Wanding Zhou, PhD
Assistant Professor of Pathology and Laboratory MedicinePerelman 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
Scalable screening of ternary-code DNA methylation dynamics associated with human traits.
Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal MS, McAuliffe L, Majounie E, Kalayil Manian M, Zhu Q, Tran C, Hansen M, Stojakovic J, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W†., Cell Genomics, 2025, PMID:40614726
Ecological Realism Accelerates Epigenetic Aging in Mice.
Zipple MN†, Zhao I, Kuo DC, Lee SM, Sheehan MJ†, Zhou W†, Aging Cell, 2025, PMID:40396452
mLiftOver: harmonizing data across Infinium DNA methylation platforms
Chen BH, Zhou W., Bioinformatics 40(): btae423, 2024, PMID:38963309
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 52(): e38, 2024, PMID:38407446
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 52(): e32, 2024, PMID:38412294
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
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
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
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
