Lei Li Associate Professor of Biological Sciences and Mathematics Contact Information E-mail: lilei@usc.edu Phone: (213) 740-2407 Office: MCB 416E LINKS Personal Website

Postdoctoral Training

• Postdoc, UCLA, Fall 2000   

Academic Appointment, Affiliation, and Employment History

• Assistant Professor, Florida State University, 08/01/1998-05/30/2002  

Description of Research

Summary Statement of Research Interests

Research Specialties

Affiliations with Research Centers, Labs, and Other Institutions

• Center for Computational and Experimental Genomics,http://www-hto.usc.edu

Publications

Book Chapter

• Li, L. M., Cheng, C. (2008). Differentiation Detection in Microarray Normalization in in DNA Microarray Normalization. CRC press.
• Li, L. M. (2003). Blind Inversion needs distribution (BIND): the general notion and case studies, in Festschrift for Professor Speed’s 60th Birthday. (Vol. 40). pp. 273-293. IMS Lecture Note Series.

Journal Article

• Cheng, C., Li, L. M., Alves, P., Gerstein, M. (2009). Systematic identification of transcription factors associated with patient survival in cancers. BMC Genomics. Vol. 10 (2009/05/16), pp. 225.
• Kim, J. H., Kim, W. C., Waterman, M. S., Park, S., Li, L. M. (2009). HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. Bioinformatics. Vol. 25 (182009/06/30), pp. 2430-1.
• Wei, M., Fabrizio, P., Madia, F., Hu, J., Ge, H., Li, L. M., Longo, V. D. (2009). Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension. PLoS Genet. Vol. 5 (52009/05/09), pp. e1000467.
• Ge, H., Wei, M., Fabrizio, P., Hu, J., Cheng, C., Longo, V. D., Li, L. M. (2009). Comparative analyses of time-course gene expression profiles of the long-lived sch9 mutant. Nucleic Acids Research.
• Ge, H., Cheng, C., Li, L. M. (2008). A Probe-Treatment-Reference (PTR) Model for the Analysis of Oligonucleotide Expression Microarrays. BMC Bioinformatics. Vol. 9, pp. 194.
• Cheng, C., Li, L. M. (2008). Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS ONE. Vol. 3, pp. e1989. doi:10.1371/journal.pone.0001989.
• Cheng, C., Li, L. M. (2008). Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics. Vol. 9, pp. 116.
• Wei, M., Fabrizio, P., Hu, J., Ge, H., Cheng, C., Li, L. M., Longo, V. D. (2008). Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9. PLoS Genet. Vol. 4 (12008/01/30), pp. e13.
• Cheng, C., Yan, X., Sun, F., Li, L. M. (2007). Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics. Vol. 8, pp. 452.
• Cheng, C., Fabrizio, P., Ge, H., Wei, M., Longo, V. D., Li, L. M. (2007). Significant and Systematic Expression differentiation in Long-lived Yeast Strains. PLoS ONE. Vol. 2 (10), pp. e1095.
• Kim, J. H., Waterman, M. S., Li, L. M. (2007). Diploid Genome Reconstruction of Ciona intestinalis and Comparative Analysis with Ciona savignyi. Genome Research. Vol. 17, pp. 1101-1110.
• Cheng, C., Fabrizio, P., Ge, H., Longo, V., Li, L. M. (2007). Inference of Transcription Modificiation in Long-live Yeast Strains from their Expression Profiles. BMC Genomics. Vol. 8, pp. 219-228.
• Kim, J. H., Waterman, M. S., Li, L. M. (2007). Accuracy Assessment of Diploid Consensus Sequences. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Vol. 4, pp. 88-97.
• Li, H., Valouev, A., Schwartz, D. C., Waterman, M. S., Li, L. M. (2007). A Quantile Method for Sizing Optical Maps. Journal of Computational Biology. Vol. 14 (3), pp. 255–266.
• Kitsantas, P., Hollander, M., Li, L. M. (2007). Assessing the stability of classification trees using Florida birth data. Journal of Statistical Planning and Inference. Vol. 137 (12), pp. 3917-3929.
• Kitsantas, P., Hollander, M., Li, L. M. (2006). Using classification trees to assess low birth weight outcomes. Journal Artificial Intelligence in Medicine. Vol. 38, pp. 275—289.
• Cheng, C., Ma, X., Yan, X., sun, F., Li, L. M. (2006). MARD: A New Method to Detect Differential Gene Expression in Treatment-Control Time Courses. Bioinformatics. Vol. 21, pp. 2650-2657.
• Nicolas, P., Sun, F., Li, L. M. (2006). A model-based approach to selection of tag SNPs. BMC Bioinformatics. Vol. 7, pp. 303.
• Li, L. M. (2006). Some Notes on Mutual Information between Past and Future. Journal of Time Series Analysis. Vol. 27, pp. 309–322.
• Valouev, A., Li, L. M., Liu, Y., Schwartz, D. C., Yang, Y., Zhang, Y., Waterman, M. S. (2006). Alignment of Optical Maps. Journal of Computational Biology. Vol. 13, pp. 442–462.
• Cheng, C., Li, L. M. (2005). Sub-array Normalization Subject to Differentiation. Nucleic Acids Research. Vol. 33(17), pp. 5565-5573.
• Li, L. M. (2005). Factorization of moving-average spectral densities by state-space representations and stacking. Journal of Multivariate Analysis. Vol. 96, pp. 425-438.
• Li, L. M., Lu, H. (2005). Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks. Journal of Computational Biology. Vol. 12, pp. 170-185.
• Fabrizio, P., Li, L. M., Longo, V. D. (2004). Analysis of Gene Expression Profile in Yeast Aging Chronologically. Mechanisms of Ageing and Development. Vol. 126, pp. 11-16.
• Li, M. L., Nordborg, M., Li, L. M. (2004). Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Research. Vol. 32, pp. 5183-5191.
• Li, L. M. (2004). An Algorithm for computing exact least trimmed squares estimate of simple linear regression with constraints. Computational Statistics and Data Analysis. Vol. 48, pp. 717-734.
• Li, L. M., Kim, J. K., Waterman, M. S. (2004). Haplotype reconstruction from SNP alignment. Journal of Computational Biology. Vol. 11, pp. 505-516.
• Li, L. M., Speed, T. P. (2004). Deconvolution of sparse positive spikes. Journal of Computational and Graphical Statistics. Vol. 13 (1-18)
• Rosenberg, N. A., Li, L. M., Ward, R., Pritchard, J. K. (2003). Informativeness of genetic markers for inference of ancestry. Journal of American Human Genetics. Vol. 73, pp. 1402-1422.
• Li, L. (2002). DNA sequencing and parametric deconvolution. Statistica Sinica. Vol. 12, pp. P179-202.
• Li, L. M., Speed, T. P. (2000). Parametric Deconvolution of Positive Spike Trains. Annals of Statistics. Vol. 28, pp. 1279-1301.
• Li, L. M., Yu, B. (2000). Iterated-logarithmic Expansion of the Pathwise Code Lengths for Exponential Families. IEEE Transactions on Information Theory. Vol. 46, pp. 2683-2689.
• Li, L. M., Speed, T. P. (2000). Estimation of the Color Separation Matrix in Four-dye Fluorescence-based DNA Sequencing. Electrophoresis. Vol. 20, pp. 1433-1442.
• Kheterpa, I., Li, L. M., Speed, T. P., Mathies, R. A. (1998). A three-color labeling Approach for DNA sequencing using energy transfer primers and capillary electrophoresis. Electrophoresis. Vol. 19, pp. 1403-1414.
• Li, L. M., Xie, Z. (1996). Model selection and order determination for time series by information between the past and the future. Journal of Time Series Analysis. Vol. 17, pp. 65-84.
• Li, L. M. (1994). A method to factorize spectral densities of multiple moving average processes. Journal of Systems Sciences and Mathematics. Vol. 7, pp. 169-176.