Publications

Human Population Genomics

• Cai JJ, Macpherson M, Sella G, and Petrov DA (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genetics, 2009 Jan;5(1):e1000336 | PubMed | Full Text | i | ii | iii |
• Chang CL, Cai JJ, Park JI, Lo C, Amigo J, Cheng PJ, Chueh HY, and Hsu SYT (2010) Adaptive selection of a cryptic incretin hormone in human populations. submitted.

Natural Selection and Evolution of Protein-coding Genes

• Cai JJ* and Petrov DA (2010) Relaxed purifying selection and higher rates of adaptation in human lineage-specific genes. Genome Biology and Evolution, doi:10.1093/gbe/evq019 | Abstract |
• Cai JJ, Borenstein E, and Petrov DA (2010) Distinct network properties of human disease genes. submitted.
• Cai JJ, Borenstein E, Rong C, and Petrov DA (2009) Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biology and Evolution, Vol. 2009, 131-144; doi:10.1093/gbe/evp013 | Full Text | PDF | PubMed |
• Cai JJ*, Woo PCY, Lau SKP, Smith DK and Yuen KY (2006) Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycetes. Journal of Molecular Evolution 2006 Jul;63(1):1-11 | Abstract | Full Text | PDF | PubMed |

Gene Expression and Alternative Splicing

• Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL and Xing Y (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genetics, 2008 October; 4(10): e1000225. | PubMed | Full Text | i | ii | iii | iv | v | vi |

Software Development

• Cai JJ* (2008) PGEToolbox: A Matlab toolbox for sequence and polymorphism data analysis in population genetics and evolution. Journal of Heredity 99(4):438-440; doi:10.1093/jhered/esm127 | PubMed |
• Cai JJ*, Smith DK, Xia X and Yuen KY (2006) MBEToolbox 2: an enhanced Matlab toolbox for molecular biology and evolution. Evolutionary Bioinformatics Online, 2:189-192 | Abstract | PDF | PubMed |
• Cai JJ*, Smith DK, Xia X and Yuen KY (2005) MBEToolbox: a MATLAB^TM toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics 6:64 | PDF | PubMed | Media Report |

Microbial Genomics

• Woo PC, Tam E, Chong KT, Cai JJ, Tung E, Lau SK, and Yuen KY (2010) Genomic evidence of a high diversity of polyketide synthases and characterization of melanin biosynthesis gene cluster in Penicillium marneffei. FEBS Journal 2010 Aug 13 | PubMed |
• Tse H, Cai JJ, Tsoi HW, Lam EPT, and Yuen KY (2010) Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. BMC Genomics 11:491
• Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, Lok S, and Yuen KY (2009) The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS genetics, 2009 Mar;5(3):e1000416. | PubMed | Full Text |
• Woo PC, Chong KT, Cai JJ, Tse H, Lau CC, Zhou AC, Lau SK, and Yuen KY (2006) Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei. FEBS Letters, 580(14):3409-3416 | PubMed |
• Woo PC, Zhen H, Cai JJ, Yu J, Lau SKP, Wang J, Teng JLL, Wong SS, Tse RH, Chen R, Yang H, Liu B and Yuen KY (2003) The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Letters, 555 (3): 469-77 | PDF | PubMed | Genome |
• Yuen KY, Pascal G, Wong SS, Glaser P, Woo PC, Kunst F, Cai JJ, Cheung EY, Medigue C, Danchin A (2003) Exploring the Penicillium marneffei genome. Archives of Microbiology, 179 (5): 339-53 | PDF | PubMed |
• Woo PC, Lau SKP, Chan KH, Tsoi HW, Huang Y, Wong BHL, Cai JJ, Wong SSY, Peiris JSM, Chu C and Yuen KY (2005) Characterization and complete genome sequence of a novel coronavirus from a patient with pneumonia. Journal of Virology p. 884-895, Vol. 79, No. 2 | PDF | PubMed |