James J Cai

Summary

Affiliation: The University of Hong Kong
Country: China

Publications

  1. ncbi MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution
    James J Cai
    Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong, China
    BMC Bioinformatics 6:64. 2005
  2. ncbi Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota
    James J Cai
    Department of Microbiology, Faculty of Medicine, University of Hong Kong, University Pathology Building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong SAR, China
    J Mol Evol 63:1-11. 2006
  3. ncbi High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei
    Patrick C Y Woo
    State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China
    FEBS J 277:3750-8. 2010
  4. ncbi Draft genome sequence of Penicillium marneffei strain PM1
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, Hong Kong
    Eukaryot Cell 10:1740-1. 2011
  5. ncbi Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
    FEBS Lett 580:3409-16. 2006
  6. ncbi Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes
    Herman Tse
    Carol Yu Centre for Infection, Department of Microbiology, The University of Hong Kong, Hong Kong, China
    BMC Genomics 11:491. 2010
  7. ncbi Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
    J Virol 79:884-95. 2005
  8. ncbi The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, PR China
    FEBS Lett 555:469-77. 2003
  9. ncbi Diverse splicing patterns of exonized Alu elements in human tissues
    Lan Lin
    Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
    PLoS Genet 4:e1000225. 2008
  10. ncbi PGEToolbox: A Matlab toolbox for population genetics and evolution
    James J Cai
    Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
    J Hered 99:438-40. 2008

Collaborators

Detail Information

Publications10

  1. ncbi MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution
    James J Cai
    Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong, China
    BMC Bioinformatics 6:64. 2005
    ..However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution...
  2. ncbi Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota
    James J Cai
    Department of Microbiology, Faculty of Medicine, University of Hong Kong, University Pathology Building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong SAR, China
    J Mol Evol 63:1-11. 2006
    ..These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes...
  3. ncbi High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei
    Patrick C Y Woo
    State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China
    FEBS J 277:3750-8. 2010
    ..marneffei and 6 min for the alb1 knockdown mutant of P. marneffei, implying that the melanin-biosynthesis gene cluster contributed to virulence through decreased susceptibility to killing by hydrogen peroxide...
  4. ncbi Draft genome sequence of Penicillium marneffei strain PM1
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, Hong Kong
    Eukaryot Cell 10:1740-1. 2011
    ..We report the 28,887,485-bp draft genome sequence of P. marneffei, which contains its complete mitochondrial genome, sexual cycle genes, a high diversity of Mp1p homologues, and polyketide synthase genes...
  5. ncbi Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, Queen Mary Hospital, Hong Kong
    FEBS Lett 580:3409-16. 2006
    ..We speculate that P. marneffei can potentially be a heterothallic fungus that does not switch mating type...
  6. ncbi Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes
    Herman Tse
    Carol Yu Centre for Infection, Department of Microbiology, The University of Hong Kong, Hong Kong, China
    BMC Genomics 11:491. 2010
    ..Given such a functional significance, we expect statistically overrepresented OSCs in coding sequences as a result of a widespread selection. Accordingly, we examined available prokaryotic genomes to look for evidence of this selection...
  7. ncbi Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
    J Virol 79:884-95. 2005
    ..13 x 10(6) copies per ml, from a 35-year-old woman with pneumonia. Our data support the existence of a novel group 2 coronavirus associated with pneumonia in humans...
  8. ncbi The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts
    Patrick C Y Woo
    Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, PR China
    FEBS Lett 555:469-77. 2003
    ..Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts...
  9. ncbi Diverse splicing patterns of exonized Alu elements in human tissues
    Lan Lin
    Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
    PLoS Genet 4:e1000225. 2008
    ..Our results imply that some Alu exonization events may have acquired adaptive benefits during the evolution of primate transcriptomes...
  10. ncbi PGEToolbox: A Matlab toolbox for population genetics and evolution
    James J Cai
    Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
    J Hered 99:438-40. 2008
    ..For academic uses, PGEToolbox is available free of charge at http://bioinformatics.org/pgetoolbox...