| System Biology - Lang Li Lab |
Research
Develop molecular network for estrogen signaling pathways for cancer cells
- Estrogen receptor regulatory network
- Estrogen signal pathway
- eQTL network
Software and Databases
GenePattern Data integration tool
http://www.broad.mit.edu/cancer/software/genepattern/
GSEA Gene Set Enrichment Analysis
http://www.broad.mit.edu/gsea/
MAT Tiling array data analysis
http://chip.dfci.harvard.edu/~wli/MAT/
MDscan TF binding site scan
http://ai.stanford.edu/~xsliu/MDscan/
MotifModeler Motif identification
http://motifmodeler.org/
Mixture Model Motif pattern identification
SAM, PAM, and GSA Significant analysis of microarray
http://www-stat.stanford.edu/~tibs
Selected Publications
Wang G., Wang Y., Wang, C., Huang Y, Huang K., Huang T., Nephew K., Li L., and Liu Y. RNA Polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation, Plos One 2010 (in press).
Jeong J., Li L., Liu Y., Nephew K.P., Huang T., Shen C. An Empirical Bayes Model for Gene Expression and Methy- lation Pro files in Antiestrogen Resistant Breast Cancer. BMC Biomedical Genetics, 2010, 3: 55.
Wang G., Yadong Wang, Mingxiang Teng, Denan Zhang, Li L, and Yunlong Liu, Signal Transducers and Activators of Transcription-1 (STAT1) Regulates microRNA Transcription in Interferon gamma-Stimulated HeLa Cells. Plos One, 2010 July 26; 5(7):e11794.
Feng W., Liu Y., Wu J., Nephew K.P., Huang T., Li L. A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology. BMC Genomics, 2008, 9, s23.
Shen C., Wang Z., Shanker G., Zhang X., and Li L. A Hierarchical Statistical Model to Assess the Confidence of Peptides and Proteins Inferred from Tandem Mass Spectrometry. Bioinformatics 2008, 24, 202-208.
Wang G., Wang X., Li L., Nephew N.P., Edenberg H.J., Zhou F.C., Liu Y. Identification of Transcription Factor and microRNA Binding Sites from Array-derived Gene Expression Data, BMC Genomics 2008 9 Suppl 1: p. S17.
Wang X., Wang G., Shen C., Li L., Edenberg H.J., Sanford J., Liu Y., Refining Detection of Protein Binding Regions Using Pyrosequencing-derived RNA Fragments, BMC Genomics 2007 2008 9 Suppl 1: p. S19.
Khalili A., Potter D., Yan P., Li L., Gray J., Huang T., Lin S. Gamma-Normal-Gamma Mixture Model for Detecting Differentially Methylated Loci in three cancer cell lines. Cancer Informatics 2007, http://la-press.com/journals.php?pa=toc&journal_id=10&folder_id=15.
Fan M., Yan P. S., Hartman-Frey C., Chen L., Paik H., Abbosh P., Cheng A. S. L, Li L., Huang H. M. T., and Nephew K. Breast cancer cells with acquired resistance to 4-hydroxytamoxifen and fulvestrant display divergent gene expression and DNA methylation signatures. 2006, Cancer Research, 66, 11964-11966
Li L., Cheng A. S. L., Jin V., Paik H. H., Fan M., Li X., Zhang W., Robarge J., Balch K., Davuluri R. V., Kim S., Huang T., Nephew K. A Mixture Model Based Discriminate Analysis for Identifying Ordered Transcription Factor Binding Site Pairs in Gene Promoters Directly Regulated by Estrogen Receptor-a. Bioinformatics, 2006, 22: 2210-2216.
Lim Y., Li L., Desta D., Zhao Q., Rae, J., Flockhart D. A., and Skaar T. Endoxifen, a secondary metabolite of tamoxifen, and 4-OH-tamoxifen induce similar changes in global gene expression patterns in MCF-7 breast cancer cells. Journal of Pharmacology and Experimental Therapeutics, 2006, 318: 502-513.
Shen, C., Li L., and Chen J. A statistical framework to discover true associations from multi-protein complex pull-down proteomics data sets. Proteins: Structure, Function, and Bioinformatics 2006, 64, 436-443.
Li L, Shi H, Yiannoutsos C, Huang Tim and Nephew K. Epigenetic hypothesis tests for methylation and acetylation in a triple microarray system. Journal of Computational Biology. 2005, 12, 370-390.
Shen C, Huang Y, Liu Y, Wang G, Zhao Y, Wang Z, Teng M, Wang Y, Flockhart DA, Skaar TC, Yan P, Nephew KP, Huang TH, Li L. A Modulated Empirical Bayes Model for Identifying Topological and Temporal Estrogen Receptor α Regulatory Networks in Breast Cancer. BMC Syst Biol. 2011 May 9; 5(1):67.
Jeong J., Li L., Liu Y., Nephew K.P., Huang T., Shen C. An Empirical Bayes Model for Gene Expression and Methy- lation Pro files in Antiestrogen Resistant Breast Cancer. BMC Biomedical Genetics, 2010, 3: 55.
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Wang G., Wang Y., Shen C., Huang Y., Huang K., Huang T., Nephew K., Li L., and Liu Y., RNA Polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation, PloS One 2010, 5(11); e13798.
Wang G., Wang Y., Teng M., Zhang D., Li L., and Liu Y. Signal Transducers and Activators of Transcription-1 (STAT1) Regulates microRNA Transcription in Interferon gamma-Stimulated HeLa Cells. PloS One, 2010 July 26; 5(7):e11794.
