616.234.5000

Wanding Zhou, Ph.D.

Wanding Zhou, Ph.D.
Postdoctoral fellow, Laird Laboratory, Shen Laboratory & Jones Laboratory
616.234.5320

Biography

Dr. Wanding Zhou is an expert in bioinformatics and the development of custom software applications for the analysis of large, complex datasets. He earned his B.S. in bioengineering from Fudan University followed by his Ph.D. in bioengineering from Rice University, where he developed methods for modeling and analyzing microbial metabolism. He has extensive experience in both genomic and epigenomic sequencing and analytical techniques, and has contributed to several multi-institutional collaborations, including the 1000 Genome Project, The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium. In 2015, he joined the labs of Drs. Peter Laird, Hui Shen and Peter Jones in Van Andel Research Institute’s Center for Epigenetics.

Current research focus

Dr. Zhou studies the epigenome in human and other mammalian organisms with a focus on its alteration during organismal development and disease onset and progression. He relies on computational methods to investigate the epigenetic hallmarks of different cell types as they differentiate and branch out from stem cells. The perceived epigenetic hallmarks of cancer are seen as an abnormal acceleration of the same ongoing process occurring during the healthspan. He is also interested in the evolution of epigenetic modifications during ontogeny as well as phylogeny.

Education & Training

Odyssey Research Fellow, University of Texas, MD Anderson Cancer Center

Ph.D. in bioengineering, Rice University (Adviser: Dr. Luay K. Nakhleh)

B.S. in biological sciences, Fudan University

Awards & External Funding

Odyssey Fellowship, MD Anderson Cancer Center (awarded to five outstanding employees out of 20,000 each year) (2014)

Graduate Scholarship, Rice University (2009–2013)

Scholarship of Chinese Academy of Science, Fudan University (2006)

Kerry Scholarship, Fudan University (2005)

People’s Scholarship of China, Fudan University (2004 and 2007)

Society Memberships

Publications

To view a list of selected publications click below.

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Carpenter BL*, Zhou W, Madaj Z, DeWitt AK, Ross JP, Grønbaek K, Liang G, Clark SJ, Molloy PL, Jones PA. 2018. Mother-child transmission of epigenetic information by tunable polymorphic imprinting. Proc Natl Acad Sci U S A
*Co-first authors

Thorsson V…Zhou W, Shen H…Shmulevich I. 2018. The immune landscape of cancer. Immunity 48(4):812–830.

Sanchez-Vega F, Mina M, Armenia J…Zhou W, Shen H, Laird PW…Schultz N. 2018. Oncogenic signaling pathways in The Cancer Genome Atlas. Cell 173(2):321–337.
*One of three theme papers for the PanCancer Atlas

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

Martin KR, Zhou W, Bowman MJ, Shih J, Au KS, Dittenhafer-Reed KE, Kellie AS, Koeman J, Weisenberger DJ, Cottingham SL, DeRoos ST, Devinsky O, Winn ME, Cherniack AD, Shen H, Northrup H, Krueger DA, MacKeigan JP. 2017. Genomic landscape of tuberous sclerosis complex. Nat Comm 8:15816.

Chong Z, Ruan J, Gao M, Zhou W, Chen T, Fan X, Ding L, Lee AY, Boutros P, Chen J, Chen K. 2017. novoBreak: Glocal assembly for breakpoint detection in cancer genomes.
Nat Methods 14(1):65–67.

Zhou W, Laird PW, Shen H. 2017. Comprehensive characterization, annotation and innovative use of Infinium DNA Methylation BeadChip probes.
Nucleic Acid Res 4(4):e22. 


Liu M, Otani H, Zhou W, Ørskov A, Charlet J, Shen H, Baylin SB, Liang G, Grønbæk K, Jones PA. 2016. Vitamin C increases viral mimicry induced by 5-aza-2′-deoxycytidine.
Proc Natl Acad Sci U S A 113(37):10238–10244.

Chen T, Wang Z, Zhou W, Chong Z, Meric-Bernstam F, Mills GB, Chen K. 2016. Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types.
BMC Genomics 17(Suppl 2):394. 


Sudmant PH…Zhou W…Korbel JO. 2015. An integrated map of structural variation in 2,504 human genomes. Nature 526(7571):75–81.

Liu S, Meric-Bernstam F, Parinyanitikul N, Wang B, Eterovic AK, Zheng X, Gagea M, Chavez-MacGregor M, Ueno NT, Lei X, Zhou W, Nair L, Tripathy D, Brown PH, Hortobagyi GN, Chen K, Mendelsohn J, Mills GB, Gonzalez-Angulo AM. 2015. Functional consequence of the MET-T1010I polymorphism in breast cancer. Oncotarget 6(5):2604–2614.  


Chenetal K, Meric-Bernstam F, Zhao H, Ezzeddine N, Tang LY, Qi Y, Mao Y, Chen T, Chong Z, Zhou W, Zheng X, Johnson A, Aldape KD, Routbort MJ, Luthra R, Kopetz S, Bavies MA, de Groot J, Moulder S, Vinod R, Farhangfar CJ, Shaw KM, Mendelsohn J, Mills GB, Eterovic AK. 2015. Clinical actionability enhanced through deep targeted sequencing of solid tumors. Clin Chem 61(3):544–553. 


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

Zhou W, Zhao H, Chong Z, Mark R, Eterovic AK, Meric-Bernstam F, Chen K. 2015. ClinSeK: a targeted variant characterization framework for clinical sequencing.
Genome Med 7(1):1–9. 


Zhou W, Chen T, Zhao H, Eterovic AK, Meric-Bernstam F, Mills GB, Chen K. 2014. Bias from removing read duplication in ultra-deep sequencing experiments.
Bioinformatics 30(8):1073–1080. 


Fan X, Zhou W, Chong Z, Nakhleh L, Chen K. 2014. Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinformatics. 15:299. 


Berestovsky N, Zhou W, Nagrath D, Nakhleh L. 2013. Modeling integrated cellular machinery using hybrid Petri-Boolean networks.
PLoS Comput Biol 9(11):e1003306. 


Zhou W, Nakhleh L. 2012. Convergent evolution of modularity in metabolic networks through different community structures.
BMC Evol Biol 12(1):181. 


Zhou W, Nakhleh L. 2012. Quantifying and assessing the effect of chemical symmetry in metabolic pathways. J Chem Infor Modeling 52(10):2684–2696. 


Zhou W, Nakhleh L. 2011. Properties of metabolic graphs: biological organization or representation artifacts? BMC Bioinformatics 12:132. 

*Featured as a highly accessed paper by BioMed Central

Zhou W, Nakhleh L. 2011. The strength of chemical linkage as a criterion for pruning metabolic graphs. Bioinformatics 27(14):1957–1963. 


Abstracts & presentations

To view a list of abstracts and presentations click below.

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Whole-genome DNA methylation universally predicts 3-D topological domains across cell types. Poster, International Society for Computational Biology (2016)

Genome-wide DNA methylation analysis of benign prostate hyperplasia. Poster, Society for the Study of Reproduction (2016)

The long-range domain structure of DNA hypomethylation reveals regulatory changes in common cancers. Poster, AACR Epigenetics (2015)

Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types. Poster, Varl-SIG (2015)

TransVar: a trans-level variant annotator for precision genomics. Poster, Varl-SIG (2015)

Developing and validating a targeted exome sequencing platform for routine cancer patient care. Poster, HITSeq (2014)

ClinSeK: Targeted clinical variant identification from high-throughput sequencing data. Poster, HITSeq (2014)

Functional consequence of the METT1010I polymorphism in breast cancer. Poster, European Society for Medical Oncology (2014)

Introduction to Hadoop and MapReduce. Presentation, VARI Computational Technical Meeting (2014)

ClinSeK: a targeted variant characterization framework for clinical sequencing. Poster, American Society of Human Genetics (2014)

ClinSeK: a targeted genomic variant caller for cancer clinics. Presentation, University of Texas MD Anderson Cancer Center Odyssey Annual Mini-Symposium (2014)

Genotyping the BreakDancer deletion call set and small deletions. Presentation, The 1000 Genome Projects SV Group Meeting, Cold Spring Harbor Laboratory (2014)

Bias from re-moving read duplication in ultra-deep sequencing experiments. Poster, 7th Annual Bayesian Biostatistics and Bioinformatics Conference (2014)

Bias from removing read duplication in ultra-deep sequencing experiments. Poster, AGBT (2014)

Atom-tracing and modular evolution of metabolic networks. Presentation, Rice University, hosted by Prof. Lydia Kavraki (2013)

Analysis of epistatic interactions in Staphylococcus aureus using flux balance analysis. Poster, NSF REU BioNetwork Summer Undergraduate Programs (2011)