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Michael Qiwei Zhang
Professor-Biological Sciences
Office MailstopMail Box: RL11, Room No.: RL4748 
Email Address    Primary Phone Number 972-883-2523    Media Contact
 Professional Preparation
 Ph.D.Statistical PhysicsRutgers University1987
 B.S.Mechanical EngineeringUniversity of Science and Technology of China1981
Collapse Section Expand Section Research and Expertise
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.
Collapse Section Expand Section Publications
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  YearPublication  Type
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
Akerman M., Zhang M.Q., Krainer A. (2013) ProteoMirExpress: inferring microRNA-centered regulatory networks from high throughput proteomic and mRNA expression data. MCP, Submitted.
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.
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.
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.
Collapse Section Expand Section Affiliations
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
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. 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 [] (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 [] (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
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
Collapse Section Expand Section Appointments
DurationRankDepartment / SchoolCollege / OfficeUniversity / Company
2009Visiting Professor  HKU Med School
2009Green Distinguished Chair ProfessorDepartment of Biology UT Dallas
2008Qian Ren Ji Hua scholarInstitute of BioinformaticsSchool of Information Science and TechnologyTsinghua University
2005Chang Jiang Chair ProfessorInstitute of BioinformaticsSchool of Information Science and TechnologyTsinghua University
2004Guest Chair ProfessorInstitute of BioinformaticsSchool of Information Science and TechnologyTsinghua University
 News Articles
Scientist Strengthens Systems Biology Initiative
UT Dallas News Center
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.

       Teaching HelpHelp  
toggle toggle Invited Talks
Invited Talks
  • Genome-wide gene expression and promoter analysis, CSHL course on Computational Genomics, Nov., 1998.
  • Deciphering the book of life, Rutgers Univ., Nov., 1998.
  • Genome expression analysis of yeast cell cycle genes and promoter regulatory elements. IBC's 2nd Annual
  • Conference on Maving gene expression technology & analysis towards drug discovery, Berkeley, CA. May, 1999.
  • On large-scale genome expression data analysis, International conference on Computational Biology and Bioinformatics, Beijing, China. Jul, 1999.
  • Genome expression analysis and promoter regulatory elements, After Genome V, Jackson Hole, WM. Oct, 1999.
  • Genome expression analysis and promoter regulatory elements, Medical University of South Carolina, Charleston, SC. Oct, 1999.
  • Large-scale genome expression analysis, Tularik Genomics, NY. Nov, 1999.
  • Cluster, Function and Promoter: Analysis of Yeast Expression Array, Honolulu, HW. Jan, 2000.
  • Large-scale gene expression analysis, USC, LA, CA. Jan, 2000.
  • Exploring large-scale gene expression data, NYU Med. School, NYC, NY. Feb, 2000.
  • Exploring large-scale gene expression data, Columbia U. Genome Center, NYC, NY. Mar. 2000.
  • Bridging the gap between clinical informatics and bioinformatics, Columbia U. Medical School, NYC, NY. May. 2000.
  • Invited lecture on "Exploring Pattern of Gene Expression and Regulation", celebrating Prof. Joel Lebowitz 70th birthday, Rutgers, NJ, May. 2000.
  • EBI Workshop on Genome Based Gene Structure Determination, Cambridge, UK. Jun. 2000.
  • Super-Paramagnetic Clustering (SPC): A New Tool for Large-scale Gene Expression Analysis, San Francisco, CA. Jun. 2000.
  • Chinese American Academic & Professional Society 2000 Annual Convention (CAAPS'2000), Biotechnology session. Microarray: A Powerful Tool in Functional Genomics, NYC. Aug. 2000.
  • The third annual bioinformatics meeting - Trends in Bioinformatics on Sep 12, 2000. Helsinki, Finland
  • Exploring gene structure, expression and regulation in silico. Oct.16, 2000. SUNY Stony Brook Genetics Program Retreat
  • Computational analysis of large-scale gene expression data. International Symposium on Bioinformatics, Nov.22-23, 2000. Pohang, Korea.
  • Extracting functions from genomic regulatory regions. IPAM Workshop on Mathematical and Statistical Challenges from Computational Biology. Dec.11-15, 2000. Lake Arrowhead, CA.
  • Exploring untranslated regions. ValiGen, Apr. 9, 2001, Paris, France.
  • Computational Molecular Biology of Gene Expression and Regulation. Dept. of Biology, UPenn. Mar. 8, 2001, Philadelphia, PA.
  • Promoter Analysis in silico. NIDDK Workshop on Genomics and Proteomics in Kidney and Urological Diseases. Jul. 8-10, 2001, Washington DC.
  • RPI Bioinformatics Summer Workshop. Aug. 1, 2001, RPI, NY.
  • Computational Approaches To Gene Expression and Regulation. The 9th SCBA International Symposium. Aug.5-10, 2001 Taipei, Taiwan.
  • Microarray Data Analysis Workshop. Yang Ming Medical School, Aug. 8-9, 2001 Taipei, Taiwan.
  • Computational molecular biology problems. University of Hong Kong, Aug. 13, 2001 Hong Kong, China.
  • Genomics and bioinformatics. National University, Aug. 15-17, 2001, Singapore.
  • The first virtual conference in Genomics and Bioinformatics, Oct. 15-16, 2001 Fargo, ND.
  • CART classification of human 5'UTR sequences in Beyond the Identification of Transcribed Sequences (BIT): Function and expression analysis. Nov. 9-12, 2001, Washington DC.
  • NFS workshop on Genomics approaches to cis-element/TF interactions, Jan. 15-16, 2002. Virginia.
  • Computational biology of genome expression and regulation, Yale Med. School, Mar. 26-27, 2002, New Haven, CT.
  • Computational biology of genome expression and regulation, Institute of Genomics and Bioinformatics, Indiana University, Mar. 28-29, 2002. Bloomington, IN.
  • Computational genomics lectures, Peking (Beida) University, April 10, 2002. Beijing, China.
  • Computational prediction of first exons and promoters in the human genome. HGM'2002, April 14-17. Shanghai, China.
  • Computational genomics lecture, Fudan Univeristy, April 18, 2002. Shanghai, China.
  • Annotation of promoters and first exons in the human genome, (Presented by Ramana), May 8, 2002. CSH, NY.
  • Computational genomics lecture, Genetics Program, UCR, May 14. Riverside, CA.
  • Computational genomics lecture, Genomics Therapeutics Corp. Jun 17-18, 2002, Boston, MA.
  • 1% Workshop, NHGRI, Jul 23-24, 2002, Bethesda, MD.
  • Bio Expo Korea Sept. 26-27, 2002, Seoul, Korea.
  • Computational genomics lecture, Oak Ridge National Lab., Oct. 11, 2002.
  • Differential Gene Expression 2002, Vanderbilt University, Oct. 12-15, 2002. Nashville, TN.
  • Computational genomics lecture, Biomedical Engineering Department, SUNY at Stony Brook, Oct. 16, 2002. Stony brook, NY.
  • Genomics Revolution and Bioinformatics Frontier, Open ceremony at Korea Biotech VC company BiNEXT HiTEC, DAESUNG GROUP, Oct. 17, 2002. Seoul, Korea.
  • Combinatorial Analysis of Transcription Regulation in Yeast, IFBT'02 (International Forum on Biochip Technologies), Nov. 9-13, 2002. Beijing, China.
  • Bioinformatic approach to genetic networks, Feb 24 - Mar 1, 2003, Institute for Theoretical Physics, Santa Barbara, CA.
  • Genomics of Transcriptional Regulation, Mar. 6-9, 2003, Cold Spring Harbor, NY.
  • Computational Molecular Biology of Gene Expression and Regulation. NIH/NIEHS/RTP, Mar. 21, 2003. Raleigh, NC.
  • Center for Bioinformatics and Computational Biology (CBCB), Colleges of Engineering and Medicine, University of Iowa, Mar. 26, 2003. Iowa City, Iowa.
  • Keynote speaker, Symposium on the prospects for computational and interdisciplinary biology, May 18-20, 2003. Harvard, Cambridge, MA.
  • GENOMICS AND CANCER: Integrating Genomics with Clinical Research and therapy. May 25-28, 2003. Heidelberg, Germany.
  • 68th CSHL Symposium on Quatitative Biology: The Genome of Homo sapiens (May 27 - Jun 2, 2003, Cold Spring Harbor, NY)
  • Genomic Microarrays for the study of transcription factors in neoplasia workshop (Jun 5-6, 2003, NCI/NIH, Bethesda, MD)
  • 2003 Xiangshan Science Symposium on Genomics and Evolution (Oct. 28-30,2003, Beijing, China)
  • Six lectures in Computational Genomics at Tsinghua University (Nov.2003), Beijing, China.
  • Transcriptome 2003: From functional genomics to system biology, followed by IMAGE/EPIC Consortium Invitational Workshop (Nov. 16-19, 2003, Tokyo, Japan)
  • 50 Anniversary DNA: How many genes in the Human Genome? Fundation La Caixa, Barcelona, Spain, Nov. 21-22, 2003.
  • U Penn. Jan. 21, 2004. Philadelphia, PA.
  • Physics Colloquium, SUNY Stony Brook, Jan. 27, 2004. Stony Brook, NY.
  • Systems Biology: Genomic Approaches to Transcriptional Regulation (March 4 - 7, 2004, Cold Spring Harbor, NY)
  • Keystone Symposium: Biological Discovery Using Diverse High-Throughput Data (Mar. 30 - Apr. 4, 2004), Steamboat Springs, Colorado.
  • Functional Genomics of Ageing 2004, Keynote Lecture, Crete, Greece, April 28th-May 1st, 2004.
  • Invited Talks at Tsinghua/Beijing Jun 6-8, CAS/Shanghai Jun 8-10, Huada/Zhejiang University Jul 15 and Huada/Beijing Jul. 15-17.
  • SCBA2004: 10th SCBA International Symposium. (Jul. 18-23, 2004 ), Beijing, China
  • Proteomics and Systems Biology Symposium in Turk u,Finland (Sep. 20-22, 2004)
  • Computational Biology Seminar, NLBL, Berkeley, (Nov. 5, 2004)
  • Genomics Workshop: Identification of Functional Elements in Mammalian Genomes (November 11 - 14, Cold Spring Harbor, NY)
  • MaxPlanckGroup-ChineseAcademy of Sciences joint Computational Biology Symposium in Shanghai, China (Dec. 19-20, 2004).
  • Institute for Genetic Medicine, Los Angeles, CA. Jan. 25-27, 2005.
  • Department of Biological Sciences, UNLV, Las Vegas, NV. Feb. 10-12, 2005.
  • Philips Research USA. Briarcliff Manor, NY. Feb. 16, 2005.
  • UMDNJ-New Jersey Medical School, Newark, NJ. Mar. 10, 2005.
  • Department of Biology, Brookhaven National Laboratory, NY. Mar 24, 2005.
  • Network: From Biology To Theory Sponsored by Sino-German Centre (Beijing , China 04 - 08 April, 2005 ). Lectures in Tsinghua U., Apr. 28, Nov 4-29; CPUMS, May 10; PKU, May 11.; 301 Hospital Dec.12)
  • Molecular & Human Genetics Seminar Series. Baylor College of Medicine, TX, May 24, 2005.
  • Gene Regulation Network Workshop, Nov. 6, Trieste, Italy.
  • Keynote, the First International Conference on Pattern Recognition and Machine Intelligence (PReMI'05),
  • Indian Statistical Institute (ISI), Dec 18-22, Kolkata, India.
  • IPK Gatersleben Lecture, Germany, May 4, 2006.
  • International Bioinformatics Workshop, Jun 10-12, 2006, Zhong Nan University, Changsha, Hunan, China.
  • Systems Properties and Evolution in Cell Signaling, Jun. 25-27, 2006. Peking U., Beijing, China.
  • The First International Conference on Computational Systems Biology CAS-MPI, Shanghai, China, July 20-23, 2006.
  • The 11th SCBA International Symposium (San Francisco, July 19-23, 2006)
  • University of Michigan Bioinformatics Program Seminar Series, Ann Arbor, MI, Oct. 11, 2006.
  • Invited lecture series on Advances in Computational Genomics, School of Medicine, Hong Kong University, Jan 11-30, 2007. Also seminar at CUHK on Jan 24, 2007.
  • Center for Cancer System Biology (CCSB) at Dana-Farber Cancer Institute, Harvard Med. School, Feb. 8-9, 2007.
  • Invited talk at Symposium on Recent Advances in Biomedical Sciences, Inst. of Biomedical Sciences, Scientific Sinica, Taipei, Taiwan. Mar. 28, 2007.
  • Invited talk at Xiang Shan Meeting on Structural Biology, April 14-15, 2007.
  • Invited lecture on genome regulation in CSHL course, June 24, 2007.
  • Summer School of Bioinformatics, Jul 26 - Aug 24, seminar: Computational Epigenomics. Tsinghua, Beijing.
  • Military Medical College of China, Jul 17, seminar: Computational Dissection of Gene Regulation networks. Beijing.
  • ISMB/ECCB 2007 (Jul 21-25, Viena, Austria) Special Session on Epigenomics: Insulator (CTCF) binding site motif and its distribution in the human genome.
  • Seminar at Simon Fraser University sponsored by the Michael Smith Foundation for Health Research and SFU, Vancouver, Canada. Sep 21, 2007.
  • Invited speaker, Seminar at C2B2/MAGNet, Columbia University, Nov. 14, 2007.
  • CSBS2008, 3rd Annual Computational & System Biology Symposium, Mar. 12, 2008, Athens, Georgia.
  • Invited speaker, Systems Biology, CSH, NY, Mar. 27-30, 2008.
  • Seminar, Department of Biostatistics and Epidemiology University of Pennsylvania School of Medicine. April 22, 2008.
  • Invited speaker, The CAS International Symposium on Developmental System Biology, Beijing, China. May 18-20, 2008.
  • IBW2008, The 6th International Bioinformatics Workshop (funded by DragonStar bioinformatics program),June 7-9, 2008, Yunnan University, Kunming, China.
  • Seminar at Dept. of Mol. And Cell Biol., UT Dallas, Jun. 26, 2008.
  • Seminar on Next-generation sequencing and its application in epigenomics, Beijing Normal U., Oct. 10, 2008.
  • Lecture series on Advances in Computational Genomics, Tsinghua U., Beijing, China, Sep. 20- Oct. 19, 2008.
  • Second visit to UT Dallas - UTSW, Nov. 12-16, 2008.
  • Invited speaker, Workshop on Computational Systems Biology Approaches to Analysis of Genome Complexity and Regulatory Gene Networks (20 -25 Nov 2008), Singapore.
  • Invited seminar, Beijing Med. College, PKU, Jan. 5, 2009.
  • Invited speaker, HKU, Jan. 19, 2009.
  • Invited talk, Department of Molecular, Cell and Developmental Biology, UCLA, Apr 20, 2009.
  • CSH Integrative Statistical Analysis of Genome Scale Data (summer workshop), Jun 15, 2009

 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.

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