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James J Cai

Assistant Professor

Curriculum Vitae

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Phone: (979) 458-5482

Mailstop: 4458

Department: VIBS

Photo of Cai, James


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

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.


Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort.
Wang G, Yang E, Brinkmeyer-Langford CL, Cai JJ.
Genetics. 2014 Feb; 196(2):413-25.
PMID: 24298061 [PubMed - in process]
Population-level expression variability of mitochondrial DNA-encoded genes in humans.
Wang G, Yang E, Mandhan I, Brinkmeyer-Langford CL, Cai JJ.
Eur J Hum Genet. 2014 Jan; .
PMID: 24398800 [PubMed - as supplied by publisher]
Microsatellite variation in the equine MHC.
Brinkmeyer-Langford CL, Cai JJ, Gill CA, Skow LC.
Anim Genet. 2013 Jun; 44(3):267-75.
PMID: 23051181 [PubMed - in process]
Draft genome sequence of Penicillium marneffei strain PM1.
Woo PC, Lau SK, Liu B, Cai JJ, Chong KT, Tse H, Kao RY, Chan CM, Chow WN, Yuen KY.
Eukaryot Cell. 2011 Dec; 10(12):1740-1.
PMID: 22131218 [PubMed - in process]
Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation.
Chang CL, Cai JJ, Cheng PJ, Chueh HY, Hsu SY.
Diabetes. 2011 Mar; 60(3):726-34.
PMID: 21300845 [PubMed - indexed for MEDLINE]
Widespread establishment and regulatory impact of Alu exons in human genes.
Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y.
Proc Natl Acad Sci U S A. 2011 Feb; 108(7):2837-42.
PMID: 21282640 [PubMed - indexed for MEDLINE]
Context-dependent robustness to 5' splice site polymorphisms in human populations.
Lu ZX, Jiang P, Cai JJ, Xing Y.
Hum Mol Genet. 2011 Mar; 20(6):1084-96.
PMID: 21224255 [PubMed - indexed for MEDLINE]
Adaptive selection of an incretin gene in Eurasian populations.
Chang CL, Cai JJ, Lo C, Amigo J, Park JI, Hsu SY.
Genome Res. 2011 Jan; 21(1):21-32.
PMID: 20978139 [PubMed - indexed for MEDLINE]
Broker genes in human disease.
Cai JJ, Borenstein E, Petrov DA.
Genome Biol Evol. 2010 ; 2:815-25.
PMID: 20937604 [PubMed - indexed for MEDLINE]
Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes.
Tse H, Cai JJ, Tsoi HW, Lam EP, Yuen KY.
BMC Genomics. 2010 Sep; 11:491.
PMID: 20828396 [PubMed - indexed for MEDLINE]
High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei.
Woo PC, Tam EW, Chong KT, Cai JJ, Tung ET, Ngan AH, Lau SK, Yuen KY.
FEBS J. 2010 Sep; 277(18):3750-8.
PMID: 20718860 [PubMed - indexed for MEDLINE]
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes.
Cai JJ, Petrov DA.
Genome Biol Evol. 2010 ; 2:393-409.
PMID: 20624743 [PubMed - indexed for MEDLINE]
The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.
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.
PLoS Genet. 2009 Mar; 5(3):e1000416.
PMID: 19283063 [PubMed - indexed for MEDLINE]
Pervasive hitchhiking at coding and regulatory sites in humans.
Cai JJ, Macpherson JM, Sella G, Petrov DA.
PLoS Genet. 2009 Jan; 5(1):e1000336.
PMID: 19148272 [PubMed - indexed for MEDLINE]
Similarly strong purifying selection acts on human disease genes of all evolutionary ages.
Cai JJ, Borenstein E, Chen R, Petrov DA.
Genome Biol Evol. 2009 May; 1:131-44.
PMID: 20333184 [PubMed]
Diverse splicing patterns of exonized Alu elements in human tissues.
Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y.
PLoS Genet. 2008 Oct; 4(10):e1000225.
PMID: 18841251 [PubMed - indexed for MEDLINE]
PGEToolbox: A Matlab toolbox for population genetics and evolution.
Cai JJ.
J Hered. 2008 Jul; 99(4):438-40.
PMID: 18310616 [PubMed - indexed for MEDLINE]
MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution.
Cai JJ, Smith DK, Xia X, Yuen KY.
Evol Bioinform Online. 2007 Feb; 2:179-82.
PMID: 19455210 [PubMed]
Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota.
Cai JJ, Woo PC, Lau SK, Smith DK, Yuen KY.
J Mol Evol. 2006 Jul; 63(1):1-11.
PMID: 16755356 [PubMed - indexed for MEDLINE]
Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei.
Woo PC, Chong KT, Tse H, Cai JJ, Lau CC, Zhou AC, Lau SK, Yuen KY.
FEBS Lett. 2006 Jun; 580(14):3409-16.
PMID: 16714021 [PubMed - indexed for MEDLINE]
MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.
Cai JJ, Smith DK, Xia X, Yuen KY.
BMC Bioinformatics. 2005 Mar; 6:64.
PMID: 15780146 [PubMed - indexed for MEDLINE]
Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia.
Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y, Wong BH, Poon RW, Cai JJ, Luk WK, Poon LL, Wong SS, Guan Y, Peiris JS, Yuen KY.
J Virol. 2005 Jan; 79(2):884-95.
PMID: 15613317 [PubMed - indexed for MEDLINE]
The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts.
Woo PC, Zhen H, Cai JJ, Yu J, Lau SK, Wang J, Teng JL, Wong SS, Tse RH, Chen R, Yang H, Liu B, Yuen KY.
FEBS Lett. 2003 Dec; 555(3):469-77.
PMID: 14675758 [PubMed - indexed for MEDLINE]
Exploring the Penicillium marneffei genome.
Yuen KY, Pascal G, Wong SS, Glaser P, Woo PC, Kunst F, Cai JJ, Cheung EY, Médigue C, Danchin A.
Arch Microbiol. 2003 May; 179(5):339-53.
PMID: 12640520 [PubMed - indexed for MEDLINE]

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