James J. Cai

James J. Cai

Associate Professor
Veterinary Integrative Biosciences

Phone: 979.458.5482
TAMU Mailstop: 4458
Website: James Cai

Research and Scholarly Interests

Our research focuses on elucidation of genotype-phenotype relationships using computational and evolutionary genomics approaches. We develop computational tools and statistical tests to estimate key parameters of evolutionary processes that shape the sequence and expression variability within and between individuals, populations, and species. We apply theories to genomic diversity and divergence data in order to search for the signatures of selection in the genomes of different organisms.


  • M.S., University of New South Wales, 2001
  • Ph.D., University of Hong Kong, 2006
  • Post-doc, Stanford University, 2010

  • Genomics
  • Genetics
  • Infectious Disease
  • Microbiology

  • Wang G, Yang E, Mandhan I, Brinkmeyer-Langford CL, Cai JJ (2014). Population-level expression variability of mitochondrial DNA-encoded genes in humans. EUR J HUM GENET. 22, 1093-99
  • Yang E, Wang G, Woo PC, Lau SK, Chow WN, Chong KT, Tse H, Kao RY, Chan CM, Che X, Yuen KY, Cai JJ (2013). Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. EUKARYOT CELL. 9, 1214-24
  • Konganti K, Wang G, Yang E, Cai JJ (2013). SBEToolbox: A Matlab Toolbox for Biological Network Analysis. EVOL BIOINFORM ONLINE. 9, 355-62
  • Hulse AM, Cai JJ (2013). Genetic variants contribute to gene expression variability in humans. GENETICS. 1, 95-108
  • Yang E, Hulse AM, Cai JJ (2012). Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. EVOL BIOINFORM ONLINE. 8, 623-44
  • Chang CL, Cai JJ, Huang SY, Cheng PJ, Chueh HY, Hsu SY (2014). Adaptive Human CDKAL1 Variants Underlie Hormonal Response Variations at the Enteroinsular Axis. PLOS ONE. 9,
  • Wang G, Yang E, Brinkmeyer-Langford CL, Cai JJ (2014). Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort. GENETICS. 2, 413-25
  • Brinkmeyer-Langford CL, Cai JJ, Gill CA, Skow LC (2013). Microsatellite variation in the equine MHC. ANIM GENET. 3, 267-75
  • 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. 6,
  • 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 GENET.
  • 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
  • Zeng Y, Wang G, Yang E, Ji G, Brinkmeyer-Langford CL, Cai JJ (2015). Aberrant gene expression in humans PLOS GENET. 1,
  • Chacko N, Zhao Y, Yang E, Wang L, Cai JJ, Lin X (2015). The lncRNA RZE1 Controls Cryptococcal Morphological Transition PLOS GENET. 11,
  • Guan J, Yang E, Yang J, Zeng Y, Ji G, Cai JJ (2016). Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis HUM GENET. 7, 797-811
  • Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ (2016). Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains FRONT AGING NEUROSCI., 183
  • Brinkmeyer-Langford C, Balog-Alvarez C, Cai JJ, Davis BW, Kornegay JN (2016). Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy BMC GENOMICS., 665
  • Yang E, Wang G, Yang J, Zhou B, Tian Y, Cai JJ (2016). Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action HUM MOL GENET.