Dr. Cai's research lies at the interface of single-cell biology, computational statistics, and data science. Current research focuses on using machine learning, network science and dynamical system analysis to better understand the diverse behaviors of cells. Dr. Cai's group develops novel algorithms and analytical frameworks to study single-cell omics data from various types of cells. Dr. Cai also studies the genetic basis of phenotypic variability, identifying genetic variants that control complex traits and determine the susceptibility of genetic disorders.

selected publications
Academic Articles72
  • Osorio, D., Zhong, Y., Li, G., Xu, Q., Yang, Y., Tian, Y., ... Cai, J. J. (2022). scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation. Patterns. 100434-100434.
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  • Fink, D. L., Cai, J., Whelan, M., Monit, C., de Motes, C. M., Towers, G. J., & Sumner, R. P. (2021). HIV-2/SIV Vpx antagonises NF-κB activation by targeting p65. bioRxiv. 2021.06.26.450035.
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  • Osorio, D., Kuijjer, M. L., & Cai, J. J. (2021). rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. bioRxiv. 2021.05.28.446161.
  • Cai, J. J., & Osorio, D. (2021). Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2. ALGORITHMS AND DATA STRUCTURES, PROCEEDINGS. Computational Advances in Bio and Medical Sciences. 88-94. Springer International Publishing.
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  • J., J. (2011). Evolutionary Bioinformatics with a Scientific Computing Environment. Yang, N. S. (Eds.), Systems and Computational Biology - Bioinformatics and Computational Modeling. InTech.
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Conference Papers1
  • Al Kawam, A., Alshawaqfeh, M., Cai, J., Serpedin, E., & Datta, A. (2017). Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 762-763.
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Repository Documents / Preprints1
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chaired theses and dissertations
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mailing address
MS 4458; Veterinary Integrative Biosciences; 4458 TAMU
College Station, Texas 77843