James Cai - Systems Genetics at Texas A&M
James Cai, Ph.D.
Associate Professor
Veterinary Integrative Biosciences
Faculty of Genetics
Faculty of Electrical & Computer Engineering
Texas A&M University
4458 TAMU
College Station, TX 77843-4458
Tel (979) 458-5482 | Fax (979) 847-8981
[Faculty page | Lab website]

Research Interests

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

Select Publications [Show All]

  1. 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., 25 (22): 4911-4919. [Preprint]
    [PubMed][Full Text]

  2. 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., Aug 3. [Full Text]

  3. Guan J, Wang G, Yang E, Yang J, Zeng Y, Ji G, Cai JJ* (2016) Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Human Genetics, 135(7):797-811. [PDFPDF][PubMed][Full Text]

  4. Chacko N, Zhao Y, Yang E, Wang L, Cai JJ, Lin X (2015) The lncRNA RZE1 controls cryptococcal morphological transition. PLoS Genetics, 11(11):e1005692. [PDFPDF][Full Text]

  5. Zeng Y, Wang G, Yang E, Ji G, Brinkmeyer-Langford CL, Cai JJ* (2015) Aberrant gene expression in humans. PLoS Genetics, 11(1):e1004942. doi:10.1371/journal.pgen.1004942. [PDFPDF][PubMed][Full Text]

  6. 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][Full Text]

  7. 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, 10(10):e1004662. [PDFPDF][PubMed][Full Text]

  8. 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][Featured in "GENETICS 2014 Spotlight" booklet]

  9. 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]

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

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

  12. 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]

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

  14. 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]
[Google Cites | MyBibliography (NCBI) | SciENCV]

Book Chapter

  • 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]


  • Population Genetics & Evolution Toolbox (PGEToolbox)
  • Molecular Biology & Evolution Toolbox (MBEToolbox)
  • Systems Biology & Evolution Toolbox (SBEToolbox)
jamesjcai's Github chart
Updated on 7/10/2017