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Dan L. Duncan Cancer Center

Houston, Texas

BCM has 25 departments and more than 90 research and patient-care centers.
Dan L. Duncan Cancer Center
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Wei Li, Ph.D. - Biostatistician

Dr. Wei LiAssociate Professor
Division of Biostatistics, Dan L. Duncan Cancer Center
Department of Molecular and Cellular Biology

Phone: 713-798-7854
Fax: 713-798-2716
E-mail: WL1@bcm.edu
Website: http://lilab.openwetware.org/

Training

2004–2007 - Postdoctoral Research Fellow, Department of Biostatistics and Computational Biology,
Dana Farber Cancer Institute / Harvard School of Public Health, Boston, MA
1998–2003 - Ph.D. in Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences,
Beijing, China
1994–1998 -B.S. in Biophysics, Department of Physics, B.A. in International Finance, School of
Business, Nanjing University, Nanjing, China

Previous Positions and Experiences

2004–2007 - Dana Farber Cancer Institute / Harvard School of Public Health, Boston, MA

  • Development of statistical and computational algorithms for Affymetrix genome tiling microarrays,
    which aims to identify genome-wide transcription factor binding sites using Chromatin
    ImmunoPrecipitation coupled with DNA microarray analysis (ChIP-chip)
  • Identification of the regulatory mechanisms of key cancer transcription factors by integrating the
    data from ChIP-chip, gene expression profiling and sequence motif finding

2000–2004 - Beijing Genomics Institute, Chinese Academy of Sciences, Beijing, China

  • Bioinformatics group leader of the Sino-Danish pig genome and the anti-SARS genome projects
  • Sequence analysis of the T. tengcongensis thermophilic eubacterium genome project, China’s first
    whole genome sequencing and analysis effort
  • Participation in the human genome and Chinese hybrid-rice genome projects

1999-2003 - Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

  • Design of mathematical models for whole-genome based phylogenetic study

Other Academic Experiences

2005-present - Member, International Society for Computational Biology (ISCB)
2004-present - Reviewer, Bioinformatics, BMC Bioinformatics, Genome Research and International
conference on Intelligent Systems for Molecular Biology (ISMB)

Honors and Awards

2006 - Best Poster Award, the 3rd Annual DF/HCC Breast Cancer Symposium
2006 - Honorable Mention, the 20th Annual HSPH Poster & Exhibit Day
2005-2006 - Fellowship, Cold Spring Harbor Laboratory Systems Biology Meeting and Annual Meeting
of the International Society for Computational Biology (ISMB)
1999-2003 - President Scholarship, Chinese Academy of Sciences
1994 - First Prize, the 10th National Physics Olympics Competition in China

Peer Reviewed Publications

Selected Publications:

Johnson D*, Li W* ,…, Struhl K, Myers RM, Lieb JD, Liu XS.: Systematic evaluation of variability in simulated ChIP-chip experiments. Genome Res. accepted (* joint first authors)

Li W, Carroll JS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides. BIOCOMP'07 Accepted (acceptance rate 27%), BMC Genomics.

Wang Q, Li W, Liu XS, Carroll JS, Janne OA, Keeton EK, Chinnaiyan AM, Pienta KJ and Brown M: A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell 27 (2007) 380-392. (Featured Article)

Johnson WE*, Li W*, Meyer CA*, Gottardo R, Carroll JS, Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. U S A 103 (2006) 12457-12462. (* joint first authors)

Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS and Brown M: Genome-wide analysis of estrogen receptor binding sites. Nat. Genet.38 (2006) 1289-1297.

Ji X*, Li W*, Song J, Wei L and Liu XS: CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 34 (2006) W551-554. (* joint first authors)

Li W, Meyer CA and Liu XS: A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 21 Suppl 1 (ISMB2005) i274-i282.

Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA and Brown M: Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1. Cell 122 (2005) 33-43.

Li W, Shi J, Wang X, Han Y, Tong W, Ma L, Liu B and Cai B: Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6. Gene 336 (2004) 231-240.

A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). Chin. Sci. Bull. 48 (2003) 941-948. (joint first author).

Bao Q*, Tian Y*, Li W*, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J and Yang H: A Complete Sequence of the T. tengcongensis Genome. Genome Res. 12 (2002) 689-700. (* joint first authors)

Li W, Fang W, Ling L, Wang J, Xuan Z and Chen R: Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis. J. Biol. Phys. 28 (2002) 439-447.

International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921. (list author)

All Publications

2007

Yagi S, etc. Tissue specific gene expression profile emerged from genome-wide DNA methylation profile of T-DMRs identified with mouse promoter tiling array. Submitted (2007).

Wade JT*, Li W*, Liu XS and Struhl K: Distinguishing function from noise: identification of functional protein-DNA interactions from genome-wide binding profiles. Submitted to Molecular Cell (* joint first authors)

Xia X, Lemieux M, Li W, Carroll JS, Brown M, Liu XS and Kung A: Integration of chromatin binding and gene expression identifies 2-oxoglutarate-Fe(2+) dioxygenases as primary HIF-1 targets and reveals determinants of hypoxic responses. Submitted to Nature.

Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS and Brown M: FoxA1 translates epigenetic signatures into lineage-specific transcription. Cell (accepted 2007).

Johnson D*, Li W* ,…, Struhl K, Myers RM, Lieb JD, Liu XS.: Systematic evaluation of variability in simulated ChIP-chip experiments. Genome Res. accepted (* joint first authors)

O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser R, Wong KK, Li W, KcKenna K, Liu XS, Neuberg D, Silverman L, DeAngelo D, Kutok J, Rothstein R, DePinho R, Chin L, Lee C and Look AT: Tandem Duplication as a Novel Mechanism of MYB Activation in Human T-ALL. The Journal of Experimental Medicine (accepted 2007).

Gottardo R, Li W, Liu XS and Johnson WE: A flexible and powerful Bayesian hierarchical model for ChIP-chip experiments. Biometrics (2007).

Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R and Liu XS: Model-based analysis of two-color arrays (MA2C). Genome Biol 8 (2007) R178.

Li W, Carroll JS, Brown M and Liu XS: xMAN: extreme MApping of OligoNucleotides. Accepted, BIOCOMP'07 (acceptance rate 27%), BMC Genomics (2007).

Wang Q, Li W, Liu XS, Carroll JS, Janne OA, Keeton EK, Chinnaiyan AM, Pienta KJ and Brown M: A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell 27 (2007) 380-392. (Featured Article)

Song J, Maghsoudi K, Li W, Fox E, Quackenbush J and Liu XS: Microarray Blob-Defect Removal Improves Array Analysis. Bioinformatics 23 (2007) 966-971.

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol 8 (2007) R45. (list author)

2006

Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS and Brown M: Genome-wide analysis of estrogen receptor binding sites. Nat. Genet.38 (2006) 1289-1297.

Johnson WE*, Li W*, Meyer CA*, Gottardo R, Carroll JS, Brown M and Liu XS: Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. U S A 103 (2006) 12457-12462. (* joint first authors)

Ji X*, Li W*, Song J, Wei L and Liu XS: CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 34 (2006) W551-554. (* joint first authors)

Nelson EA, Walker SR, Li W, Liu XS and Frank DA: Identification of Human STAT5-dependent Gene Regulatory Elements Based on Interspecies Homology. J. Biol. Chem. 281 (2006) 26216-26224.

Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, Li W, Liu XS, Young RA and Look AT: Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. Blood 108 (2006) 986-992.

The DNA sequence, annotation and analysis of human chromosome 3. Nature 440 (2006) 1194-1198. (list author)

2005

Li W, Meyer CA and Liu XS: A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 21 Suppl 1 (ISMB2005) i274-i282.

Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA and Brown M: Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1. Cell 122 (2005) 33-43.

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 6 (2005) 70. (list author)

Yu Z, Li Y, Meng Q, Yuan J, Zhao Z, Li W, Hu X, Yan B, Fan B, Yu S and Li N: Comparative analysis of the pig BAC sequence involved in the regulation of myostatin gene. Sci. China C Life Sci. 48 (2005) 168-180.

The Chinese Human Genome Sequencing Consortium: “Beijing Region” (3pter-D3S3397) of the human genome: Complete sequence and analysis. Sci. China C Life Sci. 48 (2005) 311-329. (list author)

2004

Li W, Shi J, Wang X, Han Y, Tong W, Ma L, Liu B and Cai B: Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6. Gene 336 (2004) 231-240.

International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature 431 (2004) 931-945. (list author)

Li Y, Luo C, Li W, Xu Z, Zeng C, Bi S, Yu J, Wu J and Yang H: Structure-based preliminary analysis of immunity and virulence of SARS coronavirus. Viral Immunol. 17 (2004) 528-534.

Wang J, Xue Y, Feng X, Li X, Wang H, Li W, Zhao C, Cheng X, Ma Y, Zhou P, Yin J, Bhatnagar A, Wang R and Liu S: An Analysis of the Proteomic Profile for Thermoanaerobacter Tengcongensis under Optimal Culture Conditions. Proteomics 4 (2004) 136-150.

Lu H, Zhao Y, Zhang J, Wang Y, Li W, Zhu X, Sun S, Xu J, Ling L, Cai L, Bu D and Chen R: Date of origin of the SARS coronavirus strains. BMC Infect. Dis. 4 (2004).

2003

Wang J, Wen J, Li J, Yin J, Zhu Q, Wang H, Yang Y, Qin E, You B, Li W, Li X, Huang S, Yang R, Zhang X, Yang L, Zhang T, Yin Y, Cui X, Tang X, Wang L, He B, Ma L, Lei T, Zeng C, Fang J, Yu J, Yang H, West MB, Bhatnagar A, Lu Y, Xu N and Liu S: Assessment of Immunoreactive Synthetic Peptides from the Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus. Clin. Chem. 49 (2003) 1989-1996.

A complete sequence and comparative analysis of a SARS-associated virus (Isolate BJ01). Chin. Sci. Bull. 48 (2003) 941-948. (joint first author)

A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China. Genomics Proteomics Bioinformatics 1 (2003) 101-107. (joint first author)

Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04). Genomics Proteomics Bioinformatics 1 (2003) 180-192. (joint first author)

Evolution and Variation of the SARS-CoV Genome. Genomics Proteomics Bioinformatics1 (2003) 216-225. (joint first author)

Qi Z, Hu Y, Li W, Chen Y, Zhang Z, Sun S, Hu H, Zhang J, Bu D, Ling L and Chen R: Phylogeny of SARS-CoV as Inferred from Complete Genome Comparison. Chin. Sci. Bull. 48 (2003) 1175-1178.

2002

Bao Q*, Tian Y*, Li W*, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J and Yang H: A Complete Sequence of the T. tengcongensis Genome. Genome Res. 12 (2002) 689-700. (* joint first authors)

Li W, Fang W, Ling L, Wang J, Xuan Z and Chen R: Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis. J. Biol. Phys. 28 (2002) 439-447.

Ling L, Wang J, Cui Y, Li W and Chen R: Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms. Mol. Phylogenet. Evol. 25 (2002) 101-111.

Zhong L, Wang K, Tan J, Li W and Li S: Putative cytochrome P450 genes in rice genome (Oryza sativa L. ssp. indica) and their EST evidence. Sci. China C Life Sci. 45 (2002) 512-517.

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science296 (2002) 79-92. (list author)

2001

International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921. (list author)

A draft sequence of the rice (Oryza sativa ssp. indica) genome. Chin. Sci. Bull. 46 (2001) 1937-1942. (list author)

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