Gene Expression and Alternative Splicing

  • Genetics Cover
    Wang G
    Yang E, Brinkmeyer-Langford CL, Cai JJ* (2014) Additive, epistatic, and environmental effects through the lens of expression variability QTLs in a twin cohort. Genetics,  Feb;196(2):413-25. [PDFPDF][PubMed]








  • Wang G
    Yang EMandhan I, Brinkmeyer-Langford CL, Cai JJ* (2014) Population-level expression variability of mitochondrial DNA-encoded genes in humans. Eur J Hum Genet, 1-7 [PDFPDF][PubMed]




  • Hulse AM
    Cai JJ* (2013) Genetic variants contribute to gene expression variability in humans. Genetics, 193(1):95-108 [PDFPDF][PubMed][Data]









  • Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genetics, 4(10): e1000225 [i] [ii] [iii] [iv] [v[vi] [PDFPDF][PubMed]
  • Lu Z, Jiang P, Cai JJ, Xing Y (2010) Context-dependent robustness to 5’ splice site polymorphisms in human populations. Human Molecular Genetics, HMG-2010-W-01062 [PDFPDF][PubMed]
  • Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y (2011) Widespread establishment and regulatory impact of Alu exons in human genes. PNAS, 108(7):2837-42 [PDFPDF][PubMed][i][ii]

Population Genomics

  • Cai JJ, Macpherson M, Sella G, Petrov DA (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genetics, 5(1):e1000336 [PDFPDF][PubMed]

  • Chang CL, 
    Cai JJ, Park JI, Lo C, Amigo J, Cheng PJ, Chueh HY, Hsu SYT (2011) Adaptive selection of an incretin gene in Eurasian populations. Genome Research, 21(1):21-32 [PDFPDF][PubMed][Cover Article][i][ii]






  • Chang CL, Cai JJ, Cheng PJ, Chueh HY, Hsu SYT (2011) Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes, 60(3):726-34 [PDF][PubMed][Report 1][Report 2]

  • Brinkmeyer-Langford CL,
    Cai JJ, Gill CA, and Skow LC (2013) Microsatellite variation in the equine MHC. Animal Genetics, 44(3):267-75. doi:10.1111/age.12003 [PDF][PubMed]



Natural Selection and Evolution of Protein-coding Genes

  • Cai JJ*, Petrov DA (2010) Relaxed purifying selection and higher rates of adaptation in human lineage-specific genes. Genome Biology and Evolution, 2:393-409 [PDFPDF][PubMed]
  • Cai JJ*, Borenstein E, Petrov DA (2010) Broker genes in human disease. Genome Biology and Evolution, 2:1-11 [PDFPDF][PubMed][Data]
  • Cai JJ, Borenstein E, Rong C, Petrov DA (2009) Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biology and Evolution, 1:131-144 [PDFPDF][PubMed][Data]
  • Cai JJ*, Woo PCY, Lau SKP, Smith DK, Yuen KY (2006) Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycetes. Journal of Molecular Evolution, 63(1):1-11 [PDFPDF][PubMed]
  • Chang CL, Semyonov J, Cheng PJ, Huang SY, Park JI, Tsai HJ, Lin CY, Grützner F, Soong YK, Cai JJ, Hsu SY (2013) Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection. PLoS One. 8(4):e61701. [PDFPDF][PubMed]

Software Development

  • Konganti K, Wang G, Yang E, Cai JJ* (2013) SBEToolbox: a Matlab toolbox for biological network analysis. Evolutionary Bioinformatics, 9:1-8 [PDFPDF][PubMed]
  • Cai JJ* (2011) Evolutionary bioinformatics with a scientific computing environment. Systems and Computational Biology - Bioinformatics and Computational Modeling, Ning-Sun Yang (Ed.), ISBN 978-953-307-875-5, InTech. [PDFPDF][Link]
  • 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 [PDFPDF][PubMed]
  • Cai JJ*, Smith DK, Xia X, Yuen KY (2006) MBEToolbox 2: an enhanced Matlab toolbox for molecular biology and evolution. Evolutionary Bioinformatics, 2:189-192 [PDFPDF][PubMed]
  • Cai JJ*, Smith DK, Xia X, Yuen KY (2005) MBEToolbox: a MATLABTM toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics, 6:64 [PDFPDF][PubMed][Report]

Microbial Genomics

  • Yang E
    , Wang G, Woo PC, Lau SK, Chow WN, Chong KT, Tse H, Kao RY, Chan CM, Yuen KY, Cai JJ* (2013) Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. Eukaryot Cell, 12(9):1214-24[PDFPDF][PubMed][GEO DataSet]







  • Yang E, Hulse AM, Cai JJ* (2012) Evolutionary analysis of sequence divergence and diversity of duplicate genes in Aspergillus fumigatus. Evolutionary Bioinformatics, 8:1-15 [PDFPDF][PubMed]
  • Woo PC, Lau SK, Liu B, Cai JJ, Chong KT, Tse H, Kao RY, Chan CM, Chow WN, Yuen KY (2011) Draft Genome Sequence of Penicillium marneffei Strain PM1. Eukaryot Cell, 10(12):1740-1 [PDFPDF][PubMed]
  • Woo PC, Tam E, Chong KT, Cai JJ, Tung E, Lau SK, Yuen KY (2010)  High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffeiFEBS Journal, 277(18):3750-8 [PDFPDF][PubMed]
  • Tse H, Cai JJ, Tsoi HW, Lam EPT, Yuen KY (2010) Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. BMC Genomics, 11:491 [PDFPDF][PubMed]
  • 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, Yuen KY (2009) The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS genetics, 5(3):e1000416. [PDFPDF][PubMed]
  • Woo PC, Chong KT, Cai JJ, Tse H, Lau CC, Zhou AC, Lau SK, Yuen KY (2006) Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffeiFEBS Letters, 580(14):3409-3416 [PDFPDF][PubMed]
  • Woo PC, Lau SKP, Chan KH, Tsoi HW, Huang Y, Wong BHL, Cai JJ, Wong SSY, Peiris JSM, Chu C, Yuen KY (2005) Characterization and complete genome sequence of a novel coronavirus from a patient with pneumonia. Journal of Virology, 79(2):884-895 [PDFPDF][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, 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 [PDFPDF][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 [PDFPDF][PubMed]

*Corresponding Author; ___ Lab members: The names of Cai lab members at the time of the project are underlined.