Wanding Zhou, Ph.D.

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Assistant Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine

Contact information
3501 Civic Center Blvd
Philadelphia, PA 19104
Office: 215-590-0473
Ph.D. (Bioengineering)
Rice University, 2013.
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Description of 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.

- 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

Selected Publications

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#: BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nucleic Acids Res Feb 2024.

Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W: Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res Feb 2024.

Ding W, Kaur D, Horvath S, Zhou W.: Comparative epigenome analysis using Infinium DNA methylation BeadChips. Brief Bioinform 24: bbac617, Jan 2023.

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#: Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip. Epigenetics Communications 3(1): 6, Sep 2023.

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.: DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom 2: 100144, Jul 2022.

Iqbal W, Zhou W.: Computational methods for single-cell DNA methylomes. Genomics Proteomics Bioinformatics Jun 2022.

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: Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell 37(5), 2020.

Zhou W*, Liang G, Molloy PL, Jones PA*: DNA methylation enables transposable element-driven genome expansion. Proceedings of National Academy of Sciences 117(32), 2020.

Zhou W*, Triche Jr TJ., Laird PW and Shen H*: SeSAMe: Reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Research 46(20):e123, 2018.

Zhou W^, Dinh HQ^, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H*, Laird PW*, Berman BP*: DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nature Genetics 50:591–602, 2018.

Zhou W, Laird PW, Shen H*: Comprehensive characterization, annotation and innovative use of Infinium DNA Methylation BeadChip probes. Nucleic Acids Research 45(4) e22-e22, 2017.

Zhou W^, Chen T^, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K*: TransVar: a multi-level variant annotator for precision genomics. Nature Methods 12:11, 2015.

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Last updated: 03/12/2024
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