Journal Articles


Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang J, Cai JJ* (2019) Extent, heritability, and functional relevance of single cell expression variability in highly homogeneous populations of human cells. [bioRxiv 574426]

Osorio D, Yu X, Yu P, Serpedin E, Cai JJ* (2019) Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. [bioRxiv 548115]

Cai JJ* (2019) scGEApp: a Matlab app for feature selection on single-cell RNA sequencing data. [bioRxiv 544163]

Huang G, Osorio D, Guan J, Ji G, Cai JJ* (2019) Overdispersed gene expression characterizes schizophrenic brains. [bioRxiv 441527]


Guan J, Cai JJ, Ji G, Sham PC (2019) Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia and bipolar disorder. Transl Psychiatry 00:00-00 (In Press)


Lau SKP, Lo G, Chow W, Fan R, Cai JJ, Yuen KY, Woo PCY (2018) Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei. mBio, mBio00947-18 DOI PMID [Editor's Pick]

Chen J, Ke S, Zhong L, Wu J, Tseng A, Morpurgo B, Golovko A, Wang G, Cai JJ, Ma X, Li D, Tian Y (2018) Long noncoding RNA MALAT1 regulates generation of reactive oxygen species and the insulin responses in male mice. Biochemical Pharmacology, 10.1016/j.bcp.2018.03.019 DOI PMID

Brinkmeyer-Langford C, Chu C, Balog-Alvarez C, Yu X, Cai JJ, Nabity M, Kornegay JN (2018) Expression pro ling of disease progression in canine model of Duchenne muscular dystrophy. PLoS One, Mar 19;13(3):e0194485. DOI PMID

Al Kawam A, Alshawaqfeh M, Cai JJ, Serpedin E, Datta A (2018) Simulating variance heterogeneity in quantitative genome wide association studies. BMC Bioinformatics, 19(Suppl 3):72. DOI PMID

Guan J, Chen M, Ye C, Cai JJ, Ji G (2018) AEGS: identifying aberrantly expressed gene sets for differential variability analysis. Bioinformatics. Oct 11 DOI PMID


Guangzao Huang, Mingshun Yuan, Moliang Chen, Lei Li, Wenjie You, Hanji Li, James J Cai, Guoli Ji (2017) Integrating multiple fitting regression and Bayes decision for cancer diagnosis with transcriptomic data from tumor-educated blood platelets. Analyst 25: 22. 4911-4919 11. DOI PMID


Ence Yang, Gang Wang, Jizhou Yang, Beiyan Zhou, Yanan Tian, James J Cai* (2016) Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Human molecular genetics 25: 22. 4911-4919 11. DOI PMID

Jinting Guan, Ence Yang, Jizhou Yang, Yong Zeng, Guoli Ji, James J Cai* (2016) Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Human genetics 135: 7. 797-811 Jul. DOI PMID SharedIT

Candice L Brinkmeyer-Langford, Jinting Guan, Guoli Ji, James J Cai* (2016) Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Frontiers in aging neuroscience 8: 08. DOI PMID

Candice Brinkmeyer-Langford, Cynthia Balog-Alvarez, James J Cai, Brian W Davis, Joe N Kornegay (2016) Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy. BMC genomics 17: Aug. DOI PMID


N B Stafuzza, B C M Naressi, E Yang, J J Cai, M E J Amaral-Trusty (2015) A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly. Genetics and molecular research : GMR 14: 4. 13096-13104 Oct. DOI PMID

Nadia Chacko, Youbao Zhao, Ence Yang, Linqi Wang, James J Cai, Xiaorong Lin (2015) The lncRNA RZE1 Controls Cryptococcal Morphological Transition. PLoS genetics 11: 11. Nov. DOI PMID

Yong Zeng, Gang Wang, Ence Yang, Guoli Ji, Candice L Brinkmeyer-Langford, James J Cai* (2015) Aberrant gene expression in humans. PLoS genetics 11: 1. Jan. DOI PMID


Gang Wang, Ence Yang, Kerri J Smith, Yong Zeng, Guoli Ji, Richard Connon, Nann A Fangue*, James J Cai* (2014) Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Frontiers in genetics 5: 09. DOI PMID

Ence Yang, Wang-Ngai Chow, Gang Wang, Patrick C Y Woo, Susanna K P Lau, Kwok-Yung Yuen, Xiaorong Lin, James J Cai *(2014) Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. PLoS genetics 10: 10. Oct. DOI PMID

Gang Wang, Ence Yang, Candice L Brinkmeyer-Langford, James J Cai* (2014) Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort. Genetics 196: 2. 413-425 Feb. DOI PMID

Gang Wang, Ence Yang, Ishita Mandhan, Candice L Brinkmeyer-Langford, James J Cai* (2014) Population-level expression variability of mitochondrial DNA-encoded genes in humans. European journal of human genetics : EJHG 22: 9. 1093-1099 Sep. DOI PMID

Linqi Wang, Xiuyun Tian, Rachana Gyawali, Srijana Upadhyay, Dylan Foyle, Gang Wang, James J Cai, Xiaorong Lin (2014) Morphotype transition and sexual reproduction are genetically associated in a ubiquitous environmental pathogen. PLoS pathogens 10: 6. Jun. DOI PMID

Chia Lin Chang, James J Cai, Shang Yu Huang, Po Jen Cheng, Ho Yen Chueh, Sheau Yu Teddy Hsu (2014) Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis. PloS one 9: 9. 09. DOI PMID


Chia Lin Chang, Jenia Semyonov, Po Jen Cheng, Shang Yu Huang, Jae Il Park, Huai-Jen Tsai, Cheng-Yung Lin, Frank Grützner, Yung Kuei Soong, James J Cai, Sheau Yu Teddy Hsu (2013) Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. PloS one 8: 4. 04. DOI PMID

Ence Yang, Gang Wang, Patrick C Y Woo, Susanna K P Lau, Wang-Ngai Chow, Ken T K Chong, Herman Tse, Richard Y T Kao, Che-Man Chan, Xiaoyan Che, Kwok-Yung Yuen, James J Cai* (2013) Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. Eukaryotic cell 12: 9. 1214-1224 Sep. DOI PMID

C L Brinkmeyer-Langford, J J Cai, C A Gill, L C Skow (2013) Microsatellite variation in the equine MHC. Animal genetics 44: 3. 267-275 Jun. DOI PMID

Amanda M Hulse, James J Cai* (2013) Genetic variants contribute to gene expression variability in humans. Genetics 193: 1. 95-108 Jan. DOI PMID

Kranti Konganti, Gang Wang, Ence Yang, James J Cai* (2013) SBEToolbox: A Matlab Toolbox for Biological Network Analysis. Evolutionary bioinformatics online 9: 355-362 09. DOI PMID


Ence Yang, Amanda M Hulse, James J Cai* (2012) Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. Evolutionary bioinformatics online 8: 623-644 11. DOI PMID


Patrick C Y Woo, Susanna K P Lau, Bin Liu, James J Cai, Ken T K Chong, Herman Tse, Richard Y T Kao, Che-Man Chan, Wang-Ngai Chow, Kwok-Yung Yuen (2011) Draft genome sequence of Penicillium marneffei strain PM1. Eukaryotic cell 10: 12. 1740-1741 Dec. DOI PMID

Chia Lin Chang, James J Cai, Chiening Lo, Jorge Amigo, Jae-Il Park, Sheau Yu Teddy Hsu (2011) Adaptive selection of an incretin gene in Eurasian populations. Genome Res 21: 1. 21-32 Jan. DOI PMID

Zhi-xiang Lu, Peng Jiang, James J Cai, Yi Xing (2011) Context-dependent robustness to 5' splice site polymorphisms in human populations. Hum Mol Genet 20: 6. 1084-1096 Mar. DOI PMID

Shihao Shen, Lan Lin, James J Cai, Peng Jiang, Elizabeth J Kenkel, Mallory R Stroik, Seiko Sato, Beverly L Davidson, Yi Xing (2011) Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci U S A 108: 7. 2837-2842 Feb. DOI PMID

Chia Lin Chang, James J Cai, Po Jen Cheng, Ho Yen Chueh, Sheau Yu Teddy Hsu (2011) Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes 60: 3. 726-734 Mar. DOI PMID


James J Cai, Dmitri A Petrov (2010) Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol 2: 393-409 07. DOI PMID

Patrick C Y Woo, Emily W T Tam, Ken T K Chong, James J Cai, Edward T K Tung, Antonio H Y Ngan, Susanna K P Lau, Kwok-Yung Yuen (2010) High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei. FEBS J 277: 18. 3750-3758 Sep. DOI PMID

Herman Tse, James J Cai, Hoi-Wah Tsoi, Esther Pt Lam, Kwok-Yung Yuen (2010) Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. BMC Genomics 11: 09. DOI PMID

James J Cai, Elhanan Borenstein, Dmitri A Petrov (2010) Broker genes in human disease. Genome Biol Evol 2: 815-825 10. DOI PMID


James J Cai, Elhanan Borenstein, Rong Chen, Dmitri A Petrov (2009) Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol 1: 131-144 05. DOI PMID

Patrick C Y Woo, Susanna K P Lau, Herman Tse, Jade L L Teng, Shirly O T Curreem, Alan K L Tsang, Rachel Y Y Fan, Gilman K M Wong, Yi Huang, Nicholas J Loman, Lori A S Snyder, James J Cai, Jian-Dong Huang, William Mak, Mark J Pallen, Si Lok, Kwok-Yung Yuen (2009) The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet 5: 3. Mar. DOI PMID

James J Cai, J Michael Macpherson, Guy Sella, Dmitri A Petrov (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet 5: 1. Jan. DOI PMID


James J Cai (2008) PGEToolbox: A Matlab toolbox for population genetics and evolution. J Hered 99: 4. 438-440 Jul/Aug. DOI PMID

Lan Lin, Shihao Shen, Anne Tye, James J Cai, Peng Jiang, Beverly L Davidson, Yi Xing (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet 4: 10. 10. DOI PMID


James J Cai, David K Smith, Xuhua Xia, Kwok-Yung Yuen (2006) MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution. Evol Bioinform Online 2: 179-182 02. PMID

Patrick C Y Woo, Ken T K Chong, Herman Tse, James J Cai, Candy C Y Lau, Anna C Zhou, Susanna K P Lau, Kwok-yung Yuen (2006) Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei. FEBS Lett 580: 14. 3409-3416 Jun. DOI PMID

James J Cai, Patrick C Y Woo, Susanna K P Lau, David K Smith, Kwok-Yung Yuen (2006) Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol 63: 1. 1-11 Jul. DOI PMID


Patrick C Y Woo, Susanna K P Lau, Chung-ming Chu, Kwok-hung Chan, Hoi-wah Tsoi, Yi Huang, Beatrice H L Wong, Rosana W S Poon, James J Cai, Wei-kwang Luk, Leo L M Poon, Samson S Y Wong, Yi Guan, J S Malik Peiris, Kwok-yung Yuen (2005) Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol 79: 2. 884-895 Jan. DOI PMID

James J Cai, David K Smith, Xuhua Xia, Kwok-Yung Yuen (2005) MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics 6: 03. DOI PMID


Kwok-Yung Yuen, Géraldine Pascal, Samson S Y Wong, Philippe Glaser, Patrick C Y Woo, Frank Kunst, James J Cai, Elim Y L Cheung, Claudine Médigue, Antoine Danchin (2003) Exploring the Penicillium marneffei genome. Arch Microbiol 179: 5. 339-353 May. DOI PMID

Patrick C Y Woo, Hongjun Zhen, James J Cai, Jun Yu, Susanna K P Lau, Jian Wang, Jade L L Teng, Samson S Y Wong, Ronald H Tse, Ran Chen, Huanming Yang, Bin Liu, Kwok-yung Yuen (2003) The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Lett 555: 3. 469-477 Dec. PMID

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. [PDF][Link]