May., 2008

Michael Q. Zhang


Watson School of Biological Sciences
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724
E.mail: mzhang@cshl.org
Phone: (516) 367-8393
FAX: (516)367-8461


Education

B.S. University of Science and Technology of China   1981    Mechanical Engineering
Ph.D. Rutgers University       1987    Mathematical Physics
 
Ph.D. Thesis: Nonequilibrium Steady States of a Stochastic Model System.
Adviser: Prof.  Joel L. Lebowitz

Biology 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.

Professional Experience

2008-          Recruiting Committee member, Watson School of Biological Sciences, CSHL
2007-          Guest professor, Chinese Military medical College
2005-          Overseas Assessor of Chinese Academy of Sciences
2003-          Guest Professor (Chair Professor 2004, Chang Jiang Chair Professor, 2005-), Institute of Bioinformatics, School of Information Science and Technology. Tsinghua University. Beijing, China.
2002-          Scietific Council member, Center of Theoretical Biology, Peking University. Beijin, China.
2002           Full professor, CSHL, NY.
2001-          Advisor, Yang Ming Medical School, Taipei, Taiwan. 
2001-          Adjunct Faculty, Graduate Program in Biomedical Engineering and Physics, SUNYSB.
2001-          Scientific Advisory Board member of AmDEC
1999-present    Organizer of CSHL Bioinformatics Weekly Seminar
1999           Director for the graduate course: Fundamentals of Bioinformatics
1998-present    Associate Professor, CSHL, NY.
1997-present   Adjunct Faculty, Genetics program, SUNY at Stony Brook, NY.
1996-1998      Assistant Staff Investigator, CSHL, NY.
1995           Visiting Member (Sept.-Oct.), NCBI/NIH, MD.
1991-1996      Genome Research Fellow, P.I. of the K01 grant from NCHGR/NIH, CSHL, NY
1991           Visiting Lecturer, Dept. of Math. Rutgers University, NJ.
1990-1991      Visiting Member (with Peter Lax), Courant Institute of Math. Sci., NYU, NY.
1987-1990      Postdoctoral Fellow (with Jerry Percus), Courant Institute of Math. Sci., NYU, NY.
1981-1987       Ph.D. Trainee and Teaching Assistant, dept. of Physics, Rutgers University, NJ.

Professional Activities

Grant Review Panels

·         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.

  • NCRR/NIH R24 Grant Review, Jul. 2004; Jan. 2005.
  • MIT Cancer Center site visit committee, Oct. 2004
  • NCI P01 Grant Review, Feb. 2004.
  • Graduate Admission Committee, BioMedical Engineering Graduate Program, Stony Brook University, Feb. 2004.
  • Evaluation of PI performance at The School of Life Sciences, Fudan University, Dec., 2003.
  • Evaluation of PI performance at Kuming Animal Institute of CAS, Kuming, Yunnan, China, Oct. 23-27, 2003.
  • European Commission special initiative: QoL integrated projects in functional genomics relating to human health, Oct. 2001.
  • NIEHS 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.
  • 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

·         2009 APBC Conference chair, http://bioinfo.au.tsinghua.edu.cn/apbc2009/ Jan 13-16, Beijing, China.

·         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

Refereeing service

  • Bioinformatics (Acting Accosiate editor starting Jan, 2002) NAR (Editorial board member), PMC Journals (Editor), JBCB (Editor), Systems and Synthetic Biology (SSB, Editorial board member), Comparative and Functional Genomics (Editorial Board member), JMB, G&D, MCB, Yeast, GENE, Nature Genet. Genetics, Genomics, Genome Biol., BioMed Central., Plant Mol. Biol., Human Mol. Genet., Computational Biology, Genetics, The Plant Journal, Genomics, Bulletin for Math. Biol., J. Sta. Phys., J. Theor. Biol. Bulletin for Math.Biol.

Consulting Service

·         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.
  • Vitatex, 2001
  • Look4Gene.com 2000
  • SK Corporation, 2000
  • Tularik Genomics, 1999-present
  • Otsuka Amenrican Pharmaceutical, Inc. 1997-1998

Grants

     Cancer Center Development Award (2008)
     NIH R01GM74688 (2007-2012) (with Adrian Krainer)
     NSF 0324292 (2003-2008) (with Ying Xu)
     NIH (2003-2006) (with Sam Wang)
     Dart Neurogenomics grant (2003-2007)(with Tully, Zhong, Dubnau, Chiang)
     NIH 5P01CA013106 (2001-2006) CSHL Cancer Research Center (Tumor Virus Project Grant, PI: Winship Herr).
     NIH 1R01HG01696 supplemental grant for building a Beowulf Linux cluster (supporting large-scale comparative genome analyses).
     NIH 5R01DA13748 (2000-2004) Genome responses to Drosophila addiction using DNA chips. (with Tim Tully).
     NIH 1R21/R33 CA88351-01 (2000-2004) Cancer classification based on mRNA isoforms (Splicing Chip Array). (with Xiabg-dong Fu, J-B Fan and M. Gribskov)
     NIH 1R01GM60513 (2000-2007) Computational analysis of genome expression data.
     NIH 1R01HG01696 (1997-2011) Identification of protein coding genes in the human genome. (with Bing Ren after 2008)
     NIH 1R01CA81152 (1999-2002) Sequencing tumor suppressor loci. (with McCombie&Wigler)
     NIH 1R01HG98002 (1999-2000) Large-scale sequencing of chromosome 18. (with McCombie&McPherson)
     NIH 5K01HG00010 (1992-1997) Training in genomic research. sole P.I.
     Max-Planck Inst. Consultation award (1998).
     MGRI #29 (1997-2000) Identification of last exons in human and mouse genes.
     OTSUKA Consultaion award (1997-1998).
     CSHL Association award (1997,2001,2004).

Invited talks

  • Wavelet Transforms and DNA Sequence Analysis, Hilton Head, SC, 1994.
  • Theoretical Aspects of Sequence Alignment and Statistical Significance. SUNY Stony Brook, NY, 1994.
  • Gene Structure Analysis and Exon identification, Merck Research Labs, NJ, 1995.
  • Exon, Intron and Gene Splicing, Rutgers, NJ, 1995.
  • Statistical Structures of the Human Exons and Their Flanking Regions, the Jackson Lab., Jun., 1995.
  • Human exon classes and their statistical properties, NCBI/NLM/NIH, MD, Otc., 1995.
  • Correlations and Constraints within Coding Strucutres of the Human Genes, Univ. Penn., Otc., 1995.
  • What makes an exon an exon, Banbury Center conference on FINDING GENES, CSHL, Dec., 1995.
  • In search of exon definition, SmithKine Beecham R & D, PA, Oct. 1996.
  • Molecular sequence alignment, NEC Research, NJ, Mar., 1996.
  • Identification of Protein Coding Regions in the Human Genome Based on Quadratic Discriminant Analysis, Hilton Head, NC, 1996.
  • Identification of Protein Coding Region in Plant Genome, Plant and Animal Genome V Conference, San Diego, CA, 1997.
  • What do we know about core promoters, Banbury Center conference on FINDING GENES, CSHL, Feb., 1997.
  • Identification of Protein Coding Regions, CSHL Conference on Genome Mapping and Sequencing, May, 1997.
  • Searching for Protein Coding Genes in the Human Genome, Rockefeller University, Oct., 1997.
  • On A New Strategy of Promoter Recognition, Georgia Tech. Nov., 1997.
  • Human Gene Identification, U. Penn. Dec. 1997.
  • A Discrimination Study of Human Core-Promoters, Pacific Symposium on BIOCOMPUTING '98, Hawaii, Jan., 1998.
  • Finding Genes in the Human Genome, University of Tokyo, Japan. Apr., 1998.
  • Analysis of Complex Gene Expression Information in the New Era of Functional Genomics, The Special Meeting on ``The Origins of Life and Chaos - Biology as a Whole and Complex System'', Kyoto, Japan. Apr., 1998.
  • Genefinding and Promoter Recognition, Princeton Summer Lecture Series on Biophysics, NEC Research, NJ, May, 1998.
  • Analysis of Whole Genome Expression Using DNA Microarrays, University of Toronto, Jul., 1998.
  • A Promoter Database of Yeast Saccharomyces cerevisiae and its application in genome-wide expression data analysis, The First International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98), Novosibirsk, Russia, Aug., 1998.
  • Promoter Analysis of Co-regulated Genes in the Yeast Genome, Stanford Univ., Sept., 1998.
  • 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 netween 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.
  • CART classification of human 5'UTR sequences. BITS'2001 (Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis). Nov. 9-12, 2001. Washington D.C.
  • NFS workshop on Genomics approaches to cis-element/TF interactions, Jan. 15-16, 2002. Virginia.
  • Computational Molecular Biology of Gene Expression and Regulation. Yale University. School of Medicine. Mar. 26, 2002, New Haven.
  • Computational Molecular Biology of Gene Expression and Regulation. Indiana University. School of Informatics. Mar. 27-29, 2002. Bloomington.
  • Computational Molecular Biology of Gene Expression and Regulation. Peking University, Center for Bioinformatics. Apr. 8-12, 2002. Beijing, China.
  • 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. Biochip 2002, Nov. 9-13, 2002. Beijing, China. 
  • Bioinformatic approach to genetic networks (Feb 24 - Mar 1, 2003, Institute for Theoretical Physics, Santa Barbara)
  • 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.
  • 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)
  • MODELING OF PROTEIN INTERACTIONS IN GENOMES (Jun 27-30, 2003, SUNY Stony Brook, NY)
  • 2003 Xiangshan Science Symposium on Genomics and Evolution (Oct. 28-30,2003, 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, SUNYSB, Jan. 27, 2004.
  •  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, Crete, Greece, April 28th-May 1st, 2004.
  • 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.
  • Departmen 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.

·         GIW2007, 3-5 December 2007, Keynote: COMPUTATIONAL DISSECTION OF MAMMALIAN REGULATION NETWORKS, Singapore.

·         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.

Lab Publications

1.      Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ (2008) Distinct histone modifications are enriched in each type of heterochromatin. Submitted.

2.      Zhang Z, Lin H, Zhang MQ, Ma B, Li M 92008) ZOOM! Zillions of Oligos Mapped. Submitted.

3.      Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T (2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. Submitted.

4.      Zhao X, Yoon S, Zhang MQ, Ye K, Geschwind DH, Sebat J, Iakoucheva LM (2008) High Connectivity among Autism Gene Candidates in Biological Networks: Evidence for Common Pathways. Submitted.

5.      Bernard D, Prasanth KV, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Triller A, Spector DL, Bessis A (2008) A nuclear retained non-coding RNA regulates synaptogenesis. Submitted.

6.      Zhang C, Li W-H, Krainer AR, Zhang MQ (2008) An RNA landscape of evolution for optimal exon and intron discrination. Proc. Acad. Natl Sci. USA, 9:128.

7.      Smith AD, Xuan Z, Zhang MQ (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, In press.

8.      Wang Z, Rosenfeld J, Schones DE, Zang C, Barski A, Cuddapah S, Cui K, Roh T-Y, Peng W, Zhang MQ, Zhao K (2008) Genome-wide correlation analysis of histone acetylation and methylation in human T cells. Submitted. (equal contributing first author)

9.      Wu X, Jiang R., Zhang MQ, Li S (2008) Large-scale network-based prediction of human disease genes. Mol. Sys. Biol. In press.

10.  Cuddapah S, Chen X, Xuan Z, Roh T-Y, Cui K, Smith AD, Byun JS, Zhang MQ, Fuller MT, Zhao K (2008) Identification of potential human polycomb response elements in T cells. Nat. Genet, In press.

11.  Chen G, Li W, Zhang Q-S, Regulski M, Sinha N, Barditch J, Tully T, Krainer AR, Zhang MQ, Dubnau J (2008) Identification of synaptic targets of Drosophila Pumilio. PLoS Comp Biol. (joint corresponding authors). In press.

12.  Chen J, Kim YC, Jung Y-C, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM (2008) Scanning the human genome at kilobase resolution. Genome Res. In press.

13.  Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B (2008) Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res. 18:46-59.

14.  Eguchi J, Yan Q-W, Schones DE, Kamal M, Hsu C-H, Zhang MQ, Crawford GE, Rosen ED (2008) Identification of interferon-regulatory factors (IRFs) as regulators of adipocyte gene expression by mapping Dnase hypersensitive sites during adipogenesis. Cell Metabolism. 7:86-94.

15.  Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ. (2007) A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A. 104:19291-6.

16.  Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet. 39:1522-7.

17.  Yang Z, Jiang H, Zhao F, Shankar DB, Sakamoto KM, Zhang MQ, Lin S (2007) A highly conserved distal regulatory element controls hematopoietic expression of GATA-2. BMC Developmental Biology, 7:97.

18.  Fan S, Fang F, Zhang X, Zhang MQ (2007) Putative Zinc Finger Protein Binding Sites Are Over-represented in the Boundaries of Methylation-resistant CpG Islands in the Human Genome. PLoS ONE, 2(11):e1184.

19.  Wang X, Gu J, Zhang MQ, Li Y (2007) Identification of phylogenetically conserved microRNA cisregulatory elements across 12 Drosophila species. 24:165-71.

20.  Zhang MQ (2007) Computational analyses of eukaryotic promoters. Review proceeding of Otto Warburg International Summer School and Workshop on Networks and Regulation, Peter F Arndt & Martine Vingron eds. BMC Bioinformatics, 8(Suppl 6):S2.

21.  Wang X, Bandyopadhya S, Xuan Z, Zhao X, Zhang MQ, Zhang X (2007)  PREDICTION OF TRANSCRIPTION START SITES BASED ON FEATURE SELECTION USING AMOSA. Proc. Comp. Sys. Bioinf. Conference. San Diego, Aug. 2007. World Scientific. eProceedings.

22.  Zhang C, Krainer AR, Zhang MQ. (2007) Evolutionary impact of limited splicing fidelity in mammalian genes. Trends in Genetics. 23:484-8.

23.  Zhang C, Hastings ML Krainer AR, Zhang MQ. (2007) Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proc. Natl. Acad. Sci. USA 104, 15028-15033.

24.  Zhang C, Zhang MQ. (2007) Biomedical literature mining. Chap 10. in Introduction to Bioinformatics: A workbook approach. Mathura V ed. Elsevier. In press.

25.  Zhao X, Leotta A, Kustanovich V, Lajonchere C, Geschwind DH, Law K, Law P, Qiu S, Lord C, Sebat J, Ye K, Wigler M. (2007) A unified genetic theory for sporadic and inherited autism. Proc Natl Acad Sci U S A. 104:12831-6.

26.  Jiang B, Zhang MQ and Zhang X. (2007) OSCAR: One-class SVM for Accurate Recognition of Cis-elements. Bioinformatics,  23:2823-8.

27.  He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA, Hannon GJ (2007) A microRNA component of the p53 tumour suppressor network. Nature. 447, 1130-4.

28.  Yang Z, Jiang H, Zhao F, Shankar DB, Sakamoto KM, Zhang MQ, Lin S (2007) A highly conserved distal regulatory element controls hematopoietic expression of GATA-2. BMC Developmental Biology, 7:97.

29.  Kim TH, Abdullaev Z, Smith AD, Ching KA, Loukinow D, Green RD, Zhang MQ, Lobanenkov V, Ren B (2007) Analysis of the vertebrate insulator protein CTCF binding sites in the human genome. Cell 128(6):1231-45.

30.  Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, Hannon GJ (2007) Critical roles for Dicer in the female germine. Gene & Dev. 21:682-93.

31.  Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA, Gleiberman A, Zhang MQ, Enikolopov G. (2007) Neural Potential of a Stem Cell Population in the Hair Follicle. 6:2161-70. (cover image!)

32.  D. Das and M.Q. Zhang. (2007) Predictive Models of Gene Regulation: Application of Regression Methods to Microarray Data. Methods in Molecular Biology, ed. M. Korenberg.  377:95.

33.  Zhang J, Jiang B, Li M, Tromp J, Zhang X and Zhang MQ (2007) Computing exact p-values for DNA motifs (Part I). Bioinformatics. 23:531-7.

34.  Schones DE, Smith AD and Zhang MQ (2007) Statistical significance of cis-regulatory modules. BMC Bioinformatics 8:19.

35.  Jiang C, Xuan Z, Zhao F, Zhang MQ (2007) TRED: A Transcriptional Regulatory Element Database, new entries and other development. Nucleic Acid Res 35: D137-D140

36.  Zhang C, Zhao X, Zhang MQ (2007) Functional in silico analysis of gene regulatory polymorphism - Chapter 12 in: Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data, 2nd edition
(M.R. Barnes, ed.) Pp281-310 Wiley-VCH

37.  Zhao X, Xuan Z, Zhang MQ (2007) Boosting with stumps for predicting transcription start sites. Genome Biology 8:R17

38.  Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. (2007) Computational prediction of novel components of lung transcriptional networks. Bioinformatics. 23:21-29.

39.  Smith AD, Sumazin P and Zhang MQ (2007) Tissue-specific regulatory elements in mammalian promoters. Mol Sys Biol. 3:73.

40.  Zhang C, Zhang X, Zhang MQ, Li Y (2007) Neighbor number, valley seeking and clustering. Pattern Recognition Letters. 28:173-180.

41.  Zhang MQ (2007) Inferring Gene Regulatory Networks - Chapter 21 in: Bioinformatics - From Genomes to Therapies (T. Lengauer, ed.) Wiley-VCH. p807-828.

42.  Kim YC, Jung Y-C, Xuan Z, Tong H, Zhang MQ, Wang SM (2007) Pan-genome isolation of low abundant transcripts through SAGE. FEBS Lett 580:6721-6729.

43.  Schaffer JD, Dimitrova N, Zhang MQ (2006) Bioinformatics. Chap. 26 in Advances in Healthcare Technology: Shaping the Future of Medical Care. Spekowius G & Wendler T eds. Pp421-438. Springer.

44.   Li J, Zhang MQ and Zhang X (2006) A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. Am. J. Hum. Genet. 79:628-639.

45.  Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, Edwards JR, Ju J, Bestor TH, Zhang MQ (2006) Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A. 103:10713-6.

46.  Smith PJ, Zhang C, Wang J, Chew SL, Zhang MQ, Krainer AR (2006) An increased specificity score matrix for the prediction of SF2/ASF-specific exonix splicing enhancers. Hum Mol Genet 15(16):2490-2508.

47.  Fang F, Fan SC, Zhang X and Zhang MQ (2006) Predicting Methylation Status of CpG Islands in the Human Brain. Bioinformatics, 22:2204-2209.

48.  Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A (2006) Characterization of RNase R-digested DNA source that consists of lariat and circular RNAs derived from pre-mRNA splicing. Nucl. Acid. Res. 34(8):e63.

49.  Zhang C, Xuan Z, Mandel G, Zhang MQ (2006) A Clustering Property of Highly-degenerate Transcription Factor Binding Sites in the Mammalian Genome. Nucleic Acid Res 34(8):2238-2246.

50.  Zhang C, Zhang X, Zhang MQ, Li Y (2006) Neighbor number, valley seeking and clustering. Review, submitted.

51.  Benita Y, Oosting RS, Xuan Z, Wise MJ, Zhang QM, Humphery-Smith I (2006). Challenges in the prediction of small genes in the human genome. In preparation*. Review.

52.  Smith AD, Sumazin P, Xuan Z, Zhang MQ (2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc. Natl. Acad. Sci. USA, 103:6275-6280.

53.  Das D, Nahle Z, Zhang MQ (2006) Adaptively Inferring Human Transcriptional Subnetworks. Mol Sys Biol. 2:2006.0029.  Commentary1 Commentary2

54.  Zhang MQ (2006) Inferring Gene Regulatory Networks, chapter 21 in Bioinformatics – From Genomics to Therapies. T. Lengauer (ed.), Wiley-VCH.

55.  Zhang C, Li HR, Fan JB, Fu XD and Zhang MQ (2006) Profiling alternative spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics 2006 Apr;7:202.

56.  Rollins RA, Haghighi FG, Edwards JR, Das R, Zhang MQ, Ju J, Bester TH (2006) The Large-Scale Structure of Genomic Methylation Patterns.  Genome Research, 16:157-163.

57.  Zhang MQ (2005) Computational Molecular Biology of Genome Expression and Regulation. PReMI05 Lecture Notes in Computer Science, pp31-38, Springer-Verlag GMbH.

58.  Prasanth KV, Prasanth SG, Xuan ZY, Sachidandam R, Hearn S, Frier SM, Bennett CF, Zhang MQ and Spector DL (2005) Regulating Gene Expression Through RNA Nuclear Retention.  Cell, 123:249-263.

59.  Wang J, Smith PH, Krainer AR, Zhang MQ (2005) Distribution of SR Protein Exonic Splicing Enhancer Motifs in Human Protein-Coding Genes.  Nucl Acid Res, 33:5053-5062.

60.  Xuan ZY, Zhao F, Wang JH, Chen GX and Zhang MQ (2005) Genome-Wide Protomer Extraction and Analysis in Human, Mouse and Rat. Genome Biology, 6:R74.

61.   Zhang MQ (2005) Finding Human Core Promoter Regions. in: Current Protocols in Bioinformatics. (A. D. Baxevanis & D. B. Davison, Eds.), John Wiley & Sons.

62.  Smith AD, Sumazin P, Das D and Zhang MQ (2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Accepted talk, ISMB2005. Bioinformatics. 21 Suppl 1:i403-i412

63.  Zhao F, Xuan ZY, Liu Lihua and Zhang MQ (2005) TRED: a Transcription Regulatory Element Database and a platform for in silico gene regulation studies. Nucl Acid Res, 33:D103-107.

64.  Xuan ZY and Zhang MQ (2005) From worm to human:Bioinformatics approaches to identify FOXO target genes. Special issue on Functional Genomics of Ageing 2004. Mech. Ageing Dev. 126:209-215.

65.  Smith AD, Sumazin P and Zhang MQ (2005) Identifying tissue-specific transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci USA, 102:1560-1565.

66.  Schones DE, Sumazin P and Zhang MQ (2005) Similarity of Position Frequency Matrices for Transcription Factor Binding Sites. Bioinformatics, 21:307-313.

67.  Sumazin P, Chen GX, Hata N, Smith AD and Zhang MQ (2005) DWE: Discriminant Word Enumerator. Bioinformatics, 21:31-38.

68.  Zhang J, Li F, Li J,  Zhang MQ and  Zhang XG (2004) Evidence and Characteristics of Putative Human α Recombination Hotspots. Hum. Mol. Genet. 13:2823-2828.

69.  Long F, Liu H, Hahn C, Sumazin P, Zhang MQ and Zilberstein A (2004) Genome-wide Prediction and Analysis of Function-Specific Transcription Factor Binding Sites. In Silico Biology, 4:0033.

70.  Banerjee N and Zhang MQ (2005) Transcription Regulatory Networks in Yeast Cell Cycle. A chapter in Microarray expression profiling and transcriptional regulatory networks, Shannon F and Rao S eds. In press.

71.  Guigo R and Zhang MQ (2005) Gene predictions and annotations, Chap17 in Mammalian Genomics, eds. A. Ruvinsky and J.A. Marshall Graves. Pp 429 Wallingford:CAB International.

72.  Das D, Banerjee N and Zhang MQ (2004) Interacting Models of Cooperative Gene Regulation. Proc. Natl Acad Sci. USA, 101:16234-16239.

73.  Chen J, Lee S, Sun M, X ZY, Zhou G, Zhang RS, Rowley JD, Zhang MQ and Wang SM (2004) Exhaustive identification of novel transcription units in the human genome using novel SAGE tags. Unpublished.

74.  Dike S, Vivekanand S. Balija, Lidia Gnoj, Zhenyu Xuan, Jacqueline Ou, Theresa Zutavern, Lance E. Palmer, Greg Hannon, Michael Q. Zhang, W. Richard McCombie (2004). The Mouse Genome: Experimental examination of gene predictions and transcriptional start sites. Genome Res 14:2424-2429..

75.  Guigo R, Birney E, Brent M, Dermitzakis E, Pachter L, Roest Crollius H, Solovyev V and Zhang M (2004) Completion of the catalog of protein coding genes in the human genome. Quantitative Biology. Online, http://arxiv.org/abs/q-bio.GN/0410008

76.  Wang JH, Hata N, Fu XD and Zhang MQ (2004). Searching for tissue specific splicing cis-elements in human alternatively spliced genes. Unpublished.

77.  Kato M, Hata N, Banerjee B and Zhang MQ (2004). Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology 5:R56.

78.  Chen GX, Hata N and Zhang MQ (2004). Transcription factor binding element detection using functional clustering of mutant expression data. Nucl. Acid Res. 32:2362-2371.

79.  Banerjee N and Zhang MQ (2003) Identification of cooperativity among transcription factors controlling cell cycle in yeast. Nucl. Acid Res. 31:7024-7031.

80.  Wang, JH, Xuan ZY, Fu XD and Zhang, MQ (2004). Cross-species comparison of alternative splicing between human and mouse. Unpublished.

81.  Zhang MQ (2003) Prediction, Annotation and Analysis of Human Promoters. Cold Spring Harbor Symposium Quantitative Biology 68:217-225, Cold Spring Harbor Press.

82.  Davuluri R and Zhang MQ (2003) Computer software to find genes in plant genomic DNA.
Methods Mol Biol. 236:87-108.

83.  Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ and Ren B (2003) A global transcriptional Regulatory role for c-myc in Burkitt’s lymphoma cells. Proc. Natl. Acad. Sci. USA 100:8164-8169.

84.  Cartegni L, Wang JH, Zhu ZW, Zhang MQ and Krainer AR (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucl. Acid. Res. 31:3568-3571.

85.  Davuluri R, Grosse I and Zhang MQ (2003) Annotation of promoters and first exons in the human genome. Submitted.

86.  Carmell M, Xuan ZY, Zhang MQ and Hannon GJ (2002)  Argonaute proteins :  tentacles that reach into RNAi, stem cell maintenance and tumorigenesis. G&D, 16:2733-2742.

87.  Xuan ZY, Wang JH and Zhang MQ (2002) Computational comparison of two mouse draft genomes and the human goldenpath. Genome Biology, 4(1):R1.

88.  Zhang MQ (2002) Extracting functional information from microarrays: A challenge for functional genomics.
Proc Natl Acad Sci U S A 99:12509-12511.

89.  Nahle Z, Polyakoff J, Davuluri RV, Jacobson MD, McCurrach ME, Narita M, Zhang MQ, Lazebnik Y, Bar-Sagi D and Lowe SW (2002) Direct coupling of the cell cycle and cell death machinery by E2F. Nat. Cell Biol. 4:859-864.

90.  Zhang MQ (2002) Computational prediction of eukaryotic protein-coding genes. Nat. Rev Genet. 3:698-709.

91.  Grosse I, Zhang MQ and Herzel H (2002) On the dynamic origin of isochores. (presented at the CSHL Genome Meeting in May 2001) Submitted.

92.  Saied A. Jaradat, Tetsuya S. Tanaka, Lydia O'Neill, G. Chen, N. Banerjee, Kevin G. Becker, Michael Q. Zhang, Kenneth R. Boheler and Minoru S.H. Ko (2002) Dynamic genetic reprogramming of pluripotent embryonic stem cells during differentiation. Unpublished.

93.  Zhang Y, Mei PC, Lou R, Zhang MQ, Wu G, Qiang B, Zhang ZG and Shen Y(2002). Gene expression profiling in developing human hippocampus.  J. Neurosci. Res. 70:200-208.

94.  Zhang MQ (2003) Using MZEF to Find Internal Coding Exons. In Current Protocols in Bioinformatics, Baxevanis A et al. eds. John Wiley & Sons.

95.  Zhang MQ (2002) Predicting full-length transcripts. Trends Biotechnol. 20:275.

96.  Xuan ZY, McCombie WR and Zhang MQ (2002) GFScan: a gene family search tool at genomic DNA sequence level. Genome Res. 12:1142-1149.

97.  Banerjee N and Zhang MQ (2002) Functional genomics as applied to mapping transcription regulatory networks. Curr. Op. Microbiol. 5:313-317.

98.  Weinmann AS, Bartley SM, Zhang T, Zhang MQ and Farnham PJ (2001). Use of chromatin immunoprecipitation to clone novel e2f target promoters. Mol. Cell Biol. 21:6820-6832.

99.  Davuluri R, Grosse I and Zhang MQ. (2001). Computational identification of promoters and first exons in the human genome. Nat. Genet. 29:412-417.

100.          Zhang T and Zhang MQ (2001). Promoter extraction from GenBank (PEG): automatic extraction of promoter sequences in large sets of genes. Bioinformatics, 12:1232-1233.

101.          Chen G, Jaradat SA, Banerjee N, Tanaka TS, Ko MSH and Zhang MQ (2002). Cluster analysis of microarray gene expression data: application to and evaluation with NIA mouse 15K array on ES cell differentiation. Statistica Sinica, 12:241-262.

102.          Kel AE, Kel-Margoulis OV, Farnham PJ, Stephanie MB, Wingender E and Zhang MQ (2001). Computer-assisted identification of cell cycle-related genes - new targets for E2F transcription factors. J. Mol. Biol. 309:99-120.

103.          Zhang MQ (2001). Computational methods for promoter recognition. Chapter 10 in Current Topics in Computational Biology (Jiang T, Smith T, Xu Y and Zhang MQ eds). pp249-268. MIT Press and TUP.

104.          Wu Q, Zhang T, Cheng J-F, Kim Y, Grimwood J, Schmulz J, Dickson M, Noonan JP, Zhang MQ, Myers RM and Maniatis T. (2001) Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 11:389-404.

105.          Tabaska JE, Davuluri R and Zhang MQ (2001). A novel 3'-Terminal exon recognition algorithm. (Result was presented at CSHL Computational Biology Workshop 9/99). Bioinformatics 17:602-607.

106.          Liu H-X, Cartegni L, Zhang MQ and Krainer AR. (2001) Mechanism of exon skipping caused by a nonsense mutation in the BRCA1 gene. Nature Genetics, 27:55-58.

107.          Zhang MQ (2001). Discriminant analysis and its application in DNA sequence motif recognition. Based on a lecture given at the EBI Symposium: Genome Based Gene Structure Determination.(Jun 1-2,2000, Cambridge, UK) Briefings in Bioinformatics, 1(4)331-342.

108.          Ando S, Sarlis N, Krishnan J, Feng X, Refetoff S, Zhang MQ, Oldfield EH and Yen PM (2001). Brief report: A berrant alternative-splicing of thyroid hormone receptor is a mechanism for thyroid hormone resistance in a thyrotropin-producing pituitary tumor. Molecular Endocrinology, 15:1529-1538.

109.          Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O and Zhang MQ. (2000) A database and statistical analysis of aternative exons. DNA & Cell Biol., 19:739-756.

110.          Davuluri R, Suzuki Y, Sugano S and Zhang MQ. (2000) CART classification of human 5'UTR sequences. Genome Res. 10:1807-1816.

111.          Ioshikhes I and Zhang MQ (2000). Large-scale human promoter mapping using CpG islands. discrimination. Nature Genetics, 26:61-63.

112.          Zhu J and Zhang MQ (2000). Cluster, function and promoter: analysis of yeast expression array. In Proceedings of Pacific Symposium on Biocomputing 2000. R.B. Altman et al. eds., 5:476-487.

113.          Liu, H-X, Chew SL, Cartegni L, Zhang MQ and Krainer AR, (2000). Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. MCB, 20:1063-1071.

114.          Getz G, Levine E, Domany E and Zhang MQ (2000). Super-paramagnetic clustering  of yeast gene expression profiles. Physica A. 279:457-464.

115.          Mayeda A, Badolato J, Kobayashi R, Zhang MQ, Gardiner EM and Krainer AR.(1999) Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing, EMBL 18:4560-4570.

116.          Machida M, Yamazaki S, Kunihiro S, Tanaka T, Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S, Sekine M, Ogudhi A, Nagai Y, Sakai M, Aoki K, Ogura K, Kudoh Y, Kikuchi H, Zhang MQ and Yanagida M.(2000) A. 38 kb segment containing cdc2 gene from the left arm of fission yeast chromosome II: sequence analys is and characterization of the genomic DNA and cDNAs encoded on the segment, Yeast, 16:71-80.

117.          Zhang, M.Q.(1999) Large scale gene expression data analysis: a new challenge to computational biologists, Genome Res. 9:681-688.

118.          Tabaska, J.E. and Zhang, M.Q.(1999), Detection of polyadenylation signals in human DNA sequences. Gene, 231:77-86.

119.          Ioshikhes, I., Trifonov, E.N. and Zhang, M.Q. (1999) Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc. Natl. Acad. Sci. USA, 96:2891-2895.

120.          Zhang, M.Q., (1999) Promoter Analysis of Co-regulated Genes in the Yeast Genome. Computers and Chemistry, 23:233-250.

121.          Zhu, J. and Zhang, M.Q., (1999) SCPD: A Promoter Database of Yeast Saccharomyces cerevisiae, Bioinformatics, 15:607-611.

122.          Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998). Comprehensive Identification of Cell Cycle Regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Mol. Biol. Cell. 9:3273-3297.

123.          Liu, H.-X., Zhang, M.Q. and Krainer, A.R., (1998). Identification of Functional Exonic Splicing Enhancer Motifs Recognized by Individual SR Proteins. Gene & Dev. 12:1998-2012.

124.          Zhang, M.Q., (1998). Identification of Protein Coding Regions in Arabidopsis thaliana Genome Based on Quadratic Discriminant Analysis. Mol. Plant. Biol., 37:803-806.

125.          Zhang, M.Q., (1998). Identification of Human Gene Core-promoters In Silico. Genome Res., 8:319-326.

126.          Zhang, M.Q., (1998). Statistical Features of Human Exons and Their Flanking Regions. Hum. Mol. Genet., 7:919-932.

127.          Zhang, M.Q.,(1998). A Discrimination Study of Human Core-promoters, in Proceedings of Pacific Symposium on Biocomputing 1998. R.B. Altman et al. eds. pp240-251, World Scientific, Singapore.

128.          Chen, T., and Zhang, M.Q. (1998). POMBE: A Fission Yeast Gene-finding and Exon-intron Structure Prediction System. Yeast, 14:701-710.

129.          Zhang, M.Q. (1997). Identification of Protein Coding Regions in the Human Genome Based on Quadratic Discriminant Analysis. Proc. Natl. Acad. Sci. USA, 94:565-568.

130.          N.Kaplan, M.Lodhi, A.Johnson, M.Q.Zhang, T.G.Marr and W.R.McCombie (1995), The Schizosaccharomyces Pombe Genome Project, Cold Spring Harb. Symp., Genome Mapping and Sequencing.

131.          M.Q.Zhang and T.G.Marr (1995), Molecular Sequence Alignment Seen as Random Path Analysis, J. Theor. Biol., 174:119-130.

132.          M.Q.Zhang and T.G.Marr (1995), Exploratory Analysis of Long Genomic DNA Sequences using the Wavelet Transform: Examples using Polyomavirus Genomes, Genome Sequencing and Analysis Conference VI, Hilton Head, NC, pp.72, Mary Ann Liebert, Inc..

133.          S.Stamm, M.Q.Zhang, T.G.Marr and D.M.Helfman (1994), A Sequence Compilation and Comparison of Exons That Are Alternatively Spliced in Neurons, Nucl. Acid. Res., 22:1515-1526.

134.          M.Q.Zhang and T.G.Marr (1994), Statistical Analysis of the fission yeast genomic DNA sequences and gene recognition, Nucl. Acid. Res., 22:1750-1759.

135.          M.Q.Zhang and T.G.Marr (1994), Genome Mapping with Random Anchored Clones: A Discrete Theoretical Analysis, J. Stat. Phys., 73:611-623.

136.          M.Q.Zhang and T.G.Marr (1993), Large-scale Structure of Yeast Chromosome III: Implications in Genome Evolution, Cold Spring Harb. Symp., Genome Mapping and Sequencing.

137.          M.Q.Zhang and T.G.Marr (1993), A Weight Array Method for Splicing Signal Analysis, CABIOS 9:499-509.

138.          M.Q.Zhang and T.G.Marr (1993),Genome Mapping by Nonrandom Anchored Clones: A Discrete Theoretical Analysis, Proc. Natl. Acad. Sci. USA, 90:600-604.

139.          M.Q.Zhang (1991), How to Find the Lax Pairs from the Yang-Baxter Equations, Comm. Math. Phys.141:523.

140.          M.Q.Zhang (1991), The Nonuniform Hard Rod Fluids Revisited, J. Stat. Phys.342:1191.

141.          M.Q.Zhang (1991), Exact Response Functions of a 2D Fermion Fluid, J. Math. Phys. 32:1344.

142.          M.Q.Zhang (1991), Crystallization of One-dimensional Hard Rods with a Periodic Interaction, J. Phys. A24:3949.

143.          M.Q.Zhang (1990), Zero-thickness Membrane Interface and Schrodinger Equation, {\em Phys. Rev.,A42:4588.

144.          M.Q.Zhang and J.K.Percus (1990), A Recursive Density Functional Formalism of Nonuniform Fluids, J. Chem. Phys. 92:6779.

145.          M.Q.Zhang (1990), Entropy Functional of a Nonuniform Ising Model on a Two Row Lattice, J. Phys., A23:1.

146.          J.K.Percus and M.Q.Zhang (1989), The Quasi-One Dimensional Hard Square Gas, Mol. Phys.,69:347.

147.          M.Q.Zhang (1989). Inhomogeneous Ising Model on a Multiconnected Networks, J.Stat.Phys., 56:695.

148.          M.Q.Zhang and J.K.Percus (1989), Direct Correlations of the Capillary Wave Model and Construction of Free Energy Density Functional for the Liquid-Vapor Interface System, J. Chem. Physics, 90:3795.

149.          M.Q.Zhang (1989), A Fast Vectorized Multispin Coding Algorithm for 3D Monte Carlo Simulations Using Kawasaki Spin-exchange Dynamics, J.Stat.Phys., 56:939.

150.          M.Q.Zhang and J.K.Percus (1988), 1-D Inhomogeneous Ising Model with Periodic Boundary Condition, Phys.Rev., B38:11737.

151.          G.Ord, J.K.Percus and M.Q.Zhang (1988), Energetics of a Discrete Interface, Nucl.Phys., B305[FS23]:271.

152.          M.Q.Zhang (1988), Exact Pair Correlation Function for Ising Spins with Competing Dynamics,J.Stat.Phys., 53:1217.

153.          M.Q.Zhang, J.S.Wang, J.L.Lebowitz and J.L.Valles (1988), Power Law Decay of Correlations in Stationary Nonequilibrium Lattice Gases with Conservative Dynamics, J.Stat.Phys., 52:1461.

154.          M.Q.Zhang (1988), Nonequilibrium Steady States of Some Stochastic Lattice Gas Models, Nucl.Phys.,B(Proc.Suppl.)5A:278.

155.          M.Q.Zhang (1987), Supersymmetrical Approach to Critical Dynamics of Relaxational Models, Phys.Rev., B36:3824.

156.          M.Q.Zhang (1987), Exact Results on the Steady State of a Hopping Model,Phys.Rev., A35:2266.

157.          J.Krug,J.L.Lebowitz, H.Spohn and M.Q.Zhang (1986), The Fast Rate Limit of Diffusive System, J.Stat.Phys., 44:535

Teaching Experience

 

1991         Teaching in mathematics, Department of Mathematics, University of Rutgers
1998         Invited lecture for CSH course on Computational Genomics (organizers: Pearson&Smith)
1999-       Teaching in Computational Biology and Bioinformatics, Watson School of Biological Sciences
2007        The Croucher Foundation Advanced Study Institute: Genome Informatics: From gene finding to systems biology, Hong Kong University, Faculty of Medicine
2007        Graduate Summer School on Bioinformatics in China or GSSBC2007, Tsinghua University, Beijing
2008          Pre-workshop on Systems Biology: Global Regulation of Gene Expression, Mar 26

Students Supervised

 

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-       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, (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-       Chaolin Zhang (Grad. Student, Biomedical Engineering, FUNY/Stony Brook)
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-       Herry Lin (URP'2003 from Harvard)
2003-       Alexey Smirnov (SUNYSB Ph.D. student from Physics)
2003        Chris Maher (SUNYSB, Rotation gratuate student from Biomedical Engineering)
2002-2003   Mamoru Kato (vsiting Ph.D. student from u. Tokyo)
2002-summer Jackie Ou (URP'2003 from Duke)
2002-2003   Lihua Liu (SUNY/Stony Brook, Computer Science M.S. student)
2001-2002   Zhengwei Zhu (SUNY/Stony Brook rotation and Ph.D. student from BioMedical Engineering Program)
2001        Elaine Shum (PFF high school student)
2001-summer Joe Markson (URP'2001 student, co-supervised with Josh Huang)
2001-summer Michael Hoffman (URP'2001 student)
2000-2001   William Palumbo (High School Student)
2000-2001   Apra Mattoo (High school student)
2000 summer Chris Brunson (High school student in NY Academy of Sciences program.
2000 summer         Maria Vichnevskaia (URP'2000 student)
2000-       Nila Banerjee (Ph.D. student, Department of Bioinformatics, George Masson University)
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 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

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-       Dr. Li Wang (co-supervisor, Tsinghua U.)
2006-2007   Dr. Fei Li (visiting from Tsinghua University)
2005-       Dr. Xiaoyue Zhao
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-       Dr. Andrew Smith
2003-2005   Dr. Pavel Sumazin (NSF fellow, on leave from Portland StateUniversity, now a Research assist professor, Columbia U.)
2003-2005   Dr. Debopryia Das (Staff Scientist, NLBL)
2003-2005   Dr. Rajdeep Das
2002-2005   Dr. Fang Zhao 
2001-2005   Dr. Jinhua Wang (Assistant Professor, NYU, Med. School)
2000-2003   Dr. Naoya Hata
2000-2003    Dr. Ivo Grosse (CSHL Asssociation Fellow)
2000-2008   Dr. Zhenyu Xuan (Now, Research Assistant Professor, Bioinformatics Core Manager, CSHL)
1999-2001   Dr. Nathalie Pavy (NATO postdoc, co-supervised with Lincoln Stein)          
1999-2001   Dr. D.V.V. Ramana (Head, Computational Biology, Wistar Institute)
1999-2001   Dr. Theresa Zhang
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 Coolege of Medcine
1997-1999   Dr. Jack Tabaska, moved on to a Bioinformatic Scientist position at Monanto
 



Programmers Supervised

 

2005        Giri Pemmasani
2002-2003   Lihua Liu
2001-       Vsevolod (Simon) Ilyushchenko (a Google program analyst)
2000-       Dr. Gengxin Chen
1999-2000   Dmitri Priimak 
1997-1998   Zhanna Ioschikhes, moved on to a programmer position at Computer Associate
 
 
 
 
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