Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics. 2011 Nov 1;27(21):3010-6. Epub 2011 Sep 6. PubMed PMID: 21896509; PubMed Central PMCID: PMC3198574. 2011 - Publication
Yang S, Yalamanchili HK, Li X, Yao KM, Sham PC, Zhang MQ, Wang J. Correlated evolution of transcription factors and their binding sites. Bioinformatics. 2011 Nov 1;27(21):2972-8. Epub 2011 Sep 6. PubMed PMID: 21896508. 2011 - Publication
Zhirui Hu, Minping Qian and Michael Q. Zhang. Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. BMC Systems Biology, 2011. 2011 - Publication
Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ , Sedel F, Jourdren L, Coulpier F, Triller A, Spector DL, Bessis A (2010)
“ A long nuclear -retained non-coding RNA regulates synaptogenesis by modulating gene expression. ”EMBO J, 29:3082-93. 2010 - Publication
Wang SM, Zhang MQ. (2010) “Transcriptome study for early hematopoiesis - achievement, challenge and new opportunity.” J Cell Physiol 223(3):549-52. 2010 - Publication
Kinney JB, Murugan A, Callan CG Jr, Cox EC. (2010) “Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence.” PNAS May 3. [Epub ahead of print] 2010 - Publication
Wang SM, Zhang MQ. (2010) “Transcriptome study for early hematopoiesis - achievement, challenge and new
opportunity.” J Cell Physiol 223(3):549-52. 2010 - Publication
Mitra R, Bandyopadhyay S, Maulik U, Zhang MQ . (2010)
“ SFSSClass: an integrated approach for miRNA based tumor classification.BMC Bioinformatics. ” 2010 Jan 18;11 Suppl 1:S22. 2010 - Publication
Chicas A, Wang X, Zhang C, McCurrach M, Zhao Z, Mert O, Dickins RA, Narita M, Zhang M, Lowe SW. (2010) “Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence.” Cancer Cell 17(4):376-87. 2010 - Publication
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ , Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. (2010) 2010 - Publication
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.
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.
Genome Therapeutics Corp. 2002.
Advisor, Yang Ming Medical School, Taipei, Taiwan. Aug. 2001.
SK Corporation, 2000.
Tularik Genomics, 1999-present
Otsuka Amenrican Pharmaceutical, Inc. 1997-1998.
Visiting member at NCBI, NLM/NIH, Sept-Oct, 1995.
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 [email@example.com] (Grad. Student, Biology, NYU)
2005- Fang Fang, Jun Li, Jing Zhang, Shicai Fan, Tingting Li, Bo Jiang, Xi Wang, Xuebing Wu, Xiaowo Wang, Yunzhang Zhu, (MS. And Ph.D. students, Tsinghua U. China)
2005 Vineeta Agarwala (URP-05 from Stanford).
2005 Evan Santo (Rotation graduate student, Watson School of Biological Sciences, Cold Spring Harbor Lab)
2004-2008 Chaolin Zhang (Grad. Student, Biomedical Engineering, SUNY/Stony Brook; now postdoc at Rockeffeler)
2004 Siddharth Srivastava (URP-04 from Columbia)
2003-2004 Yair Benita (Grad. Student, Pharmaceutical Proteomics, Utrecht University, The Netherlands. Now postdoc at Harvard)
2003-2006 Dustin Schones (SUNYSB Ph.D. student from Physics, now postdoc at NIH)
2003 Henry Lin (URP-03 from Harvard)
2003 Chris Maher (SUNY/Stony Brook rotation and Ph.D graduate student from Biomedical Engineering program).
2002-2003 Mamoru Kato (one-year visiting Ph.D. graduate student from U. of Tokyo)
2002-summer Jackie Ou (URP-02 from Duke)
2001 Elaine Shum (PFF high school student)
2001-2002 Zhenwei Zhu (SUNY/Stony Brook rotation and Ph.D. student from BioMedical Engineering Program)
2001-summer Joe Markson (URP'01 student, co-supervised with Josh Huang)
2001-summer Michael Hoffman (URP'2001 from UT)
2000-2001 William Palumbo (High School Student)
2000-2001 Apra Mattoo (High school student)
2000 Johannes (Yogi) Jaeger (Rotation graduate student, Genetics, SUNYSB)
2000 summer Chris Brunson (High school student in NY Academy of Sciences program).
2000 summer Maria Vichnevskaia (URP'00 student)
2000-2004 Nila Banerjee (Ph.D. student, Department of Bioinformatics, George Masson University. Move on as a postdoc at Columbia University Genome Center. Now a research scientist at Philip Research)
2000- Yan Zhang (Ph.D. student, Department of Biomedical Engineering, School of Basic Medicine, Peking Union Medical College)
2000 Elizabeth Thomas (Rotation Graduate Student from Watson School)
2000 Jenny Hizver (SUNY/Stony Brook rotation and Ph.D graduate student from Genetics Program)
1999 Adriano Costa de Alcantara (URP-99 student, went back to Brazil)
1998-1999 Brain Chang, Junior-Senior, Dept. of Molecular Biology, Harvard University (Thesis advisor: Tom Maniatis).
1997 Robert Klein, Senior, Dept. of Molecular Biology, Harvard University (Thesis advicor: Walter Gilbert) (went onto graduate student at Wash. U.)
1996-1997 Tim Chem, Ph.D., Dept. of Computer Science, SUNY at Stony Brook (Thesis advisor: Steve Skiena). (went onto Harvard Med. School as a postdoc in George Church's Lab. He became a faculty member at USC in 2000.).
1996 Will Orrick, Ph.D. Dept. of Physics, SUNY at Stony Brook (Thesis advisor: Barry McCoy). (went onto Australia for a postdoctoral position).
Postdoctoral Fellows and Visiting Scientists
2009- Dr. Justin Kinney (from Princeton U)
2009- Dr. Monica Sleumer (Tsinghua U. from UBC)
2009 Dr. Kaz Wrzeszcynski (from Colombia U)
2009- Dr. Martin Akerman (Joint postdoc with Krainer)
2009- Dr. Eric Man-Hung Tang (from U. Copenhagen)
2009- Dr. Zhihua Zhang (from Michigan U)
2009- Dr. Kato Mamoru (Tokyo U/Riken)
2009- Dr. Wenyu Chung (from Penn State U)
2008- Dr. Darrin Lewis (From Columbia U)
2008-2009 Dr. Michaela Oswald-Pisarski
2008- Dr. Chenghai Xue (from Tsinghua U)
2008 Dr. Vladimir A. Kuznetsov, visiting scientist from Bioinformatics Institute of Singapore.\
2007 Dr. Xinying Ren, (now working for Dutch Embassy in China) (jointly supervised with Doreen Ware)
2006 Prof. Sue Brown (co-supervisor, CAPS awardee at KSU)
2006 Dr. Sanghamitra Bandyopadhyay [firstname.lastname@example.org] (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
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
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