Human Population Genomics
- Cai JJ, Macpherson M, Sella G, and Petrov DA (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genetics, 5(1):e1000336 [PDF
 ][PubMed]
- Chang CL, Cai JJ, Park JI, Lo C, Amigo J, Cheng PJ, Chueh HY, and Hsu SYT (2011) Adaptive selection of an incretin gene in Eurasian populations. Genome Research, 21(1):21-32 [PDF][PubMed][Cover Article][i][ii]
- Chang CL, Cai JJ, Cheng PJ, Chueh HY, and Hsu SYT (2011) Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes, 60(3):726-34 [PDF
 ][PubMed][Report][Report]
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, 2:393-409 [PDF][PubMed]
- Cai JJ*, Borenstein E, and Petrov DA (2010) Broker genes in human disease. Genome Biology and Evolution, 2:1-11 [PDF][PubMed]
- 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, 1:131-144 [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, 63(1):1-11 [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, 4(10): e1000225 [i] [ii] [iii] [iv] [v] [vi] [PDF][PubMed]
- Lu Z, Jiang P, Cai JJ, and Xing Y (2010) Context-dependent robustness to 5’ splice site polymorphisms in human populations. Human Molecular Genetics, HMG-2010-W-01062 [PDF][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 [PDF][PubMed][i][ii]
Software Development
- 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. [PDF][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 [PDF][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 [PDF][PubMed]
- 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][Report]
Microbial Genomics
- Woo PC, Lau SK, Liu B, Cai JJ, Chong KT, Tse H, Kao RY, Chan CM, Chow WN, and Yuen KY (2011) Draft Genome Sequence of Penicillium marneffei Strain PM1. Eukaryot Cell, 10(12):1740-1 [PDF][PubMed]
- Woo PC, Tam E, Chong KT, Cai JJ, Tung E, Lau SK, and Yuen KY (2010) High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei. FEBS Journal, 277(18):3750-8 [PDF][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 [PDF][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, and 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. [PDF][PubMed]
- 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][PDF]
- 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, 79(2):884-895 [PubMed][PDF]
- 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[PubMed][Genome][PDF]
- 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]
*Corresponding Author.
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