Epernicus: Zhong Wang, Ph.D.

Zhong Wang, Ph.D.

Position:
Career Computational Biologist Staff scientist, Group lead for genome analysis

Research and Development

DOE Joint Genome Institute (Walnut Creek, CA)
Degrees:

Ph.D., Cell Biology, Duke University (Durham, NC)

M.S., Cell Biology, Institute of Cell Biology, Chinese Academy of Sciences

B.S., Microbiology, Shandong University (Jinan, China)
Past Advisors:

Michael Snyder (as Senior Scientist)

Huntington F. Willard (as Post Doctoral Fellow)

Haifan Lin (as Graduate Student - Ph.D.)

Debiao Zhao (as Graduate Student - Masters)
Research:
RNA-Seq informatics; metagenome informatics; short read assembly
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Developing algorithms for high-throughput data analysis
Data visualization
Modeling
Stem cell biology
Cancer biology
Epigenetics
Other Experience:
2000-2002 Certificate for Genome Technology and Bioinformatics, Duke University
Honors:
1997-2004 Jame B. Duke Fellowship

Communities:

Zhong Wang's Genealogy

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Zhong Wang's Publications (16)

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM

Science (New York, N.Y.). 2011 Jan 28;331(6016):463-7
Next-generation transcriptome assembly.
Martin JA, Wang Z

Nature reviews. Genetics. 2011;12(10):671-82
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.
Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M

Genome research. 2010 Oct;20(10):1451-8
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics.
He S, Wurtzel O, Singh K, Froula JL, Yilmaz S, Tringe SG, Wang Z, Chen F, Lindquist EA, Sorek R, Hugenholtz P

Nature methods. 2010 Oct;7(10):807-12
Close association of RNA polymerase II and many transcription factors with Pol III genes.
Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M

Proceedings of the National Academy of Sciences of the United States of America. 2010 Feb 23;107(8):3639-44
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z

BMC genomics. 2010;11:663
The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe.
Ni T, Tu K, Wang Z, Song S, Wu H, Xie B, Scott KC, Grewal SI, Gao Y, Zhu J

PloS one. 2010;5(12):e15271
RNA-Seq: a revolutionary tool for transcriptomics.
Wang Z, Gerstein M, Snyder M

Nature reviews. Genetics. 2009 Jan;10(1):57-63
The transcriptional landscape of the yeast genome defined by RNA sequencing.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M

Science (New York, N.Y.). 2008 Jun 6;320(5881):1344-9
Sex-lethal is a target of Bruno-mediated translational repression in promoting the differentiation of stem cell progeny during Drosophila oogenesis.
Wang Z, Lin H

Developmental biology. 2007 Feb 1;302(1):160-8
Evidence of influence of genomic DNA sequence on human X chromosome inactivation.
Wang Z, Willard HF, Mukherjee S, Furey TS

PLoS computational biology. 2006 Sep 1;2(9):e113
A novel class of small RNAs in mouse spermatogenic cells.
Grivna ST, Beyret E, Wang Z, Lin H

Genes & development. 2006 Jul 1;20(13):1709-14
The division of Drosophila germline stem cells and their precursors requires a specific cyclin.
Wang Z, Lin H

Current biology : CB. 2005 Feb 22;15(4):328-33
Regulatory relationship among piwi, pumilio, and bag-of-marbles in Drosophila germline stem cell self-renewal and differentiation.
Szakmary A, Cox DN, Wang Z, Lin H

Current biology : CB. 2005 Jan 26;15(2):171-8
Nanos maintains germline stem cell self-renewal by preventing differentiation.
Wang Z, Lin H

Science (New York, N.Y.). 2004 Mar 26;303(5666):2016-9
The arrest gene is required for germline cyst formation during Drosophila oogenesis.
Parisi MJ, Deng W, Wang Z, Lin H

Genesis (New York, N.Y. : 2000). 2001 Apr;29(4):196-209

Zhong Wang's Posters and Presentations (8)

BioPig, a hadoop based analytic toolkit for next-gen sequence data analysis (presentation)
Zhong Wang

Finish in the future at Santa Fe, NM; 06/2011
RNA-Seq: technology and applications (presentation)
Zhong Wang

Merck Inc, New Jersey; 05/2011
From microbial communities to functional biomass degrading enzymes (presentation)
Zhong Wang

LNNL, Livermore, CA; 04/2011
Massive Discovery of Biomass Degrading Genes and Genomes in Rumen (presentation)
Zhong Wang

DOE JGI User Meeting 06, Walnut Creek, CA; 03/2011
Massive Metagenomic Discovery of Biomass-Degrading Genes and Genome from Cow Rumen (presentation)
Zhong Wang

AGBT 2011, Marco Island, FL; 02/2011
Assembly of biomass degrading genes and genomes from cow rumen (presentation)
Zhong Wang

2010 ILLUMINA SAN FRANCISCO USER MEETING, San Francisco, CA; 06/2010
Assembly Cellulolytic Genes from Deep Metagenomic Sequencing of a Cow Rumen Microbiome (presentation)
Zhong Wang

CSHL Genome Informatics Meeting, New York, NY; 11/2009
RNA-Seq for Cancer Transcriptome (presentation)
Zhong Wang

“Crack the Code with the Bear” Research Symposium, Chicago, IL; 11/2008

One Figure

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