Lab News

Daniel will be joining the Kuijjer lab at University of Oslo as a postdoctoral fellow through the Marie Curie Scientia Fellows II program to work on regulatory network modeling in single-cell data. Here's a CVM News to learn more.
Preprint "scTenifoldKnk: a machine learning workflow performing virtual knockout experiments on single-cell gene regulatory networks" is posted at BioRxiv.
Dr. Cai presents at the 2021 Genetics and Epigenetics Cross-Cutting Research Team (GECCRT) Meeting.
Daniel receives Marie Skłodowska-Curie Actions Research Fellowship.
Dr. Cai speaks at the 3d Workshop on Computational Advances for Single-Cell Omics Data Analysis (CASCODA 2020).
Dr. Cai speaks at the 7th NCHU GEAR UP forum.
Dr. Cai speaks at the 2020 TAMU-NCHU research forum.
scTenifoldNet is published online in Patterns.
Dr. Cai speaks at the 1st Annual Gulf Coast Consortia (GCC) Single Cell Omics Cluster Symposium.
Dr. Cai speaks at EUSTM-2020 on COVID-19 - 7th Annual Congress of the European Society for Translational Medicine on Covid-19 (EUSTM-2020 21-25 September, 2020 (Virtual Congress).
Daniel publishes on Bioinformatics.
Preprint: Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2. [] [ResearchGate]
npj Schizophrenia paper published: Overdispersed gene expression in schizophrenia
Dr. Cai speaks at The 20th International Conference on Systems Biology (ICSB2019).
Opening for graduate student is available.
Dr. Cai speaks at the 10x Genomics User Group meeting in Houston.
We release three preprints: [bioRxiv 544163] [bioRxiv 548115] and [bioRxiv 574426].
Preprint 'Overdispersed gene expression characterizes schizophrenic brains' posted at BioRxiv.
Dr. Cai attends SMBE18 in Yokohama.
Ahmad publishes vQTL/vGWAS simulator at BMC Genomics.
Welcome to new members of the team, Daniel and Ahmad!
Guangzao, as lead author, publishes at Analyst.
We attend SMBE17 in Austin.
We are part of PoreCamp USA 2017. Read The Eagle report.
We participate the 2nd Southeast Texas Evolutionary Genetics and Genomics (STEGG) Symposium at Texas A&M University at Galveston.
Postdoc position is available immediately.
Opening for graduate student is available.
This new lab website is launched. Lab news on the old site is still accessible here.


Leverage structure of knowledge to learn its interaction with the unknown.

Our research lies at the interface of human genetics, computational statistics, and data science. Current research focuses on understanding diverse behaviors of cells using machine learning, network science and dynamical system analysis. We develop analytical frameworks to study single-cell transcriptome data from various types of cells. We also study the genetic basis of phenotypic variability or randomness in the human population and develop computational tools to identify genetic variants that control complex traits and determine the susceptibility of genetic disorders.


We apply our integrated knowledge of molecular biology, genetics, and informatics, to provide insights into data in language diverse team understands.


  • Cai JJ, Osorio D. Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2. OSFPreprints. 2020 [PDF][Link]
  • Osorio D, Zhong Y, Li G, Qian X, Hillhouse A, Chen J, Davidson LA, Tian Y, Chapkin RS, Huang JZ, Cai JJ. scTenifoldKnk: a machine learning workflow performing virtual knockout experiments on single-cell gene regulatory networks. bioRxiv. 2021.03.22.436484; doi:

Journal Articles

  1. Zhu B, Guo X, Xu H, Jiang B, Li H, Wang Y, Yin Q, Zhou T, Cai JJ, Glaser S, Meng F, Francis H, Alpini G, Wu C. Adipose tissue inflammation and systemic insulin resistance in mice with diet-induced obesity is possibly associated with disruption of PFKFB3 in hematopoietic cells. Lab Invest. 2021 Mar;101(3):328-340. doi: 10.1038/s41374-020-00523-z. Epub 2021 Jan 18. PMID: 33462362; PMCID: PMC7897240.
  2. Osorio D, Zhong Y, Li G, Huang JZ, Cai JJ. scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data. Patterns (N Y). 2020 Nov 5;1(9):100139. doi: 10.1016/j.patter.2020.100139. PMID: 33336197; PMCID: PMC7733883.
  3. Kumar V, Ivens A, Goodall Z, Meehan J, Doharey PK, Hillhouse A, Hurtado DO, Cai JJ, Zhang X, Schnaufer A, Cruz-Reyes J. Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes. RNA. 2020 Dec;26(12):1862-1881. doi: 10.1261/rna.076513.120. Epub 2020 Sep 1. PMID: 32873716; PMCID: PMC7668249.
  4. Osorio D, Cai JJ. Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control. Bioinformatics. 2020 Aug 25:btaa751. doi: 10.1093/bioinformatics/btaa751. Epub ahead of print. PMID: 32840568.
  5. Eldridge R, Osorio D, Amstalden K, Edwards C, Young CR, Cai JJ, Konganti K, Hillhouse A, Threadgill DW, Welsh CJ, Brinkmeyer-Langford C. 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.
  6. Huang G, Osorio D, Guan J, Ji G, Cai JJ. Overdispersed gene expression in schizophrenia. NPJ Schizophr. 2020 Apr 3;6(1):9. doi: 10.1038/s41537-020-0097-5. PMID: 32245959; PMCID: PMC7125213.
  7. Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ, Cai JJ. Single-Cell Expression Variability Implies Cell Function. Cells. 2019 Dec 19;9(1):14. doi: 10.3390/cells9010014. PMID: 31861624; PMCID: PMC7017299.
  8. Cai JJ. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics. 2019 Nov 7:btz830. doi: 10.1093/bioinformatics/btz830. Epub ahead of print. PMID: 31697351.
  9. Osorio D, Yu X, Yu P, Serpedin E, Cai JJ. Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. Sci Data. 2019 Jul 4;6(1):112. doi: 10.1038/s41597-019-0116-4. PMID: 31273215; PMCID: PMC6609777. Data Set - [SRA | GDrive]
  10. Guan J, Cai JJ, Ji G, Sham PC. Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder. Transl Psychiatry. 2019 May 24;9(1):152. doi: 10.1038/s41398-019-0488-4. PMID: 31127088; PMCID: PMC6534650.
  11. Lau SKP, Lo GCS, Chow FWN, Fan RYY, Cai JJ, Yuen KY, Woo PCY. Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei. mBio. 2018 Jun 12;9(3):e00947-18. doi: 10.1128/mBio.00947-18. PMID: 29895639; PMCID: PMC6016240.
  12. Al Kawam A, Alshawaqfeh M, Cai JJ, Serpedin E, Datta A. Simulating variance heterogeneity in quantitative genome wide association studies. BMC Bioinformatics. 2018 Mar 21;19(Suppl 3):72. doi: 10.1186/s12859-018-2061-1. PMID: 29589560; PMCID: PMC5872534.
  13. Chen J, Ke S, Zhong L, Wu J, Tseng A, Morpurgo B, Golovko A, Wang G, Cai JJ, Ma X, Li D, Tian Y. Long noncoding RNA MALAT1 regulates generation of reactive oxygen species and the insulin responses in male mice. Biochem Pharmacol. 2018 Jun;152:94-103. doi: 10.1016/j.bcp.2018.03.019. Epub 2018 Mar 22. PMID: 29577871.
  14. Brinkmeyer-Langford C, Chu C, Balog-Alvarez C, Yu X, Cai JJ, Nabity M, Kornegay JN. Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. PLoS One. 2018 Mar 19;13(3):e0194485. doi: 10.1371/journal.pone.0194485. Erratum in: PLoS One. 2020 Jul 23;15(7):e0236916. PMID: 29554127; PMCID: PMC5858769.
  15. Guan J, Chen M, Ye C, Cai JJ, Ji G. AEGS: identifying aberrantly expressed gene sets for differential variability analysis. Bioinformatics. 2018 Mar 1;34(5):881-883. doi: 10.1093/bioinformatics/btx646. PMID: 29040376; PMCID: PMC6192207.
  16. Huang G, Yuan M, Chen M, Li L, You W, Li H, Cai JJ, Ji G. Integrating multiple fitting regression and Bayes decision for cancer diagnosis with transcriptomic data from tumor-educated blood platelets. Analyst. 2017 Oct 7;142(19):3588-3597. doi: 10.1039/c7an00944e. Epub 2017 Aug 30. PMID: 28853484.
  17. Yang E, Wang G, Yang J, Zhou B, Tian Y, Cai JJ. Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Hum Mol Genet. 2016 Nov 15;25(22):4911-4919. doi: 10.1093/hmg/ddw314. PMID: 28171656; PMCID: PMC6078589.
  18. Brinkmeyer-Langford C, Balog-Alvarez C, Cai JJ, Davis BW, Kornegay JN. Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy. BMC Genomics. 2016 Aug 22;17(1):665. doi: 10.1186/s12864-016-2948-z. PMID: 27549615; PMCID: PMC4994242.
  19. Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ. Aging Shapes the Population- Mean and -Dispersion of Gene Expression in Human Brains. Front Aging Neurosci. 2016 Aug 3;8:183. doi: 10.3389/fnagi.2016.00183. PMID: 27536236; PMCID: PMC4971101.
  20. Guan J, Yang E, Yang J, Zeng Y, Ji G, Cai JJ. Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Hum Genet. 2016 Jul;135(7):797-811. doi: 10.1007/s00439-016-1673-7. Epub 2016 Apr 30. PMID: 27131873.
  21. Chacko N, Zhao Y, Yang E, Wang L, Cai JJ, Lin X. The lncRNA RZE1 Controls Cryptococcal Morphological Transition. PLoS Genet. 2015 Nov 20;11(11):e1005692. doi: 10.1371/journal.pgen.1005692. PMID: 26588844; PMCID: PMC4654512.
  22. Zeng Y, Wang G, Yang E, Ji G, Brinkmeyer-Langford CL, Cai JJ. Aberrant gene expression in humans. PLoS Genet. 2015 Jan 24;11(1):e1004942. doi: 10.1371/journal.pgen.1004942. PMID: 25617623; PMCID: PMC4305293.
  23. Yang E, Chow WN, Wang G, Woo PC, Lau SK, Yuen KY, Lin X, Cai JJ. Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. PLoS Genet. 2014 Oct 16;10(10):e1004662. doi: 10.1371/journal.pgen.1004662. PMID: 25330172; PMCID: PMC4199489.
  24. Wang G, Yang E, Smith KJ, Zeng Y, Ji G, Connon R, Fangue NA, Cai JJ. Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Front Genet. 2014 Sep 11;5:312. doi: 10.3389/fgene.2014.00312. PMID: 25309574; PMCID: PMC4160998.
  25. Chang CL, Cai JJ, Huang SY, Cheng PJ, Chueh HY, Hsu SY. Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis. PLoS One. 2014 Sep 15;9(9):e105410. doi: 10.1371/journal.pone.0105410. PMID: 25222615; PMCID: PMC4164438.
  26. Wang L, Tian X, Gyawali R, Upadhyay S, Foyle D, Wang G, Cai JJ, Lin X. Morphotype transition and sexual reproduction are genetically associated in a ubiquitous environmental pathogen. PLoS Pathog. 2014 Jun 5;10(6):e1004185. doi: 10.1371/journal.ppat.1004185. PMID: 24901238; PMCID: PMC4047104.
  27. Wang G, Yang E, Mandhan I, Brinkmeyer-Langford CL, Cai JJ. Population-level expression variability of mitochondrial DNA-encoded genes in humans. Eur J Hum Genet. 2014 Sep;22(9):1093-9. doi: 10.1038/ejhg.2013.293. Epub 2014 Jan 8. PMID: 24398800; PMCID: PMC4135407.
  28. Wang G, Yang E, Brinkmeyer-Langford CL, Cai JJ. Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort. Genetics. 2014 Feb;196(2):413-25. doi: 10.1534/genetics.113.157503. Epub 2013 Dec 2. PMID: 24298061; PMCID: PMC3914615.
  29. Konganti K, Wang G, Yang E, Cai JJ. SBEToolbox: A Matlab Toolbox for Biological Network Analysis. Evol Bioinform Online. 2013 Sep 1;9:355-62. doi: 10.4137/EBO.S12012. PMID: 24027418; PMCID: PMC3767578.
  30. Yang E, Wang G, Woo PC, Lau SK, Chow WN, Chong KT, Tse H, Kao RY, Chan CM, Che X, Yuen KY, Cai JJ. Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. Eukaryot Cell. 2013 Sep;12(9):1214-24. doi: 10.1128/EC.00159-13. Epub 2013 Jul 12. PMID: 23851338; PMCID: PMC3811563.
  31. Chang CL, Semyonov J, Cheng PJ, Huang SY, Park JI, Tsai HJ, Lin CY, Grützner F, Soong YK, Cai JJ, Hsu SY. Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. PLoS One. 2013 Apr 16;8(4):e61701. doi: 10.1371/journal.pone.0061701. PMID: 23613906; PMCID: PMC3628338.
  32. Yang E, Hulse AM, Cai JJ. Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. Evol Bioinform Online. 2012;8:623-44. doi: 10.4137/EBO.S10372. Epub 2012 Nov 19. PMID: 23225993; PMCID: PMC3510868.
  33. Hulse AM, Cai JJ. Genetic variants contribute to gene expression variability in humans. Genetics. 2013 Jan;193(1):95-108. doi: 10.1534/genetics.112.146779. Epub 2012 Nov 12. PMID: 23150607; PMCID: PMC3527258.
  34. Woo PC, Lau SK, Liu B, Cai JJ, Chong KT, Tse H, Kao RY, Chan CM, Chow WN, Yuen KY. Draft genome sequence of Penicillium marneffei strain PM1. Eukaryot Cell. 2011 Dec;10(12):1740-1. doi: 10.1128/EC.05255-11. PMID: 22131218; PMCID: PMC3232717.
  35. Chang CL, Cai JJ, Cheng PJ, Chueh HY, Hsu SY. Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes. 2011 Mar;60(3):726-34. doi: 10.2337/db10-1331. Epub 2011 Feb 7. PMID: 21300845; PMCID: PMC3046833.
  36. Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y. Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2837-42. doi: 10.1073/pnas.1012834108. Epub 2011 Jan 31. PMID: 21282640; PMCID: PMC3041063.
  37. Lu ZX, Jiang P, Cai JJ, Xing Y. Context-dependent robustness to 5' splice site polymorphisms in human populations. Hum Mol Genet. 2011 Mar 15;20(6):1084-96. doi: 10.1093/hmg/ddq553. Epub 2010 Dec 28. PMID: 21224255; PMCID: PMC3043661.
  38. Chang CL, Cai JJ, Lo C, Amigo J, Park JI, Hsu SY. Adaptive selection of an incretin gene in Eurasian populations. Genome Res. 2011 Jan;21(1):21-32. doi: 10.1101/gr.110593.110. Epub 2010 Oct 26. PMID: 20978139; PMCID: PMC3012923.
  39. Cai JJ, Borenstein E, Petrov DA. Broker genes in human disease. Genome Biol Evol. 2010;2:815-25. doi: 10.1093/gbe/evq064. Epub 2010 Oct 11. PMID: 20937604; PMCID: PMC2988523.
  40. Tse H, Cai JJ, Tsoi HW, Lam EP, Yuen KY. Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. BMC Genomics. 2010 Sep 9;11:491. doi: 10.1186/1471-2164-11-491. PMID: 20828396; PMCID: PMC2996987.
  41. Woo PC, Tam EW, Chong KT, Cai JJ, Tung ET, Ngan AH, Lau SK, Yuen KY. High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei. FEBS J. 2010 Sep;277(18):3750-8. doi: 10.1111/j.1742-4658.2010.07776.x. Epub 2010 Aug 13. PMID: 20718860.
  42. Cai JJ, Petrov DA. Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol. 2010 Jul 12;2:393-409. doi: 10.1093/gbe/evq019. PMID: 20624743; PMCID: PMC2997544.
  43. 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. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet. 2009 Mar;5(3):e1000416. doi: 10.1371/journal.pgen.1000416. Epub 2009 Mar 13. PMID: 19283063; PMCID: PMC2652115.
  44. Cai JJ, Macpherson JM, Sella G, Petrov DA. Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet. 2009 Jan;5(1):e1000336. doi: 10.1371/journal.pgen.1000336. Epub 2009 Jan 16. PMID: 19148272; PMCID: PMC2613029.
  45. Cai JJ, Borenstein E, Chen R, Petrov DA. Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol. 2009 May 27;1:131-44. doi: 10.1093/gbe/evp013. PMID: 20333184; PMCID: PMC2817408.
  46. Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet. 2008 Oct 17;4(10):e1000225. doi: 10.1371/journal.pgen.1000225. PMID: 18841251; PMCID: PMC2562518.
  47. Cai JJ. PGEToolbox: A Matlab toolbox for population genetics and evolution. J Hered. 2008 Jul-Aug;99(4):438-40. doi: 10.1093/jhered/esm127. Epub 2008 Feb 29. PMID: 18310616.
  48. Cai JJ, Woo PC, Lau SK, Smith DK, Yuen KY. Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol. 2006 Jul;63(1):1-11. doi: 10.1007/s00239-004-0372-5. Epub 2006 Jun 3. PMID: 16755356.
  49. Woo PC, Chong KT, Tse H, Cai JJ, Lau CC, Zhou AC, Lau SK, Yuen KY. Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei. FEBS Lett. 2006 Jun 12;580(14):3409-16. doi: 10.1016/j.febslet.2006.05.014. Epub 2006 May 11. Erratum in: FEBS Lett. 2006 Sep 4;580(20):4976-7. PMID: 16714021.
  50. Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox enhanced version of a MATLAB toolbox for molecular biology and evolution. Evol Bioinform Online. 2007 Feb 6;2:179-82. PMID: 19455210; PMCID: PMC2674653.
  51. Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics. 2005 Mar 22;6:64. doi: 10.1186/1471-2105-6-64. PMID: 15780146; PMCID: PMC1274259.
  52. 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. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005 Jan;79(2):884-95. doi: 10.1128/JVI.79.2.884-895.2005. PMID: 15613317; PMCID: PMC538593.
  53. 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. The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Lett. 2003 Dec 18;555(3):469-77. doi: 10.1016/s0014-5793(03)01307-3. PMID: 14675758.
  54. Yuen KY, Pascal G, Wong SS, Glaser P, Woo PC, Kunst F, Cai JJ, Cheung EY, Médigue C, Danchin A. Exploring the Penicillium marneffei genome. Arch Microbiol. 2003 May;179(5):339-53. doi: 10.1007/s00203-003-0533-8. Epub 2003 Mar 15. PMID: 12640520.

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]

Meet Our Team

These people are being in the superposition of the known and the unknown.


Dianel Osorio

Marie Skłodowska-Curie Actions Research Fellow


Qian Xu

Creating purpose-built tools, rapidly prototype pipelines, and scale and adapt them to meet what we need.


Yongjian Yang

Solving complex bioinformatics problems from signal processing through biological interpretation.

We strive to execute stellar projects with cross-team collaboration

Contact Form

The Cai lab is located in Texas A&M University, College Station.