Journal Articles


Osorio D, Yu X, Zhong Y, Li G, Huang J, Cai JJ* (2020) scTenifoldNet: a machine learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from single-cell data. [bioRxiv 441527]


Eldridge R, Osorio D, Amstalden K, Edwards C, Young CR, Cai JJ, Konganti K, Hillhouse A, Threadgill DW, Welsh CJ, Brinkmeyer-Langford C. (2020) Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies. Sci Rep. 2020 May 13;10(1):7918. doi: 10.1038/s41598-020-64862-z. PMID: 32404926; PMCID: PMC7220920.

Huang G, Osorio D, Guan J, Ji G, Cai JJ*. (2020) Overdispersed gene expression in schizophrenia. NPJ Schizophr. 6(1):9. doi: 10.1038/s41537-020-0097-5. PMID: 32245959; PMCID: PMC7125213. [bioRxiv 441527]

Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ*, Cai JJ* (2020) Single-cell expression variability implies cell function. Cells, 9(1) [Full Text] [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. Scientific Data, 6:112. [Full Text] [bioRxiv 548115]

Cai JJ* (2019) scGEApp: a Matlab app for feature selection on single-cell RNA sequencing data. Bioinformatics, bez830. [Full Text] [bioRxiv 544163]

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, 9 (1), 152


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]