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  • Wanding Zhou
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Faculty

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Wanding Zhou, Ph.D.

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Assistant Professor of Pathology and Laboratory Medicine
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Department: Pathology and Laboratory Medicine
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1f Graduate Group Affiliations 8 a
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46 Contact information
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3501 Civic Center Blvd
Philadelphia, PA 19104
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2e Office: 215-590-0473
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Email: wanding.zhou@pennmedicine.upenn.edu
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18 Publications
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13 Education:
21 a Ph.D. 1b (Bioengineering) c
28 Rice University, 2013.
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Links
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Description of Research Expertise

631 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.
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11 Keywords:
23 - epigenetics and chromatin
25 - bioinformatics and genomics
29 - transcriptional gene regulation
31 - cancer genetics and signal transduction
20 - developmental genetics
18 - human genetics
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1a Rotation Projects:
2a - AI for DNA methylation BeadChips
3b - Reconstructing Epigenetic Tree of Differentiation
41 - Long-read sequencing-based detection of DNA modification
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Selected Publications

193 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†.: Scalable screening of ternary-code DNA methylation dynamics associated with human traits. Cell Genomics Jul 2025.

 114 Yehya N†, Till JE, Srivastava N, Zhang D, Christie JD, Carpenter EL, Mangalmurti NS, Zhou W†: Cell-free DNA methylomics identify tissue injury patterns in pediatric ARDS. JCI Insight 10(2), Sep 2025.

 f4 Goldberg DC†, Fu H, Atkins D, Moyer E, Lee CN, Deng Y, Zhou W†: KnowYourCG: Facilitating base-level sparse methylome interpretation. Science Advances 11(43), Oct 2025.

 e9 Lee SM, Goldberg DC, Cloud C, Parker JB, Krapp C, Loo CE, Kim E, Zhao I, Jin C, Porecha R, Bartolomei MS, Kohli RM†, Zhou W†.: A ternary-code DNA methylome atlas of mouse tissues 3f Genome Biology 7;26(1): 343, Oct 2025.

 e9 CN Lee†, H Fu, A Cardilla, W Zhou†, Y Deng†: Spatial joint profiling of DNA methylome and transcriptome in tissues. Nature 646(8087): 1261-1271, Oct 2025.

 d7 Zipple MN†, Zhao I, Kuo DC, Lee SM, Sheehan MJ†, Zhou W†: Ecological Realism Accelerates Epigenetic Aging in Mice. Aging Cell May 2025.

 c7 Chen BH, Zhou W.: mLiftOver: harmonizing data across Infinium DNA methylation platforms. Bioinformatics 40: btae423, Jul 2024.

 f6 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 52: e38, Apr 2024.

 17c 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 52: e32, Apr 2024.

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

 13c 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.

 1f1 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.

 f5 Zhou W*, Liang G, Molloy PL, Jones PA*: DNA methylation enables transposable element-driven genome expansion. Proceedings of National Academy of Sciences 117(32), Aug 2020.

 10a 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, Nov 2018.

 11f 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, Apr 2018.

 fe 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, Feb 2017.

 125 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, Nov 2015.

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