Cai, James
individual record
Associate Professor
Positions:
- Faculty, Center for Statistical Bioinformatics, College of Science
- Associate Professor (affiliated), Electrical and Computer Engineering, College of Engineering
- Associate Professor, Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences
overview
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.
education and training
- Stanford University - (Stanford, California, United States), Postdoctoral Training
- Ph.D. in Genomics, University of Hong Kong - (Hong Kong, Hong Kong, China) 2006
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.
- 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. Bioinformatics.
- 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.
- Osorio, D., & Cai, J. J. (2021). Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control.. Bioinformatics. 37(7), 963-967.
- 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.
Chapters2
- 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.
- J., J. (2011). Evolutionary Bioinformatics with a Scientific Computing Environment. Yang, N. S. (Eds.), Systems and Computational Biology - Bioinformatics and Computational Modeling. InTech.
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.
Repository Documents / Preprints1
- Cai, J. J., & Hurtado, D. (2020). Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2.
in the news
- CVMBS GRADUATE STUDENT RECEIVES FELLOWSHIP TO STUDY GENETIC DRIVERS OF BREAST CANCER IN NORWAY CVMBS NEWS April 1, 2021
researcher on
Principal Investigator2
Investigator2
recent teaching activities
- BIOT684 Direct Prof Internship: In-ab Instructor
- BIOT684 Directed Pro Internship: In-ab Instructor
- BIOT684 Directed Prof Internship Instructor
- BIOT684 Directed Prof Internship:in-ab Instructor
- BIOT684 Directed Prof Internshp Instructor
chaired theses and dissertations
- Osorio Hurtado, Daniel C. (2021-03). Single-Cell Gene Expression Variability: Functional Assessment and Applications in Functional Genomics. (Doctoral Dissertation)
- Osorio Hurtado, Daniel C. (2021-05). Single-Cell Gene Expression Variability: Functional Assessment and Applications in Functional Genomics. (Doctoral Dissertation)
- Wang, Gang (2016-05). Effects of Genetic Variants on Gene Expression Variability. (Doctoral Dissertation)
Email
jcai@tamu.edu
First Name
James
Last Name
Cai
mailing address
MS 4458; Veterinary Integrative Biosciences; 4458 TAMU
College Station, Texas 77843
USA