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Drug Dependence
Contacts
Fellows
Oscar M. Harari, Ph.D.
Xin Zhou, Ph.D.
Sean D. Kristjansson, Ph.D.
Ruth Huang Miller, Ph.D.
Wei (Will) Yang, Ph.D.
Bo Zhang, Ph.D.
Sumithra Sankararaman
Ni Huang, Ph.D.
  

Xin Zhou, Ph.D. 

 
 

Xin Zhou, Ph.D. 

Year in Program:   Currently on additional fellowship year, Feb 2014. 
     
Completed 3-year fellowship, May 2013

Primary Mentor:

  Ting Wang, Ph.D. 
  Assistant Professor 
  Department of Genetics 
  Washington University School of Medicine 
                           Website: http://wang.wustl.edu 

  Symposium Presentation 
  Video Link 
 
(viewable via Windows Media Player  
  click "open" to play) 

 

Project Description

Dr. Xin Zhou is a bioinformatist with a background in bioinformatics web server construction and genetic network modeling (Ph.D. Thesis) , originally from China, who is being mentored by Drs. Ting Wang (bioinformatics and molecular research as related to epigenetics and transposable genetic elements; Dept. of Genetics) and Elliot Nelson (Psychiatrist with a background in alcohol and opiate addiction genetics research, and an interest in GxE interactions, especially with respect to histories of trauma; Dept. of Psychiatry).

Dr. Zhou is housed in Dr. Wang’s lab where he is primarily working on computational and data analytic tools to assist addiction investigators in epigenetic research (i.e., computational biology: program development). More specifically: 1) based on the UCSC Cancer Genomics Browser previously designed by mentor Dr. Wang, to develop functions to enable display of currently available epigenome data. His goal is to create a fully functional epigenome browser that includes a data transformation function so that high throughput sequencing data can be properly displayed. 2)  Transposable elements (TEs) carry important regulatory functions. Different epigenetic modification patterns for TEs, e.g., DNA methylation patterns, correlate with cell and tissue type, as well as certain disease states.

In order to investigate genome-wide impact of TEs, Dr. Zhou plans to develop together with Dr. Wang, a Genomics Browser function to display TE data on a genome-wide scale.; and 3) under the guidance of Dr. Wang, Dr. Zhou plans to develop a data analysis method using the statistical framework of “conditional random field”, to incorporate data from MeDIP-seq and MRE-seq to make accurate DNA methylation cells. MeDIP (methyl-DNA chromatin immunioprecipitation) and MRE (methylation-sensitive restriction enzyme digestion) are cost-competititve approaches to study DNA methylation on a genome-wide scale. It is hoped that a combination of these two approaches can lead to accurate DNA methylation calls, but effective algorithms are yet to be invented. Dr. Zhou has only recently become a postdoctoral fellow, and both manuscripts and computational and statistical tools outlined above are still under development.

 

Product Description

Projects including Roadmap Epigenomics and ENCODE have carried out large number of sequencing experiments and resulting data are publicly available. To help explore such valuable and diverse data sets, we are developing the Human Epigenome Browser (http://epigenomegateway.wustl.edu/). It extends the UCSC Genome Browser and is built with “bigBed/bigWig” and HTML5 technologies to achieve high performance. The Browser displays genomic data as heatmaps or wiggle tracks, in parallel with samples’ metadata. Genome annotations and statistical analysis results are displayed as decorative tracks along with genomics maps. The Browser enables investigators to pan and zoom in smooth and intuitive operations, and allows dynamic view angle switching (from whole-genome to gene set/pathway views). The Browser is expanding its support on well-studied model organisms so that wider research community can benefit from this useful tool.

Weblink:  http://epigenomegateway.wustl.edu/

 

Program Presentations

Zhou X. Oral presentation: Human Epigenome Browser. Wash U Genetics Department Retreat, St. Louis, MO, September 2010.

Zhou X. Oral presentation: Human Epigenome Browser. Center for Genome Sciences Research, St. Louis, MO, January 2011.

Zhou X.  Poster Presentation: Human Epigenome Browser. 11th Annual Guze Symposium on Alcoholism, Midwest Alcoholism Research Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, February 2011.

Zhou X, Xie M, Nielsen C, Hirst M, Farnham P, Kuhn R, Zhu J, Kent J, Haussler D, Costello J, Wang T. Poster presentation: The Human Epigenome Browser at Washington University. Visualization of Biological Data (VIZBI) Conference, Broad Institute, Boston, MA, March 2011.

Zhou X, Xie M, Nielsen C, Hirst M, Farnham P, Kuhn R, Zhu J, Kent J, Haussler D, Costello J, Wang T. Poster presentation: The Human Epigenome Browser At Washington University, 7th Annual Postdoc Symposium, Washington University, St. Louis, MO, March 2011.

Zhou X, Xie M, Nielsen C, Hirst M, Farnham P, Kuhn R, Zhu J, Kent J, Haussler D, Costello J, Wang T. Poster presentation: The Human Epigenome Browser At Washington University. DNA Day Symposium (organized by the Genome Institute, Washington University), St. Louis, MO,  April 2011.

Zhou X, Xie M, Nielson C, Hirst M, Farnham P, Kuhn R, Zhu J, Kent J, Haussler D, Costello J, Wang T. Poster presentation: The Human Epigenome Browser at Washington University. Biology of Genomes Conference, Cold Spring Harbor, NY, May 2011.

Zhou X, Xie M, Nielson C, Hirst M, Farnham P, Kuhn R, Zhu J, Kent J, Haussler D, Costello J, Madden PAF, Wang T. Oral presentation: The Human Epigenome Browser at Washington University. 41st Annual Meeting of the Behavior Genetics Association (BGA), Newport, RI, June 2011.

Zhou X, Human Epigenome Browser, Oral presentation, Center for Genome Sciences Research Talk, St. Louis, June 2011.

Zhou X, Human Epigenome Browser, Oral presentation, Center for Genome Sciences Research Talk, St. Louis, September 2011.

Zhou X. Human Epigenome Browser, Oral presentation, NIH/NIDA Genetics Consortium Meeting, Rockville, MD, 30 November 2011.

Zhou X, Xie M, Nielson C, Hirst M, Farnham P, Kuhn R, Zhu J, Kent J, Haussler D, Costello J, Madden P, Wang T. Poster Presentation: The Human Epigenome Browser at Washington University in St. Louis. 12th Annual Guze Symposium on Alcoholism, Midwest Alcoholism Research Center, Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, February 2012

Zhou X. Oral presentation: The Human Epigenome Browser at Washington University. Generic Model Organism Database, 2012 GMOD Meeting, Washington, DC, April 2012.

Zhou X. Oral presentation: Visualizing genomics data using WashU EpiGenome Browser. Department of Psychiatry Seminar Series, WUSTL, St. Louis, MO, January 2013.

Zhou X. Oral presentation: Visualizing Roadmap Epigenomics Consortium data using WashU EpiGenome Browser. 6th Genboree Workshop for Epigenome Informatics, Baylor College of Medicine, Houston, TX, March 2013.

Zhou X, Nielsen C, Hirst M, Farnham P, Madden P, Costello J, Wang T. Poster presentation: WashU EpiGenome Browser. Visualization of Biological Data (VIZBI) Conference, Broad Institute, Boston, MA, March 2013.

Zhou X. Oral presentation: WashU EpiGenome Browser. Research seminar at Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, March 2013.

Zhou X. Oral presentation: Visualizing genomics data using WashU EpiGenome Browser. Department of Genetics Seminars, WUSTL, St. Louis, MO, April 2013.

Zhou X, Lowdon R, Li DF, Madden P, Costello J, Wang T. Poster presentation: WashU EpiGenome Browser Suite: powerful tool for genomics/epigenomics data visualization. Biology of Genomes Meeting, Cold Spring Harbor Laboratory, Long Island, NY, May 2013.

Zhou X. Oral presentation: Visualizing Roadmap Epigenomics Consortium data using WashU EpiGenome Browser. Roadmap Epigenome Mapping Center Meeting, University of California in San Francisco, San Francisco, CA, June 2013.

Zhou X. Oral presentation: Visualizing genomics data using WashU EpiGenome Browser. Research seminar at Stanford Center for Genomics & Personalized Medicine, Stanford University, Stanford, CA, June 2013.

Zhou X., Wang T., (Poster presentation): WashU EpiGenome Browser, A Roadmap to the Living Genome Meeting, Boston, MA, October 2013

Zhou, X. (Oral Presentation): WashU EpiGenome Browser, Research seminar at Dana Farber Cancer Institute, Harvard University, Boston, MA, December 2013

Zhou, X. (Oral Presentation): Exploring genomics data sets through WashU EpiGenome Browser. R25 Fellowship Symposium: Statistical and Computational Innovation in Addiction Genetics, Washington University School of Medicine, Saint Louis, MO, December 2013.

 

Program Publications

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28:1097-105. Epub 2010 Sep 19. PMID: 20852635. PMC2955169.

Zhou X, Xie M, Maricque B, Sundaram V, Nielsen C, Hirst M, Farnham P, Kuhn R, Zhu J, Smirnov I, Kent J, Haussler D, Madden PAF, Costello JAF, Wang T. The human epigenome browser at Washington University. Nat Methods. 2011 Nov; 8:989-90. doi: 10.1038/nmeth.1772.). PMID: 22127213. PMC3552640.

Zhou X, Wang T. Using the Wash U Epigenome Browser to examine genome-wide sequencing data. Curr Protoc Bioinformatics. 2012 Dec; Chapter 10:Unit10.10. doi: 10.1002/0471250953.bi1010s40. PMID: 23255151. PMC3643794.

Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T. Exploring long-range genome interactions using the WashU EpiGenome Browser. Nat Methods. 2013 May; 10(5):375-376. doi: 10.1038/nmeth.2440. PMID: 23629413.