Genomes and Genes
James J Cai
Affiliation: The University of Hong Kong
- MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolutionJames 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...
- Draft genome sequence of Penicillium marneffei strain PM1Patrick 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...
- Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffeiPatrick 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...
- High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffeiPatrick 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...
- Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumoniaPatrick 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...
- Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycotaJames 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...
- Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotesHerman 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...
- The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeastsPatrick 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...
- Diverse splicing patterns of exonized Alu elements in human tissuesLan 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...
- PGEToolbox: A Matlab toolbox for population genetics and evolutionJames 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...