Welcome to James J. Cai [CAIJing]'s Homepage!
Dr. James J. Cai

  

The Petrov Lab, Dept. of Biology
Stanford University
Stanford, CA 94305, USA
e-mail: jamescai[at]stanford.edu
phone: 1-650-736-2249

I am interested in a diverse set of problems in population genetics and molecular evolution. I apply theories to modern biological data, develop statistical tests and computational tools to investigate evolutionary processes shaping genome variability patterns within and between species.

Recent Publications

    Human Population Genomics

  1. 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]

    Natural Selection and Evolution of Protein-coding Genes

  2. Cai JJ* and Petrov DA (2009) Relaxed purifying selection and higher rates of adaptation in human lineage-specific genes. Genome Biology and Evolution, submitted.

  3. 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 [Abstract] [FREE Full Text] [PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS

  4. 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]

    Alternative Splicing and Gene Expression

  5. 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

  6. 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] [Download]

  7. Cai JJ*, Smith DK, Xia X and Yuen KY (2006) MBEToolbox 2: an enhanced Matlab toolbox for molecular biology and evolution. Evolutionary Bioinformatics, 2:189-192 [Abstract] [PDF][Download]

  8. Cai JJ*, Smith DK, Xia X and Yuen KY (2005) MBEToolbox: a MATLABTM toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics 6:64 [PDF] [PubMed] [Download] [Media Report]

    • Population Genetics & Evolution Toolbox (PGEToolbox)
    • Molecular Biology & Evolution Toolbox (MBEToolbox)

    Microbial Genomics

  9. 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]

  10. 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

  11. 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]

  12. 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]

  13. 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]

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