mol Biosyst 10(11):2800–2809.

Xiao Y, Liu T, Zhao H, Li X, Guan J, Xu C, Ping Y, Fan H, Wang L, Zhao T, Lv Y, Hu J, Yu X, Jin Y, Li X. 2014. Integrating epigenetic marks for identification of transcriptionally active miRNAs. Genomics 104(2):70–78.

Ping Y, Zhang H, Deng Y, Wang L, Zhao H, Pang L, Fan H, Xu C, Li F, Zhang Y, Gong Y, Xiao Y, Li X. 2014. IndividualizedPath: identifying genetic alterations contributing to the dysfunctional pathways in glioblastoma individuals. Mol Biosyst 10(8):2013–2042.

Xiao Y, Camarillo C, Ping Y, Arana TB, Zhao H, Thompson PM, Xu C, Su BB, Fan H, Ordonez J, Wang L, Mao C, Zhang Y, Cruz D, Escamilla MA, Li X, XuC. 2014. The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. PLoS One.

Zhang Y*, Fan H*, Xu J, Xiao Y, Xu Y, Li Y, Li X. 2013. Network analysis reveals functional cross-links between disease and inflammation genes. Sci Rep 3:3426.
*Co-first author

Xiao Y*, Fan H*, Zhang Y, Xing W, Ping Y, Zhao H, Xu C, Li Y, Wang L, Li F, Hu J, Huang T, Lv Y, Ren H, Li X. 2013. Systematic identification of core transcription factors mediating dysregulated links bridging inflammatory bowel diseases and colorectal cancer. PLoS One.
*Co-first author

Xiao Y, Ping Y, Fan H, Xu C, Guan J, Zhao H, Li Y, Lv Y, Jin Y, Wang L, Li X. 2013. Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. Neuro Oncol 15(7):818–828.

Xiao Y, Guan J, Ping Y, Xu C, Huang T, Zhao H, Fan H, Li Y, Lv Y, Zhao T, Dong Y, Ren H, Li X. 2012. Prioritizing cancer-related key miRNA-target interactions by integrative genomics. Nucleic Acids Res 40(16):7653–7665.  

Xiao Y, Xu C, Xu L, Guan J, Ping Y, Fan H, Li Y, Zhao H, Li X. 2012. Systematic identification of common functional modules related to heart failure with different etiologies. Gene 499(2):332–338.

Xiao Y, Xu C, Guan J, Ping Y, Fan H, Li Y, Zhao H, Li X. 2012. Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network. PLoS One.

Xiao Y, Xu C, Ping Y, Guan J, Fan H, Li Y, Li X. 2011. Differential expression pattern-based prioritization of candidate genes through integrating disease specific expression data. Genomics 98(1):64–71.