Liang Chen

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
    Sika Zheng
    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Nucleic Acids Res 37:e75. 2009
  2. pmc A two-parameter generalized Poisson model to improve the analysis of RNA-seq data
    Sudeep Srivastava
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 38:e170. 2010
  3. pmc Characterization and comparison of human nuclear and cytosolic editomes
    Liang Chen
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 110:E2741-7. 2013
  4. pmc A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 26:855-9. 2010
  5. pmc A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 38:1086-97. 2010
  6. pmc Studying alternative splicing regulatory networks through partial correlation analysis
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Genome Biol 10:R3. 2009
  7. pmc Identify alternative splicing events based on position-specific evolutionary conservation
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 3:e2806. 2008
  8. pmc Considering dependence among genes and markers for false discovery control in eQTL mapping
    Liang Chen
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
    Bioinformatics 24:2015-22. 2008
  9. pmc Emergence of daptomycin resistance in daptomycin-naïve rabbits with methicillin-resistant Staphylococcus aureus prosthetic joint infection is associated with resistance to host defense cationic peptides and mprF polymorphisms
    Nagendra N Mishra
    Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor University of California at Los Angeles Medical Center, Torrance, California, United States of America David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California, United State of America
    PLoS ONE 8:e71151. 2013
  10. pmc VERSE: a varying effect regression for splicing elements discovery
    Jing Zhang
    Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA, USA
    J Comput Biol 19:855-65. 2012

Collaborators

Detail Information

Publications30

  1. pmc A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
    Sika Zheng
    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Nucleic Acids Res 37:e75. 2009
    ..We applied BASIS to a human tiling-array data set and a mouse RNA-seq data set. Some of the predictions were validated by quantitative real-time RT-PCR experiments...
  2. pmc A two-parameter generalized Poisson model to improve the analysis of RNA-seq data
    Sudeep Srivastava
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 38:e170. 2010
    ..The usefulness of the GP model is demonstrated by applications to multiple RNA-seq data sets...
  3. pmc Characterization and comparison of human nuclear and cytosolic editomes
    Liang Chen
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 110:E2741-7. 2013
    ..This suggests that editing can mediate RNA memory on evolutionary time-scales to maintain ancestral genetic information. ..
  4. pmc A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 26:855-9. 2010
    ..It provides evidence for the link between histone modifications and transcribed exons in promoter regions...
  5. pmc A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 38:1086-97. 2010
    ..In contrast, nonsense-mediated decay is significantly more associated with the isoforms enriched in the nucleus than those enriched in the cytosol...
  6. pmc Studying alternative splicing regulatory networks through partial correlation analysis
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Genome Biol 10:R3. 2009
    ..Meanwhile, each alternative exon is controlled by multiple splicing regulators. The rapid accumulation of high-throughput data provides us with a unique opportunity to study the complicated alternative splicing regulatory network...
  7. pmc Identify alternative splicing events based on position-specific evolutionary conservation
    Liang Chen
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
    PLoS ONE 3:e2806. 2008
    ..Among those, 31,673 introns containing conditional exons and 5,294 conditional exons classified from known exons cannot be inferred from RefSeq, UCSC or Ensembl annotations. Some of these de novo predictions were experimentally verified...
  8. pmc Considering dependence among genes and markers for false discovery control in eQTL mapping
    Liang Chen
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
    Bioinformatics 24:2015-22. 2008
    ..Besides the dependence among markers, the dependence among the expression levels of genes can also have a significant impact on data analysis and interpretation...
  9. pmc Emergence of daptomycin resistance in daptomycin-naïve rabbits with methicillin-resistant Staphylococcus aureus prosthetic joint infection is associated with resistance to host defense cationic peptides and mprF polymorphisms
    Nagendra N Mishra
    Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor University of California at Los Angeles Medical Center, Torrance, California, United States of America David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California, United State of America
    PLoS ONE 8:e71151. 2013
    ....
  10. pmc VERSE: a varying effect regression for splicing elements discovery
    Jing Zhang
    Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA, USA
    J Comput Biol 19:855-65. 2012
    ..VERSE may serve as a powerful tool to not only discover SREs by incorporating additional informative signals but also precisely quantify their varying contribution under different biological contexts...
  11. pmc A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing
    Sika Zheng
    Howard Hughes Medical Institute, University of California at Los Angeles, California 90095, USA
    Genome Res 23:998-1007. 2013
    ..These results identify multiple new regulators of Dlg4 splicing, and validate an approach to isolating splicing regulators for almost any cassette exon from libraries of cDNAs, shRNAs, or small molecules...
  12. pmc The genetic basis of rapidly evolving male genital morphology in Drosophila
    John P Masly
    Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    Genetics 189:357-74. 2011
    ..These results suggest the possibility that the insulin signaling pathway might integrate size and shape genetic inputs to establish differences in overall posterior lobe morphology between D. mauritiana and D. sechellia...
  13. pmc Telavancin in therapy of experimental aortic valve endocarditis in rabbits due to daptomycin-nonsusceptible methicillin-resistant Staphylococcus aureus
    Yan Q Xiong
    Los Angeles Biomedical Research Institute, Torrance, California, USA
    Antimicrob Agents Chemother 56:5528-33. 2012
    ..0001). Together, these results demonstrate that TLV has potent bactericidal activity in vitro and in vivo against DAP-R MRSA isolates...
  14. pmc GC content around splice sites affects splicing through pre-mRNA secondary structures
    Jing Zhang
    Ming Hsieh Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    BMC Genomics 12:90. 2011
    ....
  15. pmc Improved mean estimation and its application to diagonal discriminant analysis
    Tiejun Tong
    Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
    Bioinformatics 28:531-7. 2012
    ..To obtain more accurate estimation of parameters some statistical methods, such as regularizations through shrinkage, are often desired...
  16. pmc Contribution of Panton-Valentine leukocidin in community-associated methicillin-resistant Staphylococcus aureus pathogenesis
    Binh An Diep
    Division of Infectious Diseases, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 3:e3198. 2008
    ..Taken together, our data indicate a modest and transient positive effect of PVL in the acute phase of bacteremia, thereby providing evidence that PVL contributes to CA-MRSA pathogenesis...
  17. pmc Comparison between the stochastic search variable selection and the least absolute shrinkage and selection operator for genome-wide association studies of rheumatoid arthritis
    Sudeep Srivastava
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    BMC Proc 3:S21. 2009
    ....
  18. pmc Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines
    Che Yu Lee
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 29:1713-7. 2013
    ..However, the mechanism of alternative polyadenylation selection and the involved factors is still largely unknown...
  19. pmc Extended spectrum beta-lactamase-producing Enterobacteriaceae in international travelers and non-travelers in New York City
    Scott A Weisenberg
    Department of Medicine, Alta Bates Summit Medical Center, Oakland, California
    PLoS ONE 7:e45141. 2012
    ....
  20. ncbi request reprint A statistical method for identifying differential gene-gene co-expression patterns
    Yinglei Lai
    Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
    Bioinformatics 20:3146-55. 2004
    ..In this study, we develop a statistical method for identifying differential gene-gene co-expression patterns in different cell states...
  21. ncbi request reprint Negative correlation between compositional symmetries and local recombination rates
    Liang Chen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
    Bioinformatics 21:3951-8. 2005
    ..This negative correlation pattern also held at individual chromosome levels when data only from each individual chromosome was analyzed...
  22. pmc Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains
    Liang Chen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
    BMC Genomics 6:44. 2005
    ....
  23. ncbi request reprint LKB1 modulates lung cancer differentiation and metastasis
    Hongbin Ji
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Nature 448:807-10. 2007
    ..These studies establish LKB1 as a critical barrier to pulmonary tumorigenesis, controlling initiation, differentiation and metastasis...
  24. ncbi request reprint Partial bit delay correlative modulation used to improve the dispersion tolerance of an optical duobinary system
    Zhongxi Zhang
    Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
    Opt Express 16:11344-53. 2008
    ..These conclusions are also valid for systems having non-negligible polarization-mode dispersion (PMD) and polarization dependent loss (PDL)...
  25. ncbi request reprint Capacity analysis for a two-level decoupled Hamming network for associative memory under a noisy environment
    Liang Chen
    Computer Science Department, University of Northern British Columbia, BC, Canada V2N 4Z9
    Neural Netw 20:598-609. 2007
    ..We therefore conclude that the two-level decoupled Hamming network with middle-sized windows should be an elegant associative memory model in all the senses of efficiency, hardware implementation and capacity...
  26. ncbi request reprint Epigenetic and transcriptional programs lead to default IFN-gamma production by gammadelta T cells
    Liang Chen
    Section of Rheumatology, Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
    J Immunol 178:2730-6. 2007
    ..Our results demonstrate that both epigenetic and transcriptional programs contribute to the early vigorous IFN-gamma production by gammadelta T cells...
  27. pmc FDJS03 isolates causing an outbreak of aseptic meningitis in China that evolved from a distinct Echovirus 30 lineage imported from countries of the Commonwealth of Independent States
    Ya Nan Zhao
    School of Public Health, Fudan University, Shanghai, China
    J Clin Microbiol 44:4142-8. 2006
    ..It is most likely that the ancestor of FDJS03 isolates experienced multiple recombination events in the nonstructural protein coding region, which were partly observed in the phylogenetic analysis of the 3D region...
  28. pmc Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis
    Xiaoxing Li
    Shanghai Jiao Tong University Shanghai Institutes for Biological Sciences Pennsylvania State University Joint Center for Life Sciences, Shanghai Jiao Tong University, Shanghai, People s Republic of China, 200240
    Plant Physiol 141:1167-84. 2006
    ..In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs...
  29. ncbi request reprint The impact of human EGFR kinase domain mutations on lung tumorigenesis and in vivo sensitivity to EGFR-targeted therapies
    Hongbin Ji
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Cancer Cell 9:485-95. 2006
    ..These data suggest that persistent EGFR signaling is required for tumor maintenance in human lung adenocarcinomas expressing EGFR mutants...
  30. ncbi request reprint [Niche assessment of China provincial social-economic-natural complex ecosystems in 2003]
    Liang Chen
    Research Center for Eco Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
    Ying Yong Sheng Tai Xue Bao 18:1794-800. 2007
    ..The integrated ecological niche in Guangdong, Fujian and Hainan was the highest...