Lab News

03/21/2024
Dr. Cai speaks in the TAMIDS Machine Learning, AI, and Health Collaborations Workshop -- Unveiling the Cellular Universe: Where Machine Learning Meets Single-Cell Biology.
03/20/2024
Shreyan speaks at the Texas Single Cell (TXSC) Working Group Seminar -- Beyond Averages: Exploring the Individuality and Meaningful Chaos of Single-Cell Gene Expression.
01/11/2024
Dr. Cai talks about how computation is changing the life sciences as a panelist at the MathWorks Biomed Roundtable.
12/11/2023
Dr. Cai speaks in the Seminar Series - Regional Center for Excellece in Cancer Research at TAMU.
11/20/2023
TAMU Today News -- Researchers Use Quantum Computing To Predict Gene Relationships.
10/18/2023
Cai lab is at the 2023 GCC Single-Cell Symposium.
10/13/2023
Dr. Cai speaks at the Distinguished Speaker Seminar in the Department of Electrical & Computer Engineering.
09/29/2023
Dr. Cai is interviewed on the YouTube channel NiklasOPF talking about quantum gene regulatory network.
08/25/2023
Shreyan receives TAMU Walter W. Lechner Estate Scholarship!
07/29/2023
Dr. Cai presents at ICML 2023 Workshop on Computational Biology.
07/24/2023
Shreyan presents his research to the SURGe students taking the GENE 657 Command Line Skills course and Professional Development Session #5: Bioinformatics in Genetics Research, on West Campus.
07/19/2023
Dr. Cai speaks at the International Conference on Intelligent Biology and Medicine (ICIBM 2023).
07/13/2023
Our latest research on "Quantum gene regulatory networks" has just been published in @Nature_NPJ Quantum Information. Read it here: https://rdcu.be/dgIpu.
07/12/2023
Yongjian starts doing internship at Moderna.
06/24/2023
Yongjian speaks at the Artificial Intelligence and Biomedicine Society (AI2Health). Check out the recording.
05/22/2023
Dr. Cai speaks at Texas A&M Cancer Research Symposium at The George in Century Square.
05/08/2023
Yongjian publishes Gene Knockout Inference (GenKI) at NAR.
04/16/2023
Yongjian attends RECOMB 2023, Istanbul, Turkey. Check out @RECOMBconf.
03/21/2023
Dr. Cai speaks at ASN 2023, Lexington, KY. Download full program book.
02/24/2023
The GENE Executive Committee approved VIBS 675: Single-cell Data Analysis via Machine Learning as a GENE elective. It is under the area of Statistics and Bioinformatics competency (https://genetics.tamu.edu/current-students/required-courses/).
02/18/2023
Dr. Cai speaks at the Texas Symposium on Critical Topics in Immunology, Texas A&M Hotel and Conference Center, College Station, Texas. View agenda.
02/15/2023
We are generously supported by the CPRIT RP230204 to create and run a single cell 'omics core.
02/01/2023
FOX 44 News: Grant to assist A&M researchers in developing cancer drug.
01/17/2023
Dr. Cai starts teaching VIBS675/689 - Single-Cell Data Analysis via Machine Learning.
12/19/2022
Yongjian publishes research article describing scTenifoldXct at Cell Systems. Visit his twitter thread.
12/01/2022
AgriLife E-Newsletter: $1.19 million grant will leverage single-cell sequencing technology.
11/08/2022
Yongjian speaks at the TAMIDS 2022 Scientific Machine Learning (SciML) Workshop.
10/26/2022
Yongjian and Dr. Cai presents at the 3rd GCC Single Cell Omics Symposium. More...
10/13/2022
Dr. Cai speaks at the Czech University of Life Sciences Prague (CZU) in Budova Tropického Zemědělství.
10/12/2022
Dr. Cai speaks at the ICSB 2022, Berlin, Germany. Final program is here.
10/04/2022
AgriLife E-Newsletter: AgriLife Research-led study examines nonalcoholic fatty liver disease.
09/27/2022
Dr. Cai speaks at the Single Cell Omics Data Workshop at BioScience Research Collaborative. More...
08/15/2022
Qian starts working as an intern in Johnson & Johnson.
08/09/2022
Yongjian speaks at the International Conference on Intelligent Biology and Medicine (ICIBM 2022) on "GenKI: a variational graph autoencoder based virtual knockout tool for gene function predictions via single-cell gene regulatory network."
08/02/2022
Yongjian receives the travel award provided by Texas A&M Institute of Data Science Graduate Travel Grants Program. Thanks, TAMIDS!
07/13/2022
Cristhian presents the quantum GRN model in the 2nd Cycle of International Conferences about hosted by Universidad Mayor de San Simon (Bolivia) and University of Cincinnati (USA).
07/12/2022
Cristhian presents the quantum GRN model in the seminar Experiences in Scientific Research Processes hosted by Universidad Nacional de Ingenieria (Peru).
06/30/2022
Quantum gene regulatory networks preprint is on. See also in arXiv:2206.15362 [cs.ET].
06/17/2022
We are hiring! See PhD Position in Machine Learning and Single-Cell Biology.
06/06/2022
Qian starts first intern in Bristol Myers Squibb.
06/03/2022
Dr. Cai speaks at the Southeast Texas Evolutionary Genetics and Genomics (STEGG) 2022 Symposium.
05/17/2022
Qian wins the Flash Talk Award (1st Place) in the 2022 CVMBS Trainee Research Symposium.
05/11/2022
Dr. Cai speaks at FutureTox V, Chapel Hill, NC.
04/15/2022
Qian's article "Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis" published in ImmunoInformatics is online.
04/12/2022
Special Issue "Single-Cell Bioinformatics and Machine Learning" has been published in our open access journal Genes (ISSN 2073-4425).
03/01/2022
SCGEATOOL is online at https://scgeatool.github.io.
02/18/2022
Qian's article "scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation" is published in Genes as part of the Special Issue Single-Cell Bioinformatics and Machine Learning and is available online.
02/01/2022
scTenifoldKnk paper is online in Patterns.
12/09/2021
Dr. Cai speaks at TAMIDS Research Conference.
11/10/2021
Yongjian publishes at Cancer Prevention Research.
10/07/2021
Yongjian speaks at the 2nd Annual Gulf Coast Consortia (GCC) Single Cell Omics Cluster Symposium.
07/28/2021
Daniel's new tool rPanglaoDB is made public.
04/01/2021
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.
03/23/2021
Preprint "scTenifoldKnk: a machine learning workflow performing virtual knockout experiments on single-cell gene regulatory networks" is posted at BioRxiv.
03/08/2021
Dr. Cai presents at the 2021 Genetics and Epigenetics Cross-Cutting Research Team (GECCRT) Meeting.
02/04/2021
Daniel receives Marie Skłodowska-Curie Actions Postdoctoral Fellowship. How to apply?
12/10/2020
Dr. Cai speaks at the 3rd Workshop on Computational Advances for Single-Cell Omics Data Analysis (CASCODA 2020).
12/03/2020
Dr. Cai speaks at the 7th NCHU GEAR UP forum.
11/29/2020
Dr. Cai speaks at the 2020 TAMU-NCHU research forum.
11/05/2020
scTenifoldNet is published online in Patterns.
10/08/2020
Dr. Cai speaks at the 1st Annual Gulf Coast Consortia (GCC) Single Cell Omics Cluster Symposium.
09/25/2020
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).
08/25/2020
Daniel publishes on Bioinformatics.
07/19/2020
Preprint: Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2. [https://osf.io/va7ux/] [ResearchGate]
04/14/2020
npj Schizophrenia paper published: Overdispersed gene expression in schizophrenia
11/01/2019
Dr. Cai speaks at The 20th International Conference on Systems Biology (ICSB2019).
06/04/2019
Opening for graduate student is available.
04/09/2019
Dr. Cai speaks at the 10x Genomics User Group meeting in Houston.
03/11/2019
We release three preprints: [bioRxiv 544163] [bioRxiv 548115] and [bioRxiv 574426].
10/13/2018
Preprint 'Overdispersed gene expression characterizes schizophrenic brains' posted at BioRxiv.
07/08/2018
Dr. Cai attends SMBE18 in Yokohama.
09/25/2017
Ahmad publishes vQTL/vGWAS simulator at BMC Genomics.
09/01/2017
Welcome to new members of the team, Daniel and Ahmad!
08/15/2017
Guangzao, as lead author, publishes at Analyst.
07/06/2017
We attend SMBE17 in Austin.
06/09/2017
We are part of PoreCamp USA 2017. Read The Eagle report.
06/02/2017
We participate the 2nd Southeast Texas Evolutionary Genetics and Genomics (STEGG) Symposium at Texas A&M University at Galveston.
05/01/2017
Postdoc position is available immediately.
04/28/2017
Opening for graduate student is available.
04/27/2017
This new lab website is launched. Lab news on the old site is still accessible here.

Research

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 theory, and quantum computation. We develop analytical frameworks to study single-cell omics data gathered from various types of cells. We also study the genetic basis of phenotypic variability in the human population and develop computational tools to identify variants underlying susceptibility to genetic disorders.

scTenifoldNet
Network Construction & Comparison

Project Title

Hypertension

Project Title

scTenifoldKnk
Virtual Gene Knockout

Project Title

scTenifoldXct
Prediction of Cell-cell Interactions

Project Title

Autism & Schizophrenia

Project Title

Overdispersed Gene Expression in Schizophrenia

Project Title

Genetic Variants Contribute to Gene Expression Variability

Project Title

Quantum Gene Regulatory Networks

Project Title

Penicilliosis

Penicilliosis

Single-Cell Expression Variability Implies Cell Function

Expression Variability

Aberrant Gene Expression in Humans

Aberrant gene expression

SCGEATOOL
Single-Cell Gene Expression Analysis Tool

scGEAToolbox

Publications

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

Journal Articles

  1. Chen B-J, Lin C-H, Wu H-Y, Cai JJ, Chao D-Y. Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer. Microbiol Spectr. 2024 Apr 2;12(4):e0395423. doi:10.1128/spectrum.03954-23. PMID:38483513.

  2. Ferrer P, Upadhyay S, Cai JJ, Clement TM. Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported by In Vivo Characterizations and AI Facilitated In Silico Mechanistic Modeling with bioRxiv [Preprint]. 2024 Feb 29:2024. doi:10.1101/2024.02.29.582797. PMID:38464253.

  3. Ahmad I, Gupta S, Faulkner P, Mullens D, Thomas M, Sytha SP, Ivanov I, Cai JJ, Heaps CL, Newell-Fugate AE. Single-nucleus transcriptomics of epicardial adipose tissue from females reveals exercise control of innate and adaptive immune cells. bioRxiv [Preprint]. 2023 Nov 5:2023. doi:10.1101/2023.11.02.565385. PMID:37961306.

  4. Ahmad, Irshad, Faulkner, Patricia, Gupta, Shreyan, Mullens, Destiny, Thomas, Micah, Sytha, Sharanee P, Ivan, Ivanov, Cai, James J, Heaps, Cristine L, Newell-Fugate, Anne Elizabeth. FRI015 Single Nuclei Transcriptomics Of Epicardial Adipose Tissue From Female Pigs Reveals Differential Effects Of Endurance Exercise On Resident Innate And Adaptive Immune Cells. J Endocr Soc. 2023/10/05;7(Supplement_1). doi:10.1210/jendso/bvad114.027.

  5. Yang Y, Lin YT, Li G, Zhong Y, Xu Q, Cai JJ. Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet. Brief Bioinform. 2023 Sep 22;24(6):bbad342. doi:10.1093/bib/bbad342. PMID:37798250.

  6. Roman-Vicharra, Cristhian, Cai, James J.. Quantum gene regulatory networks. npj Quantum Inf. 2023/07/13;9(1)1-8. doi:10.1038/s41534-023-00740-6.

  7. Chang, Hyunwoong, Cai, James J, Zhou, Quan. Order-based structure learning without score equivalence. Biometrika. ;(). doi:10.1093/biomet/asad052.

  8. Yang W, Kim DM, Jiang W, Ai W, Pan Q, Rahman S, Cai JJ, Brashear WA, Sun Y, Guo S. Suppression of FOXO1 attenuates inflamm-aging and improves liver function during aging. Aging Cell. 2023 Oct;22(10):e13968. doi:10.1111/acel.13968. PMID:37602516.

  9. Yang Y, Li G, Zhong Y, Xu Q, Chen BJ, Lin YT, Chapkin RS, Cai JJ. Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks. Nucleic Acids Res. 2023 Jul 21;51(13):6578-6592. doi:10.1093/nar/gkad450. PMID:37246643.

  10. Yang Y, Li G, Zhong Y, Xu Q, Lin YT, Roman-Vicharra C, Chapkin RS, Cai JJ. scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs. Cell Syst. 2023 Apr 19;14(4):302-311. doi:10.1016/j.cels.2023.01.004. PMID:36787742.

  11. Li H, Zheng J, Xu Q, Yang Y, Zhou J, Guo X, Cai Y, Cai JJ, Xie L, Awika J, Han X, Li Q, Kennedy L, Francis H, Glaser S, Huo Y, Alpini G, Wu C. Hepatocyte Adenosine Kinase Promotes Excessive Fat Deposition and Liver Inflammation. Gastroenterology. 2023 Jan;164(1):134-146. doi:10.1053/j.gastro.2022.09.027. PMID:36181835.

  12. Doke M, McLaughlin JP, Cai JJ, Pendyala G, Kashanchi F, Khan MA, Samikkannu T. HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis. Mol Ther Nucleic Acids. 2022 Jul 6;29:243-258. doi:10.1016/j.omtn.2022.07.001. PMID:35892093.

  13. Chen J, Tang S, Ke S, Cai JJ, Osorio D, Golovko A, Morpurgo B, Guo S, Sun Y, Winkle M, Calin GA, Tian Y. Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice. Redox Biol. 2022 Aug;54:102377. doi:10.1016/j.redox.2022.102377. PMID:35763934.

  14. Ni N, Fang X, Mullens DA, Cai JJ, Ivanov I, Bartholin L, Li Q. Transcriptomic Profiling of Gene Expression Associated with Granulosa Cell Tumor Development in a Mouse Model. Cancers (Basel). 2022 Apr 27;14(9):2184. doi:10.3390/cancers14092184. PMID:35565312.

  15. Osorio D, Zhong Y, Li G, Xu Q, Yang Y, Tian Y, Chapkin RS, Huang JZ, Cai JJ. scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation. Patterns (N Y). 2022 Feb 1;3(3):100434. doi:10.1016/j.patter.2022.100434. PMID:35510185.

  16. Xu Q, Yang Y, Zhang X, Cai JJ. Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis. Immunoinformatics (Amst). 2022 Jun;6:100013. doi:10.1016/j.immuno.2022.100013. PMID:35434695.

  17. Willis, Stuart C., Saenz, David E., Wang, Gang, Hollenbeck, Christopher M., Portnoy, David S., Cai, James J., Winemiller, Kirk O.. Gill transcriptome of the yellow peacock bass (Cichla ocellaris monoculus) exposed to contrasting physicochemical conditions. Conservation Genet Resour. 2022/12;14(4)391-401. doi:10.1007/s12686-022-01284-1.

  18. Zhou, Fangting, He, Kejun, Cai, James J., Davidson, Laurie A., Chapkin, Robert S., Ni, Yang. A Unified Bayesian Framework for Bi-overlapping-Clustering Multi-omics Data via Sparse Matrix Factorization. Stat Biosci. 2023/12;15(3)669-691. doi:10.1007/s12561-022-09350-w.

  19. Zhou F, He K, Cai JJ, Davidson LA, Chapkin RS, Ni Y. A Unified Bayesian Framework for Bi-overlapping-Clustering Multi-omics Data via Sparse Matrix Factorization. Stat Biosci. 2023 Dec;15(3):669-691. doi:10.1007/s12561-022-09350-w. PMID:38179127.

  20. Xu Q, Li G, Osorio D, Zhong Y, Yang Y, Lin YT, Zhang X, Cai JJ. scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation. Genes (Basel). 2022 Feb 18;13(2):371. doi:10.3390/genes13020371. PMID:35205415.

  21. Pinson MR, Chung DD, Mahnke AH, Salem NA, Osorio D, Nair V, Payne EA, Del Real JJ, Cai JJ, Miranda RC. Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development. Alcohol Clin Exp Res. 2022 Apr;46(4):556-569. doi:10.1111/acer.14796. PMID:35187673.

  22. Rogovskyy AS, Bailey LK, Blazier JC, Cai JJ, Landis M, Lidbury JA, Pavlova E, Wu J. The Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient. J Clin Microbiol. 2022 Feb 16;60(2):e0045321. doi:10.1128/JCM.00453-21. PMID:35170983.

  23. Yu L, Lin YL, Yan M, Li T, Wu EY, Zimmel K, Qureshi O, Falck A, Sherman KM, Huggins SS, Hurtado DO, Suva LJ, Gaddy D, Cai J, Brunauer R, Dawson LA, Muneoka K. Hyaline cartilage differentiation of fibroblasts in regeneration and regenerative medicine. Development. 2022 Jan 15;149(2):dev200249. doi:10.1242/dev.200249. PMID:35005773.

  24. Yang Y, Osorio D, Davidson LA, Han H, Mullens DA, Jayaraman A, Safe S, Ivanov I, Cai JJ, Chapkin RS. Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon. Cancer Prev Res (Phila). 2022 Jan;15(1):17-28. doi:10.1158/1940-6207.CAPR-21-0378. PMID:34815312.

  25. Osorio D, Kuijjer ML, Cai JJ. rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. Bioinformatics. 2022 Jan 3;38(2):580-582. doi:10.1093/bioinformatics/btab549. PMID:34320637.

  26. Xu H, Zhu B, Li H, Jiang B, Wang Y, Yin Q, Cai J, Glaser S, Francis H, Alpini G, Wu C. Adipocyte inducible 6-phosphofructo-2-kinase suppresses adipose tissue inflammation and promotes macrophage anti-inflammatory activation. J Nutr Biochem. 2021 Sep;95:108764. doi:10.1016/j.jnutbio.2021.108764. PMID:33964465.

  27. 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 Lab Invest. 2021 Mar;101(3):328-340. doi:10.1038/s41374-020-00523-z. PMID:33462362.

  28. 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.

  29. 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. PMID:32873716.

  30. Osorio D, Cai JJ. Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. Bioinformatics. 2021 May 17;37(7):963-967. doi:10.1093/bioinformatics/btaa751. PMID:32840568.

  31. 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.

  32. 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.

  33. 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.

  34. Cai JJ. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics. 2019 Nov 7:btz830. doi:10.1093/bioinformatics/btz830. PMID:31697351.

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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. PMID:29577871.

  40. 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. PMID:29554127.

  41. 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.

  42. 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. PMID:28853484.

  43. 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.

  44. 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.

  45. 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.

  46. 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. PMID:27131873.

  47. 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.

  48. Stafuzza NB, Naressi BC, Yang E, Cai JJ, Amaral-Trusty ME. A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly. Genet Mol Res. 2015 Oct 27;14(4):13096-104. doi:10.4238/2015.October.26.5. PMID:26535622.

  49. 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.

  50. 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.

  51. 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.

  52. 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.

  53. 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.

  54. 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. PMID:24398800.

  55. 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. PMID:24298061.

  56. 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.

  57. 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. PMID:23851338.

  58. 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.

  59. 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. PMID:23225993.

  60. 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. PMID:23150607.

  61. Brinkmeyer-Langford CL, Cai JJ, Gill CA, Skow LC. Microsatellite variation in the equine MHC. Anim Genet. 2013 Jun;44(3):267-75. doi:10.1111/age.12003. PMID:23051181.

  62. 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.

  63. 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. PMID:21300845.

  64. 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. PMID:21282640.

  65. 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. PMID:21224255.

  66. 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. PMID:20978139.

  67. Cai JJ, Borenstein E, Petrov DA. Broker genes in human disease. Genome Biol Evol. 2010;2:815-25. doi:10.1093/gbe/evq064. PMID:20937604.

  68. 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.

  69. 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. PMID:20718860.

  70. 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.

  71. 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.

  72. Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution. Evol Bioinform Online. 2007 Feb 6;2:179-82. PMID:19455210.
  73. 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. PMID:19283063.

  74. 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. PMID:19148272.

  75. 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.

  76. 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. PMID:18310616.

  77. 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. PMID:16755356.

  78. 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. PMID:16714021.

  79. 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.

  80. 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.

  81. 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.

  82. 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. PMID:12640520.

Preprints

  • Yuko Shimamura, Junichi Tanaka, Miwako Kakiuchi, Hemanta Sarmah, Akihiro Miura, Youngmin Hwang, Anri Sawada, Zurab Ninish, Kazuhiko Yamada, James J. Cai, Munemasa Mori A developmental program that regulates mammalian organ size offsets evolutionary distance bioRxiv. 2022.10.19.512107; doi:https://doi.org/10.1101/2022.10.19.512107.

Book Chapters

  • 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] [DOI]
  • Cai JJ*, Osorio D (2021) Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2. Lecture Notes in Bioinformatics (LNBI): Computational Advances in Bio and Medical Sciences. Chapter 9, DOI: 10.1007/978-3-030-79290-9_8, Springer Nature Switzerland AG. [PDF][Link]

Data Sets & Software

Meet Our Team

We are in superposition of the known and the unknown.

James Cai

James J. Cai

Professor
| Dept of Veterinary Integrative Biosciences
| Dept of Electrical & Computer Engineering
| Faculty of Genetics
| Faculty of Statistical Bioinformatics
| Advisor for QuantA&M
| Teaching Single-cell Data Analysis via ML
| Google Cites
| ORCID (0000-0002-8081-6725)
| Kanji of the year          

Qian Xu

Qian Xu

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

Yongjian Yang

Yongjian Yang

Solving complex bioinformatics problems from signal processing through biological interpretation.
          


Shreyan Gupta

Shreyan Gupta

Tackling biological challenges by exploiting machine learning.
   

Victoria Gatlin

Victoria Gatlin

A highly-motivated go-getter within the medical and science fields always seeking ways to improve through knowledge and wisdom as well as assist others.
   

Selim S. Romero Gonzalez

Selim S. Romero Gonzalez

Quantum Computing | High Performance Computing | Software Development | Biology, Chemistry & Physics| Data analyst | Modern Fortran, C#, Python, MATLAB & R

Cagatay Bal

Cagatay Bal

Artificial Neural Networks, Artificial Intelligence, Deep Learning, Soft Computing Methods, and Fuzzy Logic
   

Past Lab Members

Daniel Osorio

Daniel Osorio

Marie Skłodowska-Curie Actions Research Fellow
      

Cristhian Roman Vicharra

Cristhian Roman Vicharra

PhD student at ECEN on computer-aided design for hardware computing systems.

Yu-Te Lin

Visiting PhD Student (2021 - 2022) from National Taiwan University   

Eric Bo-Jia Chen

Visiting PhD Student (2019 - 2020) from National Chung Hsing University

Mary Xue Yu

Graduate Research Associate (2017 - 2019)      

Jingshu Chen

Graduate Research Associate (2017 - 2019)   

Eduardo Leonardecz

Visiting Professor (2017 - 2018) from Universidade Federal de São Carlos [ResearchGate]   

Steven Guangzao Huang

Visiting PhD Student (2017 - 2018) from Xiamen University

Ahmad Kawam

Graduate Research Associate (2017 - 2018)      

Aditi Kothari

TAMU Biotechnology Program Student (2016 - 2018)   

Sawyer Smith

TAMU Genetics Program Student (2016 - 2017)   

Ence Yang

PostDoc (2011 - 2015)   

Gang Wang

PhD Student (2011 - 2016)   

Jinting Guan

Visiting PhD Student (2014 - 2015) from Xiamen University

Yong Zeng

Visiting PhD Student (2013 - 2014) from Xiamen University

Jizhou Yang

TAMU Biotechnology Program Student (2014 - 2015)   

Tomasz Koralewski

PostDoc (2011 - 2012)

We strive to execute stellar projects with cross-team collaboration

Contact Form

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