Welcome! Visit Cai Lab website at genomezoo.net 

James Cai, Ph.D.
Assistant Professor
Department of Veterinary Integrative Biosciences
Texas A&M University
4458 TAMU
College Station, TX 77843-4458
Tel (979) 458-5482 | Fax (979) 847-8981

[ Administrative profile | Lab website | SciENCV ]


Research Interests

  • Population genomics: theory, methods and applications
  • Regulation and evolution of gene expression
  • Genetic disorders, complex traits and interaction network
  • Fungal genomics
  • Scientific computing, algorithms and software tools


  1. Wang G, Yang E, Smith KJ, Zeng Y, Ji G, Connon R, Fangue NA, Cai JJ* (2014) Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Frontiers in Genetics, 5:312 doi: 10.3389/fgene.2014.00312 [PDFPDF][PubMed][Open Access]

  2. Yang E, Chow WN, Wang G, Woo PCY, Lau SKP, Yuen KY, Lin X, Cai JJ* (2014) Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. PLoS Genetics, in press [PDFPDF][PubMed]

  3. Wang L, Tian X, Gyawali1 R, Upadhyay1 S, Foyle D, Wang G, Cai JJ, Lin X (2014) Morphotype transition and sexual reproduction are genetically associated via an RNA-binding protein in a ubiquitous environmental pathogen. PLoS Pathogens,10(6): e1004185 [PDFPDF][Open Access]
  4. 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, 196:413-25 [PDFPDF][PubMed] [Featured in AJHG][Cover Article]

  5. Wang G, Yang E, Mandhan I, Brinkmeyer-Langford CL, Cai JJ* (2014) Population-level expression variability of mitochondrial DNA-encoded genes in humans. European Journal of Human Genetics, 1-7 [PDFPDF][PubMed]

  6. 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. Eukaryotic Cell, 12(9):1214-24 [PDFPDF][PubMed][Spotlight]

  7. Konganti K, Wang G, Yang E, Cai JJ* (2013) SBEToolbox: a Matlab toolbox for biological network analysis. Evolutionary Bioinformatics, 9:1-8 [PDFPDF][PubMed][Open Access][Download]

  8. 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 [PDFPDF][PubMed]

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

  10. 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]

  11. Brinkmeyer-Langford CL, Cai JJ, Gill CA, Skow LC (2012) Microsatellite variation in the equine MHC. Animal Genetics, 44(3):267-75 [PDFPDF][PubMed]

  12. 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. Eukaryotic Cell, 10(12):1740-1 [PDFPDF][PubMed]

  13. 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]

  14. 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]

  15. 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. Proceedings of the National Academy of Sciences, 108(7):2837-42 [PDFPDF][PubMed]

  16. 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]

  17. 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]

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

  19. 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]

  20. 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. FEBS Journal, 277(18):3750-8 [PDFPDF][PubMed]

  21. 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]

  22. 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]

  23. 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]

  24. 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]

  25. 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]

  26. 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]

  27. 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]

  28. 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]

  29. 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]

  30. 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]

  31. 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]

  32. 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]

  33. 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]

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


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

Updated on 8/28/2014