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Lei Li

Adjunct Associate Professor (Research) of Biological Sciences

Contact Information
E-mail: lilei@usc.edu
Phone: (213) 740-2407
Office: RRI 416E

Personal Website


Ph.D. Statistics, University of California, Berkeley, 5/1998
M.S. Probability and Statistics, Peking University, 7/1991
B.S. Mathematics, Peking University, 7/1988

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

Professor Li’s research on computational biology and genomics centers around the mathematical and statistical modeling and software development of bio-measurement and biotechnology, genome biology. (1) Detection and understanding of expression differentiation of yeast life span; (2) Improvement of DNA sequencing accuracy and polymorphism detection; (3) Information-theoretic perspective of genomic data; (4) Statistical problems in optical mapping. His research on probability and statistics include (1) time series analysis and signal processing: (2) computation.

Research Specialties

Statistical modeling and computation, Signal processing, DNA sequencing, Microarray analysis, Functional genomics

Affiliations with Research Centers, Labs, and Other Institutions

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


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.
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