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.

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