Michael Zhang

Cecil H. and Ida Green Distinguished Chair of Systems Biology Science
Professor - Biological Sciences
mqz091000@utdallas.edu
972-883-2523
RL4748
Tags: Biology Genomics, Systems and Computational Biology

Professional Preparation

Ph.D. - Statistical Physics
Rutgers University - 1987
B.S. - Mechanical Engineering
University of Science and Technology of China - 1981

Research Areas

Research Interests
The long-term goal of research in our lab is to use mathematical and statistical methods to identify functional elements in eucaryotic genomes, especially the genes and their control and regulatory elements. A genome is the program book of a life, genome research will lead to eventual decoding of the entire genetic language of life and its grammar. Driven by the Human Genome Project, our current interest is on two related problems: genome/chromatin organization and gene regulation networks. At the transcriptional level, identification of cis-elements (both genetic and epigenetic) is the key focus. We are increasingly interested post-transcriptional regulations, especially at splicing regulation and translational regulation. Constitutive coding exons are relatively easy to identify, the greatest challenge lies in the identification of end exons and alternatively spliced exons that are often tissue- and developmental specific. Since this requires the study of many important control and regulatory elements for gene expression, this link between gene structure and function at the genomic or pre-/pri- RNA level requires high-throughput functional studies. Detecting cis regulatory elements and modeling gene expression networks are difficult challenges in the functional genomics era. Working closely with bench-scientists, our investigation will undoubtedly contribute to the understanding of genome organization as well as gene expression and regulation mechanisms, which will in turn have a profound impact on biology and medicine.

Publications

Tang M.H., Varadan V., Kamalakaran S., Zhang M.Q., Dimitrova N., Hicks J. (2013) Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Front Oncol. 2:197. PMID:23293768 2013 - Publication
Akerman M., Zhang M.Q., Krainer A. (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. MCP, Submitted. 2013 - Publication
Megha Rajaram; Jianping Zhang; Tim Wang; Cem Kuscu; Mamoru Kato; Vladimir Grubor; Robert Weil; Asluag Helland; Anne-Lise Borrenson-Dale; Kathleen Cho; Douglas A Levine; Alan N Houghton; Jedd D Wolchok; Lois Myeroff; Sanford D Markowitz; Michael Zhang; Alex Krasnitz; Robert Lucito; David Mu; Scott Powers (2013) Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS ONE, submitted. 2013 - Publication
Wen-Yu Chung, Robert J. Schmitz, Tanya Biorac, Delia Ye, Miroslav Dudas, Gavin D. Meredith, Christopher C. Adams, Joseph R. Ecker and Michael Q. Zhang (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE, In press. 2013 - Publication
Xie W., Schultz M., Lister R., Hou Z., Rajagopal N., Ray P., Whitaker J.W., Tiam S., Hawkins D.R., Leung D., Yang H., Wang T., Swanson S.A., Zhang J., Zhu Y., Lee A.Y., Kim A., Nery J., Urich M.A., Kuan S., Yen C., Klugman S., Yu P., Suknuntha K., Propson N.E., Chen H., Edsall L.E., Wagner U., Li Y., Ye Z., Kulkarni A., Xuan Z., Chung W., Chi N.C., Antosiewicz-Bourget J., Slukvin I., Stewart R., Zhang M.Q., Wang W., Thomson J.A., Eckert J.R., Ren B. (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, In press. 2013 - Publication
Zhang Z., Ma X., Zhang M.Q. (2012) Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS ONE, 7:e38112. PMID:22768038. 2012 - Publication
Li R., Guo W., Gu J., Zhang M.Q., Wang X.W. (2012) Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics. 100:297-302. PMID:22824656. 2012 - Publication
Sleumer M.C., Wei G., Wang Y., Chang H., Xu T., Chen R., Zhang M.Q. (2012) Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BMC Genomics. 13:433. PMID:22401550. 2012 - Publication
Xing H.*, Mo Y., Liao W., Zhang M.Q.* (2012) Genomewide localization of protein-DNA binding and histone modification by BCP with ChIP-seq data. PLoS CB, 8:e1002613. PMID: 22844240. 2012 - Publication
Xing H., Liao W., Mo Y., Zhang M.Q. 2012 A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIP-seq Data Types. J Vis Exp, Dec 10;(70). doi:pii: 4273. 2012 - Publication

Appointments

Visiting Professor
HKU Med School [2009–2018]
Green Distinguished Chair Professor
UT Dallas [2009–2018]
Qian Ren Ji Hua scholar
Tsinghua University [2008–2018]
School of Information Science and Technology
Chang Jiang Chair Professor
Tsinghua University [2005–2018]
School of Information Science and Technology
Guest Chair Professor
Tsinghua University [2004–2018]
School of Information Science and Technology

Additional Information

Molecular Biology and Bioinformatics Training
  • Life Technology Training Center, Recombinant DNA Techniques I and II, (Lab.Course Certificate), Mar. and Sept., 1992.
  • SIAM Computational Biology Workshop (Training Certificate), Rutgers University, Aug., 1992.
  • Advanced Automated/Diagnostic DNA Sequencing Workshop, Baylor College of Medicine, Jun., 1993.
  • Molecular Genetics, Cell Biology and Cell Cycle of Fission Yeast Course, CSHL, Nov., 1993.
  • Experimenting on Differential Display (Liang and Pardee,1992) Method by Internal Dye-labeling in David Beach's Lab., 5 months,1994.
  • Advanced Genome Sequence Analysis Course, CSHL, Mar., 1995.
  • Nucleic Acid & Protein Sequence Analysis Workshop, Pittsburgh Supercomputing Center, Jun. 1995.
  • Unix (Solaris 2.5x) system administration certificate from Sun microsystems, 1997.
 

News Articles

Scientists Advance Understanding of DNA Responsible for Diseases
Researchers from the School of Natural Sciences and Mathematics at The University of Texas at Dallas have teamed with colleagues at the UT Southwestern Children’s Medical Center Research Institute to create a new method for understanding the causes of genetic diseases, such as sickle cell anemia and some cancers. 

The new system allows researchers to define the molecular structures that control the activity of regulatory DNA sequences in the human genome. 

Dr. Michael Q. Zhang and postdoctoral researcher Dr. Yong Chen from Zhang’s Computational Biology Laboratory — along with assistant professor of biological sciences Dr. Zhenyu Xuan — collaborated on the formulation of the system called CAPTURE, or CRISPR Affinity Purification in situ of Regulatory Elements. Their work was published in a recent issue of the journal Cell. 
Scientist Flourishes in Eugene McDermott Graduate Fellows Program
Doctoral student Peng Xie came to The University of Texas at Dallas primarily to follow his mentor, Dr. Michael Q. Zhang, and his passion, computational biology.

In the three years he has been on campus, Xie has exemplified the multitude of reasons that promising graduate students come to UT Dallas — opportunity, support and career advancement.

Xie is a member of the first cohort of the Eugene McDermott Graduate Fellows Program. In addition to a stipend, tuition and fees, and a research budget, the McDermott fellowship provides professional development and enrichment opportunities.
Scientist Strengthens Systems Biology Initiative
Dr. Michael Zhang, a leading scientist in computational biology and genomic research, has joined UT Dallas as professor and Cecil H. and Ida Green Distinguished Chair of Systems Biology Science. Zhang’s chaired position in the School of Natural Sciences and Mathematics begins establishment of a new Center for Systems Biology. “In attracting a researcher of the stature of Dr. Zhang to our faculty, we expect to nucleate a major effort in genomics and computational biology that focuses on the genetic underpinnings of disease,” said Myron Salamon, dean of the School of Natural Sciences and Mathematics. Computational biology bridges the life sciences and quantitative sciences – mathematics, statistics and computer science – to understand living systems.

Affiliations

Journal service
Bioinformatics (Acting associate editor before 2007, Editorial board member), NAR (Editorial board member), CSHProtocols/BMC Biology/Genomics/Bioinformatics (Associate Editor). JBCB (Editorial board member), Systems and Synthetic Biology (SSB, Editorial board Member), Comparative and Functional Genomics (Editorial Board member), Int. J. Comp. Biolsci. (Board member), JMB, G&D, MCB, Yeast, GENE, Nature Rev. Genet., Nat. Genet., Genetics, Genomics, Genome Biol., BioMed. Central, Plant Mol. Biol., Human Mol. Genet., Computational Biology, Genetics, The Plant Journal, Genomics, J. Sta. Phys., J. Theor. Biol. , Bulletin for Math.Biol, Science, Nature, Nature Technology.
Consulting Service
Scientific Advisory Board of Cold Spring Harbor Lab Conferences in Asia, 2008-2009 External Scientific Advisory Committee, Max Plank Institute, 2006-2012 External Scientific Advisory Committee, Brown University Genome Center "COBRE" grant. 2004-present. External Scientific Reviewer of the integrated cancer biology Center Grant (P50) at OSU. 2004-present. Chondrongene. 2003. Genome Therapeutics Corp. 2002. Advisor, Yang Ming Medical School, Taipei, Taiwan. Aug. 2001. Vitatex, 2001. SK Corporation, 2000. Tularik Genomics, 1999-present Otsuka Amenrican Pharmaceutical, Inc. 1997-1998. Look4Gene.com 2000. Visiting member at NCBI, NLM/NIH, Sept-Oct, 1995.
Students Supervised
2009- Xinxu Chen (Undergrad, Stony Brook U) 2009 summer Aviva Mall (URP student from Cornell U) 2009- Yifan Mo (PhD student, Stony Brook U.) 2009- Jie Wu (PhD student, Stony Brook U) 2008- Longwei Guo (Ph.D. student, Tsinghua U.) 2008 Magdalena Jurkiewicz (MD/PhD student, Stony Brook U.) 2008- Will Liao (PhD student, Stony Brook U.) 2008 summer Eric Domb (URP, from Princeton U., CS) 2007-2008 Xiaowo Wang, visiting Ph.D. student from Tsinghua U., China. 2007 Hui-Ying Wend (iffive), summer intern from Yang Ming Medical School, Taipei, Taiwan. 2006-2009 Jeffrey Rosenfeld [jeffrey.rosenfeld@gmail.com] (Grad. Student, Biology, NYU) 2005- Fang Fang, Jun Li, Jing Zhang, Shicai Fan, Tingting Li, Bo Jiang, Xi Wang, Xuebing Wu, Xiaowo Wang, Yunzhang Zhu, (MS. And Ph.D. students, Tsinghua U. China) 2005 Vineeta Agarwala (URP-05 from Stanford). 2005 Evan Santo (Rotation graduate student, Watson School of Biological Sciences, Cold Spring Harbor Lab) 2004-2008 Chaolin Zhang (Grad. Student, Biomedical Engineering, SUNY/Stony Brook; now postdoc at Rockeffeler) 2004 Siddharth Srivastava (URP-04 from Columbia) 2003-2004 Yair Benita (Grad. Student, Pharmaceutical Proteomics, Utrecht University, The Netherlands. Now postdoc at Harvard) 2003-2006 Dustin Schones (SUNYSB Ph.D. student from Physics, now postdoc at NIH) 2003 Henry Lin (URP-03 from Harvard) 2003 Chris Maher (SUNY/Stony Brook rotation and Ph.D graduate student from Biomedical Engineering program). 2002-2003 Mamoru Kato (one-year visiting Ph.D. graduate student from U. of Tokyo) 2002-summer Jackie Ou (URP-02 from Duke) 2001 Elaine Shum (PFF high school student) 2001-2002 Zhenwei Zhu (SUNY/Stony Brook rotation and Ph.D. student from BioMedical Engineering Program) 2001-summer Joe Markson (URP'01 student, co-supervised with Josh Huang) 2001-summer Michael Hoffman (URP'2001 from UT) 2000-2001 William Palumbo (High School Student) 2000-2001 Apra Mattoo (High school student) 2000 Johannes (Yogi) Jaeger (Rotation graduate student, Genetics, SUNYSB) 2000 summer Chris Brunson (High school student in NY Academy of Sciences program). 2000 summer Maria Vichnevskaia (URP'00 student) 2000-2004 Nila Banerjee (Ph.D. student, Department of Bioinformatics, George Masson University. Move on as a postdoc at Columbia University Genome Center. Now a research scientist at Philip Research) 2000- Yan Zhang (Ph.D. student, Department of Biomedical Engineering, School of Basic Medicine, Peking Union Medical College) 2000 Elizabeth Thomas (Rotation Graduate Student from Watson School) 2000 Jenny Hizver (SUNY/Stony Brook rotation and Ph.D graduate student from Genetics Program) 1999 Adriano Costa de Alcantara (URP-99 student, went back to Brazil) 1998-1999 Brain Chang, Junior-Senior, Dept. of Molecular Biology, Harvard University (Thesis advisor: Tom Maniatis). 1997 Robert Klein, Senior, Dept. of Molecular Biology, Harvard University (Thesis advicor: Walter Gilbert) (went onto graduate student at Wash. U.) 1996-1997 Tim Chem, Ph.D., Dept. of Computer Science, SUNY at Stony Brook (Thesis advisor: Steve Skiena). (went onto Harvard Med. School as a postdoc in George Church's Lab. He became a faculty member at USC in 2000.). 1996 Will Orrick, Ph.D. Dept. of Physics, SUNY at Stony Brook (Thesis advisor: Barry McCoy). (went onto Australia for a postdoctoral position).
Postdoctoral Fellows and Visiting Scientists
2009- Dr. Justin Kinney (from Princeton U) 2009- Dr. Monica Sleumer (Tsinghua U. from UBC) 2009 Dr. Kaz Wrzeszcynski (from Colombia U) 2009- Dr. Martin Akerman (Joint postdoc with Krainer) 2009- Dr. Eric Man-Hung Tang (from U. Copenhagen) 2009- Dr. Zhihua Zhang (from Michigan U) 2009- Dr. Kato Mamoru (Tokyo U/Riken) 2009- Dr. Wenyu Chung (from Penn State U) 2008- Dr. Darrin Lewis (From Columbia U) 2008-2009 Dr. Michaela Oswald-Pisarski 2008- Dr. Chenghai Xue (from Tsinghua U) 2008 Dr. Vladimir A. Kuznetsov, visiting scientist from Bioinformatics Institute of Singapore.\ 2007 Dr. Xinying Ren, (now working for Dutch Embassy in China) (jointly supervised with Doreen Ware) 2006 Prof. Sue Brown (co-supervisor, CAPS awardee at KSU) 2006 Dr. Sanghamitra Bandyopadhyay [sanghami@isical.ac.in] (Tsinghua U., visiting professor from ISI, India) 2006-2008 Dr. Li Wang (co-supervisor, Tsinghua U.) 2006-2007 Dr. Fei Li (visiting from Tsinghua University) 2005-2008 Dr. Xiaoyue Zhao (moved to Berkeley) 2005 Dr. Bin Yan (Visiting postdoc from NIH/NIDCD) 2004-2006 Dr. Sitharthan Kamalakaran 2004-2007 Dr. Nevenka Dimitrova (Visiting Scientist from Philip) 2004-2005 Dr. Cizhong Jiang (moved on as a postdoc at U. N.C.) 2004-2008 Dr. Andrew Smith (USC Assist. Prof.) 2003-2005 Dr. Pavel Sumazin (NSF fellow, on leave from Portland StateUniversity, now a Research assist professor, Columbia U.) 2003-2005 Dr. Debopryia Das (a Research Scientist at NLBL) 2003-2005 Dr. Rajdeep Das (moved on as a staff at Ei Lilly) 2002-2005 Dr. Fang Zhao (research scientist at Schering-Plough) 2001-2005 Dr. Jinhua Wang (moved on as a bioinformatics staff at Med School, U. of Menphis, Tennessee, new a research professor, NYU Med. School). 2000-2003 Dr. Naoya Hata (moved on to a software company in Tokyo). 2000-2003 Dr. Ivo Grosse (CSHL Asssociation Fellow, moved on to a faculty position in Germany). 2000-2008 Dr. Zhenyu Xuan (Promoted to Assist. Research Prof. 2008) 1999-2001 Dr. Nathalie Pavy (NATO postdoc, co-supervised with Lincoln Stein). 1999-2001 Dr. D.V.V. Ramana, started as an assistant professor at Ohio State U, now is the director, Center for Systems and Computational Biology, Wistar Institute. 1999-2001 Dr. Theresa Zhang, now a senior scientist at Merck Research 1997-2000 Dr. Jian Zhu, moved on to a Bioinformatician position at Roche. 1997-1999 Dr. Ilya Ioshikhes, moved on to a faculty position at Albert Einstein College of Medicine 1997-1999 Dr. Jack Tabaska, moved on to a Bioinformatics Scientist position at Monanto
Programmers
2008 Martin Paradesi 2008 Dr. Weijun Luo 2005 Giri Pemmasani 2002-2003 Lihua Liu 2001- Vsevolod (Simon) Ilyushchenko (a Google program analyst) 2000-2006 Dr. Gengxin Chen (a scientist at Invitrogen) 1999-2000 Dmitri Priimak 1997-1998 Zhanna Ioschikhes, moved on to a programmer position at Computer Associate
Grant Review Panels
CAS-Max Planck SAB review panel, Sep. 2009. NIH Challenge Grant second level senior review panel, Jul, 2009. New Jersey Commission on Cancer Research (NJCCR) Research Development Award (RDA) application review, Jan 9, 2009 Site visit review board member, Inst. of Biophysics, CAS, Beijing, China, Nov. 6-8, 2008. Scientific Advisory Board meeting of Cold Spring Harbor Lab Conferences in Asia, Oct. 3-5, 2008. Site visit "973" review, Aug. 12-16, 2008, Xining, China. NIH/NCI Salt Institute Cancer Research Center site visit. 2008. NIH/NHGRI ENCODE review panel. 2007. Evaluation of new Chang Jiang Professor candidates for Ministry of Education of China. 2007. Evaluation of PIs at Inst. of Biomedical Sciences, Scientific Sinica, Taiwan. Mar, 2007. OSU Integrated Cancer Biology Program (ICBP) External Scietific Review, Apr. 2006. Brown University Center of Biomedical Research Excellence (COBRE) External Advisory Committee site visit, Feb. 9, 2006. MIT Cancer Center site visit committee, Oct. 2004; Oct. 2009 NCRR/NIH R24 Grant Review, Jul. 2004; Jan. 2005. Graduate Admission Committee, BioMedical Engineering Graduate Program, Stony Brook University, Feb. 2004. SBU Graduate School China Recruiting Committee, Feb. 2005. Fudan, School of Life Science, PI evaluation, Dec. 2003. Yunnan Kuming Institute of Zoology (CAS) PI evaluation, Oct. 2003 NIDDK/NIH special review panel Aug. 2002; Dec. 2003. Taiwan NSF grant review 2002. European Commission special initiative: Integrated projects in functional genomics relating to human health, Oct. 2001. NIEHS/NIH P01 Site Visit, May. 2001. NCI Innovative Technology and Small Business Grant Review, Nov. 2000. NCI P01 Grant Review / Site visit, Oct. 2000. Genome Study Section /NIH, Regular member,1999-2003. NCI P01 Grant Review, Feb. 2000; Feb. 2004. CANADA NSERC/CRSNG grant review, December, 1999 The Wellcome Trust JIF grant review, November, 1999 Genome Study Section / NIH, Ad hoc member , February 18-19, 1999 NSF grant review, December, 1998 The Wellcome Trust grant review, March 1998 NIH K01 grant review panels, 1993-1994
Conference Organization
Jan 13-16, Beijing, China. RECOMB Regulation/Systems/DREAM3 PC member. ISMB2008 PC member. 2008 CSH System Biology, Tutorial Workshop, Mar. 27-30. 2007 ISMB Chair, Special session on Computational Epigenomics, Jul 21-25, Vienna, Austria. 2007 APBC Chair session on Microarray Data Analysis, Jan 15. 2006 IEEE EMBC Co-chair on Bioinformatics and System Biology, Aug 30, NYC. 2006 ISMB Area Co-chair on Transcriptomics (Aug 6-10, Fortaleza, Brazil) 2006 11th SCBA co-chair on Signal Network and System Biology (Jul 19-23, SF.) 2006 The Fourth Asia Pacific Bioinformatics Conference, Program Committee, Feb 13-16, Taiwan. 2005 IEEE Computational Systems Bioinformatics Conference (Aug 8-11, Stanford) Program Committee member Genomics Workshop: Identification of Functional Elements in the Mammalian Genomes (November 11 - 13, 2004, Cold Spring Harbor, NY) Systems Biology: Genomic Approaches to Transcriptional Regulation (March 4 - 7, 2004, Cold Spring Harbor, NY) Program Committee member, RECOMB2003, Apr. 11-13, 2003. Berlin, Germany. Co-chair, Systems Biology: Genomic Approaches to Transcriptional Regulation March 6 - 9, 2003. CSHL, NY. Chair, Bioinformatics symposium, International HUGO Conference, HGM2002.(Apr. 14-17, 2002. Shanghai, China ) Chair, 2nd CSHL Meeting on Computational Biology : Integrating Genome Sequence, Sequence Variation & Gene Expression, Cold Spring Harbor, New York, September,28-30, 2001 Member of the organizing Committee. The Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2000), Novosibirsk, Russia, Aug., 2000 Chair, Special PSB2000 track: Identification of Co-regulated Genes and Regulatory Sequences, Nasau, Hawaii, Jan.5-9, 2000 Chair, First CSHL Workshop on Computational Biology : Bridging the gap between sequence and function, Cold Spring Harbor, New York, September,17-19, 1999 Member of the organizing Committee. The First International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), Novosibirsk, Russia, Aug., 1998