PEOPLE

Wanding Zhou, PhD

Assistant Professor of Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania

Contact Information3501 Civic Center Blvd

Philadelphia, PA, 19104
Office: 215-590-0473

Email: wanding.zhou@pennmedicine.upenn.edu

Research Expertise

Epigenetics, mitotic-inheritable chemical modification of chromatin in eukaryotic cells, instructs interpretation of the genetic information inside the nucleus. Our research goal is to understand how cells translate epigenetic information into transcriptional regulation and eventually into phenotypical manifestation. We focus on leveraging DNA methylation as a robust readout of the chromatin state and cell identity. We are interested in developing and applying DNA methylation-based methods for the study of human, particularly children's disease including pediatric malignancies, developmental abnormalities, cognitive deficit and infectious disease. By understanding how epigenetic markers respond to environmental perturbations such as early-life stress and pathological processes, we are hoping to uncover biomarkers and to develop computational methods to aid translational research of human disease and to better patient outcomes and quality of life. Our research develops informatics to support genomic technologies. We develop methods to support versatile usage of Infinium DNA methylation microarrays and bisulfite-seq data. We are interested in developing computational methods to support emerging epigenetic, particularly DNA methylation, assays for low input, single-cell experiment. We are also interested in providing informatics support for technologies that integrate DNA methylation, DNA sequence variation, chromatin accessibility and conformation. We are seeking to build informatics that bridges genomic technologies and biological insights.

Keywords:
- epigenetics and chromatin
- bioinformatics and genomics
- transcriptional gene regulation
- cancer genetics and signal transduction
- developmental genetics
- human genetics

Rotation Projects:
- AI for DNA methylation BeadChips
- Reconstructing Epigenetic Tree of Differentiation
- Long-read sequencing-based detection of DNA modification

Education

Ph.D. (Bioengineering), Rice University, 2013

Specialty Certification

Postgraduate Training

Postdoctoral Fellow, UT MD Anderson Cancer Center, 2013-2015
Postdoctoral Fellow, Van Andel Research Institute, 2015-2019

Awards and Honors

People’s Scholarship of China, Fudan University, 2004
Kerry scholarship for outstanding undergraduates, 2005
Chinese Academy of Science Scholarship, 2006
People’s scholarship of China, Fudan University, 2007
Odyssey Fellowship, UT MD Anderson Cancer Center, 2013-2015

Memberships and Professional Organizations

American Society of Human Genetics, 2014 - 2020
American Association for Cancer Research (AACR), 2017 - present

Web Links


Selected Publications

BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.

Zhou W*, Johnson BK*, Morrison J*, Beddows I, Eapen J, Katsman E, Semwal A, Habib WA, Heo L, Laird PW, Berman BP, Triche TJ Jr#, Shen H#, Nucleic Acids Res, 2024, PMID:38412294

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Low-input and single-cell methods for Infinium DNA methylation BeadChips.

Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W, Nucleic Acids Res, 2024, PMID:38407446

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Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip

Kaur D*, Lee SM*, Goldberg D, Spix NJ, Hinoue T, Li HT, Dwaraka VB, Smith R, Shen H, Liang G, Renke N, Laird PW, Zhou W#, Epigenetics Communications 3(1): 6, 2023

Comparative epigenome analysis using Infinium DNA methylation BeadChips

Ding W, Kaur D, Horvath S, Zhou W., Brief Bioinform 24(): bbac617, 2023, PMID:36617464

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Computational methods for single-cell DNA methylomes

Iqbal W, Zhou W., Genomics Proteomics Bioinformatics, 2022, PMID:35718270

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DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW., Cell Genom 2(): 100144, 2022, PMID:35873672

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Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer

Carrot-Zhang J^, Chambwe N^, Damrauer JS^, Knijnenberg TA^, Robertson AG^, Yau C^, Zhou W^, Berger AC, Huang KL, Mashl RJ, Newberg J, Romanel A, Sayaman RW, Demichelis, Felau I, Frampton G, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Elad Z, Cancer Genome Atlas Network, Cherniack AD, Beroukhim R, Cancer Cell 37(5): , 2020, PMID:32396860

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DNA methylation enables transposable element-driven genome expansion

Zhou W*, Liang G, Molloy PL, Jones PA*, Proceedings of National Academy of Sciences 117(32): , 2020, PMID:32719115

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DNA methylation loss in late-replicating domains is linked to mitotic cell division

Zhou W^, Dinh HQ^, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H*, Laird PW*, Berman BP*, Nature Genetics 50:591–602(): , 2018

SeSAMe: Reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions

Zhou W*, Triche Jr TJ., Laird PW and Shen H*, Nucleic Acids Research 46(20):e123(): , 2018

Comprehensive characterization, annotation and innovative use of Infinium DNA Methylation BeadChip probes

Zhou W, Laird PW, Shen H*, Nucleic Acids Research 45(4) e22-e22(): , 2017

TransVar: a multi-level variant annotator for precision genomics

Zhou W^, Chen T^, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K*, Nature Methods 12:11(): , 2015

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