Welcome! Visit Cai Lab website at genomezoo.net 

James Cai, Ph.D.
Assistant Professor
Department of Veterinary Integrative Biosciences
College of Veterinary Medicine
Texas A&M University
MS 4458 | College Station, TX 77843
Tel 979.458.5482 | Fax 979.847.8981
jcai@tamu.edu
www.genomezoo.net

[ Administrative profile | Lab website ]

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Research Interests

  • Population genomics: theory, methods and applications
  • Evolutionary interpretation of genotype-phenotype links
  • Genetic disorders, complex traits and interaction network
  • Regulation and evolution of gene expression
  • Scientific computing, algorithms, and software tools

Publications

  1. Chang CL, Semyonov J, Cheng PJ, Huang SY, Park JI, Tsai HJ, Lin CY, Grutzner 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, 16;8(4):e61701. doi: 10.1371/journal.pone.0061701

  2. Hulse AM, Cai JJ* (2013) Genetic variants contribute to gene expression variability in humans. Genetics, 10.1534/genetics.112.146779 [PDFPDF][PubMed][Journal Cover][Highlight]

  3. 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]

  4. Brinkmeyer-Langford CL, Cai JJ, Gill CA, Skow LC (2012) Microsatellite variation in the equine MHC. Animal Genetics, doi:10.1111/age.12003 [PDFPDF][PubMed]

  5. 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]

  6. Cai JJ* (2011) Evolutionary bioinformatics with a scientific computing environment. Systems and Computational Biology - Bioinformatics and Computational Modeling Ning-Sun Yang (Ed.), 51-74, ISBN 978-953-307-875-5, InTech. [PDFPDF][Link]

  7. 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 [PDFPDF][PubMed]

  8. 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]

  9. Lu Z, Jiang P, Cai JJ, Xing Y (2011) Context-dependent robustness to 5' splice site polymorphisms in human populations. Human Molecular Genetics, 20(6):1084-96 [PDFPDF][PubMed]

  10. 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][Journal Cover]

  11. Cai JJ*, Borenstein E, Petrov DA (2010) Broker genes in human disease. Genome Biology and Evolution, 2:815-25 [PDFPDF][Pubmed]

  12. Tse H, Cai JJ, Tsoi HW, Lam EP, Yuen KY (2010) Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. BMC Genomics, Sep 9;11:491. [PDFPDF][PubMed]

  13. Woo PC, Tam EW, Chong KT, Cai JJ, Tung ET, Ngan AH, Lau SK, Yuen KY (2010) High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei. The FEBS journal, 277(18):3750-8 [PDFPDF][PubMed]

  14. 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]

  15. 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][i][ii][iii]

  16. Cai JJ*, Petrov DA (2009) Relaxed purifying selection and higher rates of adaptation in human lineage-specific genes. Genome Biology and Evolution, 2:393-409 [PDFPDF][PubMed]

  17. 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]

  18. 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. [PDFPDF][PubMed][i][ii][iii][iv][v][vi]

  19. 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][Download]

  20. 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 marneffei. FEBS Letters, 580(14):3409-3416 [PDFPDF][PubMed][F1000 Article]

  21. 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]

  22. 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]

  23. 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][The Scientist]

  24. 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):884-95 [PDFPDF][PubMed]

  25. 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][Mito Genome]

  26. 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]

  27. Cai JJ (2006) Understanding the Pathogenic Fungus Penicillium marneffei: A Computational Genomics Perspective. Ph.D. Thesis [PDFPDF][HKU Theses Online]

*Corresponding author

[Google Cites]  [Publication List by Topic]  [Up-to-date List from PubMed]

Software

  • Population Genetics & Evolution Toolbox (PGEToolbox)
  • Molecular Biology & Evolution Toolbox (MBEToolbox)
  • Systems Biology & Evolution Toolbox (SBEToolbox) 
Updated on 12/16/2012