Lei M Li

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc Informativeness of genetic markers for inference of ancestry
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
    Am J Hum Genet 73:1402-22. 2003
  2. pmc Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant
    Huanying Ge
    Andrus Gerontology Center, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 38:143-58. 2010
  3. pmc Significant and systematic expression differentiation in long-lived yeast strains
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 2:e1095. 2007
  4. pmc Inferring microRNA activities by combining gene expression with microRNA target prediction
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 3:e1989. 2008
  5. pmc Sub-array normalization subject to differentiation
    Chao Cheng
    Computational Biology, University of Southern California, Los Angeles, CA, USA
    Nucleic Acids Res 33:5565-73. 2005
  6. pmc Systematic identification of transcription factors associated with patient survival in cancers
    Chao Cheng
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
    BMC Genomics 10:225. 2009
  7. pmc Inference of transcription modification in long-live yeast strains from their expression profiles
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Genomics 8:219. 2007
  8. pmc Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension
    Min Wei
    Andrus Gerontology Center, University of Southern California, Los Angeles, CA, USA
    PLoS Genet 5:e1000467. 2009
  9. pmc A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays
    Huanying Ge
    Molecular and Computational Biology, Department of Biology Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Bioinformatics 9:194. 2008
  10. ncbi request reprint MARD: a new method to detect differential gene expression in treatment-control time courses
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, Computational Biology, University of Southern California Los Angeles, CA, USA
    Bioinformatics 22:2650-7. 2006

Research Grants

Detail Information

Publications21

  1. pmc Informativeness of genetic markers for inference of ancestry
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
    Am J Hum Genet 73:1402-22. 2003
    ..Our results can aid in decisions about the type, quantity, and specific choice of markers for use in studies of ancestry...
  2. pmc Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant
    Huanying Ge
    Andrus Gerontology Center, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 38:143-58. 2010
    ....
  3. pmc Significant and systematic expression differentiation in long-lived yeast strains
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 2:e1095. 2007
    ..The three yeast mutants sch9Delta, ras2Delta, tor1Delta show extended chronological life span up to three folds. Our aim is to dissect the mechanisms that lead to the yeast life span extension...
  4. pmc Inferring microRNA activities by combining gene expression with microRNA target prediction
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 3:e1989. 2008
    ..A number of computational approaches regarding miRNAs have been proposed, but most of them focus on miRNA gene finding or target predictions. Little computational work has been done to investigate the effective regulation of miRNAs...
  5. pmc Sub-array normalization subject to differentiation
    Chao Cheng
    Computational Biology, University of Southern California, Los Angeles, CA, USA
    Nucleic Acids Res 33:5565-73. 2005
    ..We illustrate the problem and solution through an Affymetrix spike-in dataset with defined perturbation and a dataset of primate brain expression...
  6. pmc Systematic identification of transcription factors associated with patient survival in cancers
    Chao Cheng
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
    BMC Genomics 10:225. 2009
    ..However, the association between transcription factors and cancers is largely dependent on the transcription regulatory activities rather than mRNA expression levels...
  7. pmc Inference of transcription modification in long-live yeast strains from their expression profiles
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Genomics 8:219. 2007
    ..However, the mechanisms of longevity, especially the underlying transcription program have not been fully understood...
  8. pmc Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension
    Min Wei
    Andrus Gerontology Center, University of Southern California, Los Angeles, CA, USA
    PLoS Genet 5:e1000467. 2009
    ....
  9. pmc A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays
    Huanying Ge
    Molecular and Computational Biology, Department of Biology Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Bioinformatics 9:194. 2008
    ..Summarization aims to estimate the transcript abundance from normalized intensities. In this paper, we consider normalization and summarization jointly by a new strategy of reference selection...
  10. ncbi request reprint MARD: a new method to detect differential gene expression in treatment-control time courses
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, Computational Biology, University of Southern California Los Angeles, CA, USA
    Bioinformatics 22:2650-7. 2006
    ..We propose a novel method to identify the differentially expressed genes between two time courses, which avoids direct comparison of gene expression patterns between the two time courses...
  11. pmc Inferring activity changes of transcription factors by binding association with sorted expression profiles
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Bioinformatics 8:452. 2007
    ..In some other models, the target genes of a TF are first determined by a significance cutoff to binding affinity scores, and then expression differentiation is checked between the target and other genes...
  12. pmc Systematic identification of cell cycle regulated transcription factors from microarray time series data
    Chao Cheng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Genomics 9:116. 2008
    ..For most species, however, large-scale ChIP-chip data are still not available...
  13. ncbi request reprint Accuracy assessment of diploid consensus sequences
    Jong Hyun Kim
    Department of Computer Science, University of Southern California, Los Angeles 90089, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:88-97. 2007
    ..2 percent) was based on Ciona intestinalis. As a result, the high accuracy of our algorithm was indicated: The true positive rate of the haplotype estimation was greater than 97 percent...
  14. pmc Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi
    Jong Hyun Kim
    Department of Computer Science, Yonsei University, Seoul, Republic of Korea
    Genome Res 17:1101-10. 2007
    ..Our results indicate 97% accuracy in haplotype estimation, based on a simulated data set. We conduct a comparative analysis with Ciona savignyi, and discover interesting patterns of conserved DNA elements in chordates...
  15. ncbi request reprint Haplotype reconstruction from SNP alignment
    Lei M Li
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    J Comput Biol 11:505-16. 2004
    ..Also, we compute the accuracy or confidence of the reconstructed haplotypes. We discuss other issues, such as alternative methods, parameter estimation, computational efficiency, and relaxation of assumptions...
  16. pmc Intervention to enhance skilled arm and hand movements after stroke: A feasibility study using a new virtual reality system
    Jill Campbell Stewart
    Division of Biokinesiology and Physical Therapy at the School of Dentistry, University of Southern California, Los Angeles, CA, USA
    J Neuroeng Rehabil 4:21. 2007
    ..We describe four VR tasks that were developed and tested to improve arm and hand movement skills for individuals with hemiparesis...
  17. ncbi request reprint Alignment of optical maps
    Anton Valouev
    Department of Mathematics, University of Southern California, Los Angeles, 90089 1113, USA
    J Comput Biol 13:442-62. 2006
    ..This allows us to achieve maximal descriminative power for the alignment score. Our scoring method is naturally embedded within a well known DP framework for finding optimal alignments...
  18. ncbi request reprint A quantile method for sizing optical maps
    Haifeng Li
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 2910, USA
    J Comput Biol 14:255-66. 2007
    ..We show that this approach is comparable to the current reference-based method as evaluated by map alignment techniques in terms of the rate of placement of optical maps to published sequence...
  19. pmc Adjust quality scores from alignment and improve sequencing accuracy
    Ming Li
    Computational Biology, University of Southern California, Los Angeles, CA, USA
    Nucleic Acids Res 32:5183-91. 2004
    ..Besides Phred scores obtained from ABI sequencers, we apply the same technique to calibrate quality values that come along with Beckman sequencers...
  20. ncbi request reprint Explore biological pathways from noisy array data by directed acyclic Boolean networks
    Lei M Li
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    J Comput Biol 12:170-85. 2005
    ....
  21. pmc A model-based approach to selection of tag SNPs
    Pierre Nicolas
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, USA
    BMC Bioinformatics 7:303. 2006
    ..It also provides a machinery for the prediction of tagged SNPs and thereby to assess the performances of tag sets through their ability to predict larger SNP sets...

Research Grants5

  1. Detection and Understanding of Expression Differentiatio
    Lei Li; Fiscal Year: 2009
    ..To serve the scientific mission, we develop and integrate statistical and computational methodologies. Our research will benefit the society by new understanding of aging. ..