HR job title
- Professor
- Contact Info
- 19794585482
- Websites
- ORCiD
- 0000-0002-8081-6725
Cai, James Professor
Positions
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 quantum computing 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, and the genetic basis of phenotypic variability to identify genetic variants that modulate complex phenotypic traits and susceptibility of genetic disorders.
Research Areas
- Overview
- Publications
- Research
- Teaching
- Works By Students
- Background
- Contact
- Other
- View All
Overview
Publications
selected publications
-
academic article
-
Yan, X., Li, C., Liu, K., Zhang, T., Xu, Q., Li, X., ... Zhang, X.
(2024).
Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis. 10(7), 1126-1143.
-
Zhong, Y., Cui, S., Yang, Y., & Cai, J. J.
(2024).
Controlled Noise: Evidence of epigenetic regulation of Single-Cell expression variability. Bioinformatics.
40(7), btae457.
-
Zhou, F., He, K., Cai, J. J., Davidson, L. A., Chapkin, R. S., & Ni, Y.
(2023).
A Unified Bayesian Framework for Bi-overlapping-Clustering Multi-omics Data via Sparse Matrix Factorization. Statistics in Biosciences.
15(3), 669-691.
-
Ahmad, I., Faulkner, P., Gupta, S., Mullens, D., Thomas, M., Sytha, S. P., ... Newell-Fugate, A. E.
(2023).
FRI015 Single Nuclei Transcriptomics Of Epicardial Adipose Tissue From Female Pigs Reveals Differential Effects Of Endurance Exercise On Resident Innate And Adaptive Immune Cells. Journal of the Endocrine Society.
7(Supplement_1), bvad114.027.
-
Yang, W., Kim, D. M., Jiang, W., Ai, W., Pan, Q., Rahman, S., ... Guo, S.
(2023).
Suppression of FOXO1 attenuates inflamm-aging and improves liver function during aging. Aging Cell.
22(10), e13968.
-
Yang, Y., Lin, Y., Li, G., Zhong, Y., Xu, Q., & Cai, J. J.
(2023).
Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet. Briefings in Bioinformatics.
24(6), bbad342.
-
Yang, Y., Li, G., Zhong, Y., Xu, Q., Chen, B., Lin, Y., Chapkin, R. S., & Cai, J. J.
(2023).
Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks. 51(13), 6578-6592.
-
Yang, Y., Li, G., Zhong, Y., Xu, Q., Lin, Y., Roman-Vicharra, C., Chapkin, R. S., & Cai, J. J.
(2023).
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs. 14(4), 302-311.e4.
-
Li, H., Zheng, J., Xu, Q., Yang, Y., Zhou, J., Guo, X., ... Wu, C.
(2023).
Hepatocyte Adenosine Kinase Promotes Excessive Fat Deposition and Liver Inflammation. Gastroenterology.
164(1), 134-146.
-
Roman-Vicharra, C., & Cai, J. J.
(2023).
Quantum gene regulatory networks. npj Quantum Information.
9(1), 67.
-
Willis, S. C., Saenz, D. E., Wang, G., Hollenbeck, C. M., Portnoy, D. S., Cai, J. J., & Winemiller, K. O.
(2022).
Gill transcriptome of the yellow peacock bass (Cichla ocellaris monoculus) exposed to contrasting physicochemical conditions. Conservation Genetics Resources.
14(4), 391-401.
-
Doke, M., McLaughlin, J. P., Cai, J. J., Pendyala, G., Kashanchi, F., Khan, M. A., & Samikkannu, T.
(2022).
HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis. Molecular Therapy : Nucleic Acids.
29, 243-258.
-
Pinson, M. R., Chung, D. D., Mahnke, A. H., Salem, N. A., Osorio, D., Nair, V., ... Miranda, R. C.
(2022).
Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development. Alcoholism: Clinical and Experimental Research.
46(4), 556-569.
-
Xu, Q., Li, G., Osorio, D., Zhong, Y., Yang, Y., Lin, Y., Zhang, X., & Cai, J. J.
(2022).
scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation. 13(2), 371-371.
-
Rogovskyy, A. S., Bailey, L. K., Blazier, J. C., Cai, J. J., Landis, M., Lidbury, J. A., Pavlova, E., & Wu, J.
(2022).
Closing the Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient. Journal of Clinical Microbiology.
60(2), e00454-e00421.
-
Rogovskyy, A. S., Bailey, L. K., Blazier, J. C., Cai, J. J., Landis, M., Lidbury, J. A., Pavlova, E., & Wu, J.
(2022).
The Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient. Journal of Clinical Microbiology.
60(2), e0045321-e00421.
-
Chen, J., Tang, S., Ke, S., Cai, J. J., Osorio, D., Golovko, A., ... Tian, Y.
(2022).
Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice. Redox Biology.
54, 102377-102377.
-
Xu, Q., Yang, Y., Zhang, X., & Cai, J. J.
(2022).
Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis. 6, 100013-100013.
-
Yu, L., Lin, Y., Yan, M., Li, T., Wu, E. Y., Zimmel, K., ... Muneoka, K.
(2022).
Hyaline cartilage differentiation of fibroblasts in regeneration and regenerative medicine. Development.
149(2), dev200249.
-
Ni, N., Fang, X., Mullens, D. A., Cai, J. J., Ivanov, I., Bartholin, L., & Li, Q.
(2022).
Transcriptomic Profiling of Gene Expression Associated with Granulosa Cell Tumor Development in a Mouse Model. Cancers.
14(9), 2184-2184.
-
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.
3(3), 100434-100434.
-
Yang, Y., Osorio, D., Davidson, L. A., Han, H., Mullens, D. A., Jayaraman, A., ... Chapkin, R. S.
(2022).
Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon. Cancer Prevention Research.
15(1), 17-28.
-
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-B activation by targeting p65. 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. 2021.05.28.446161.
-
Zhu, B., Guo, X., Xu, H., Jiang, B., Li, H., Wang, Y., ... Wu, C.
(2021).
Adipose tissue inflammation and systemic insulin resistance in mice with diet-induced obesity is possibly associated with disruption of PFKFB3 in hematopoietic cells. 101(3), 328-340.
-
Xu, H., Zhu, B., Li, H., Jiang, B., Wang, Y., Yin, Q., ... Wu, C.
(2021).
Adipocyte inducible 6-phosphofructo-2-kinase suppresses adipose tissue inflammation and promotes macrophage anti-inflammatory activation. JOURNAL OF NUTRITIONAL BIOCHEMISTRY.
95, 108764-108764.
-
Kumar, V., Ivens, A., Goodall, Z., Meehan, J., Doharey, P. K., Hillhouse, A., ... Cruz-Reyes, J.
(2020).
Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes. RNA.
26(12), 1862-1881.
-
Eldridge, R., Osorio, D., Amstalden, K., Edwards, C., Young, C. R., Cai, J. J., ... Brinkmeyer-Langford, C.
(2020).
Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies. Scientific Reports.
10(1), 7918.
-
Huang, G., Osorio, D., Guan, J., Ji, G., & Cai, J. J.
(2020).
Overdispersed gene expression in schizophrenia. npj Schizophrenia.
6(1), 9.
-
Osorio, D., Zhong, Y., Li, G., Huang, J. Z., & Cai, J. J.
(2020).
scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data. Patterns.
1(9), 100139-100139.
-
Brinkmeyer-Langford, C., Chu, C., Balog-Alvarez, C., Yu, X., Cai, J. J., Nabity, M., & Kornegay, J. N.
(2020).
Correction:Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. PLoS ONE.
15(7), e0236916-e0236916.
-
Osorio, D., & Cai, J. J.
(2020).
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control. 2020.02.20.958793.
-
Osorio, D., Zhong, Y., Li, G., Huang, J. Z., & Cai, J. J.
(2020).
scTenifoldNet: a machine learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from single-cell data. 2020.02.12.931469.
-
Osorio, D., Yu, X., Zhong, Y., Li, G., Yu, P., Serpedin, E., Huang, J. Z., & Cai, J. J.
(2019).
Single-Cell Expression Variability Implies Cell Function. Cells.
9(1), 14-14.
-
Cai, J. J.
(2019).
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics.
36(6), 1948-1949.
-
Osorio, D., Yu, X., Yu, P., Serpedin, E., & Cai, J. J.
(2019).
Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. Scientific data.
6(1), 112.
-
Guan, J., Cai, J. J., Ji, G., & Sham, P. C.
(2019).
Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder. Translational Psychiatry.
9(1), 152.
-
Osorio, D., Yu, X., Zhong, Y., Li, G., Yu, P., Serpedin, E., Huang, J., & Cai, J. J.
(2019).
Extent, heritability, and functional relevance of single cell expression variability in highly homogeneous populations of human cells. 574426.
-
Cai, J. J.
(2019).
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. 544163.
-
Osorio, D., Yu, X., Yu, P., Serpedin, E., & Cai, J. J.
(2019).
Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. 548115.
-
Roszczenko-Jasiska, P., Vu, H. N., Subuyuj, G. A., Crisostomo, R. V., Ayala, E. M., Cai, J., ... Skovran, E.
(2019).
Lanthanide transport, storage, and beyond: gene products and processes contributing to lanthanide and methanol metabolism in Methylorubrum extorquens AM1. 647677.
-
Willis, S. C., Saenz, D. E., Wang, G., Hollenbeck, C. M., Rocha, L. A., Portnoy, D. S., Cai, J. J., & Winemiller, K. O.
(2018).
Osmoregulation in freshwaters: Gene expression in the gills of a Neotropical cichlid in contrasting pH and ionic environments. 489211.
-
Brinkmeyer-Langford, C., Chu, C., Balog-Alvarez, C., Yu, X., Cai, J. J., Nabity, M., & Kornegay, J. N.
(2018).
Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. PLoS ONE.
13(3), e0194485-e0194485.
-
Al Kawam, A., Alshawaqfeh, M., Cai, J. J., Serpedin, E., & Datta, A.
(2018).
Simulating variance heterogeneity in quantitative genome wide association studies. BMC Bioinformatics.
19(Suppl 3), 72.
-
Guan, J., Chen, M., Ye, C., Cai, J. J., & Ji, G.
(2018).
AEGS: identifying aberrantly expressed gene sets for differential variability analysis. Bioinformatics.
34(5), 881-883.
-
Chen, J., Ke, S., Zhong, L., Wu, J., Tseng, A., Morpurgo, B., ... Tian, Y.
(2018).
Long noncoding RNA MALAT1 regulates generation of reactive oxygen species and the insulin responses in male mice. Biochemical Pharmacology.
152, 94-103.
-
Huang, G., Yuan, M., Chen, M., Li, L., You, W., Li, H., Cai, J. J., & Ji, G.
(2017).
Integrating multiple fitting regression and Bayes decision for cancer diagnosis with transcriptomic data from tumor-educated blood platelets. The Analyst.
142(19), 3588-3597.
-
Yang, E., Wang, G., Yang, J., Zhou, B., Tian, Y., & Cai, J. J.
(2016).
Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Human Molecular Genetics.
25(22), 4911-4919.
-
Guan, J., Yang, E., Yang, J., Zeng, Y., Ji, G., & Cai, J. J.
(2016).
Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Human Genetics.
135(7), 797-811.
-
Brinkmeyer-Langford, C., Balog-Alvarez, C., Cai, J. J., Davis, B. W., & Kornegay, J. N.
(2016).
Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy. BMC GENOMICS.
17(1), 665.
-
Brinkmeyer-Langford, C. L., Guan, J., Ji, G., & Cai, J. J.
(2016).
Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Frontiers in Aging Neuroscience.
8(AUG), 183.
-
Chacko, N., Zhao, Y., Yang, E., Wang, L., Cai, J. J., & Lin, X.
(2015).
The lncRNA RZE1 Controls Cryptococcal Morphological Transition. PLOS Genetics.
11(11), e1005692-e1005692.
-
Stafuzza, N. B., Naressi, B., Yang, E., Cai, J. J., & Amaral-Trusty, M.
(2015).
A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly. 14(4), 13096-13104.
-
Guan, J., Yang, E., Yang, J., Zeng, Y., Ji, G., & Cai, J. J.
(2015).
Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. 029488.
-
Yang, E., Wang, G., Yang, J., Zhou, B., Tian, Y., & Cai, J. J.
(2015).
Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. 026393.
-
Zeng, Y., Wang, G., Yang, E., Ji, G., Brinkmeyer-Langford, C. L., & Cai, J. J.
(2015).
Aberrant gene expression in humans. PLOS Genetics.
11(1), e1004942-e1004942.
-
Yang, E., Chow, W., Wang, G., Woo, P., Lau, S., Yuen, K., Lin, X., & Cai, J. J.
(2014).
Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. PLOS Genetics.
10(10), e1004662-e1004662.
-
Chang, C. L., Cai, J. J., Huang, S. Y., Cheng, P. J., Chueh, H. Y., & Hsu, S.
(2014).
Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis. PLoS ONE.
9(9), e105410-e105410.
-
Wang, G., Yang, E., Mandhan, I., Brinkmeyer-Langford, C. L., & Cai, J. J.
(2014).
Population-level expression variability of mitochondrial DNA-encoded genes in humans. European Journal of Human Genetics.
22(9), 1093-1099.
-
Wang, L., Tian, X., Gyawali, R., Upadhyay, S., Foyle, D., Wang, G., Cai, J. J., & Lin, X.
(2014).
Morphotype transition and sexual reproduction are genetically associated in a ubiquitous environmental pathogen. PLOS Pathogens.
10(6), e1004185-e1004185.
-
Wang, G., Yang, E., Brinkmeyer-Langford, C. L., & Cai, J. J.
(2014).
Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort. Genetics.
196(2), 413-425.
-
Wang, G., Yang, E., Smith, K. J., Zeng, Y., Ji, G., Connon, R., Fangue, N. A., & Cai, J. J.
(2014).
Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. 5(SEP), 312.
-
Yang, E., Wang, G., Woo, P., Lau, S., Chow, W., Chong, K., ... Cai, J. J.
(2013).
Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. 12(9), 1214-1224.
-
Brinkmeyer-Langford, C. L., Cai, J. J., Gill, C. A., & Skow, L. C.
(2013).
Microsatellite variation in the equine MHC. Animal Genetics.
44(3), 267-275.
-
Chang, C. L., Semyonov, J., Cheng, P. J., Huang, S. Y., Park, J. I., Tsai, H., ... Hsu, S.
(2013).
Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. PLoS ONE.
8(4), e61701-e61701.
-
Chang, C. L., Cai, J. J., Cheng, P. J., Chueh, H. Y., & Hsu, S.
(2013).
Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes 2011;60:726734. Diabetes.
62(12), 4284-4284.
-
Hulse, A. M., & Cai, J. J.
(2013).
Genetic variants contribute to gene expression variability in humans. Genetics.
193(1), 95-108.
-
Konganti, K., Wang, G., Yang, E., & Cai, J. J.
(2013).
SBEToolbox: A Matlab Toolbox for Biological Network Analysis. 9(9), 355-362.
-
Yang, E., Hulse, A. M., & Cai, J. J.
(2012).
Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. 8(8), 623-644.
-
Woo, P., Lau, S., Liu, B., Cai, J. J., Chong, K., Tse, H., ... Yuen, K.
(2011).
Draft genome sequence of Penicillium marneffei strain PM1. 10(12), 1740-1741.
-
Gustafson, A. A., Sharkey, J., Samuel-Hodge, C. D., Jones-Smith, J., Folds, M. C., Cai, J., & Ammerman, A. S.
(2011).
Perceived and objective measures of the food store environment and the association with weight and diet among low-income women in North Carolina. 14(6), 1032-1038.
-
Lu, Z., Jiang, P., Cai, J. J., & Xing, Y. i.
(2011).
Context-dependent robustness to 5' splice site polymorphisms in human populations. Human Molecular Genetics.
20(6), 1084-1096.
-
Chang, C. L., Cai, J. J., Cheng, P. J., Chueh, H. Y., & Hsu, S.
(2011).
Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes.
60(3), 726-734.
-
Shen, S., Lin, L., Cai, J. J., Jiang, P., Kenkel, E. J., Stroik, M. R., ... Xing, Y. i.
(2011).
Widespread establishment and regulatory impact of Alu exons in human genes. Proceedings of the National Academy of Sciences of the United States of America.
108(7), 2837-2842.
-
Chang, C. L., Cai, J. J., Lo, C., Amigo, J., Park, J., & Hsu, S.
(2011).
Adaptive selection of an incretin gene in Eurasian populations. Genome Research.
21(1), 21-32.
-
Woo, P., Tam, E., Chong, K., Cai, J. J., Tung, E., Ngan, A., Lau, S., & Yuen, K.
(2010).
High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei. The FEBS Journal.
277(18), 3750-3758.
-
Cai, J. J., & Petrov, D. A.
(2010).
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biology and Evolution.
2(1), 393-409.
-
Tse, H., Cai, J. J., Tsoi, H., Lam, E. P., & Yuen, K.
(2010).
Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. BMC GENOMICS.
11(1), 491.
-
Cai, J. J., Borenstein, E., & Petrov, D. A.
(2010).
Broker genes in human disease. Genome Biology and Evolution.
2, 815-825.
-
Cai, J. J., Borenstein, E., Chen, R., & Petrov, D. A.
(2009).
Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biology and Evolution.
1, 131-144.
-
Lin, L., Shen, S., Tye, A., Cai, J. J., Jiang, P., Davidson, B. L., & Xing, Y. i.
(2009).
Diverse splicing patterns of exonized Alu elements in human tissues. The FASEB Journal.
23(S1), 662.1-662.1.
-
Woo, P., Lau, S., Tse, H., Teng, J., Curreem, S., Tsang, A., ... Yuen, K.
(2009).
The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLOS Genetics.
5(3), e1000416-e1000416.
-
Cai, J. J., Macpherson, J. M., Sella, G., & Petrov, D. A.
(2009).
Pervasive hitchhiking at coding and regulatory sites in humans. PLOS Genetics.
5(1), e1000336-e1000336.
-
Lin, L., Shen, S., Tye, A., Cai, J. J., Jiang, P., Davidson, B. L., & Xing, Y. i.
(2008).
Diverse splicing patterns of exonized Alu elements in human tissues. PLOS Genetics.
4(10), e1000225-e1000225.
-
Cai, J. J.
(2008).
PGEToolbox: A Matlab toolbox for population genetics and evolution. 99(4), 438-440.
-
Cai, J. J., Smith, D. K., Xia, X., & Yuen, K.
(2007).
MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution. Evolutionary Bioinformatics.
2, 179-182.
-
Woo, P., Chong, K., Tse, H., Cai, J. J., Lau, C., Zhou, A. C., Lau, S., & Yuen, K.
(2006).
Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei (vol 580, pg 3409, 2006). 580(20), 4976-4977.
-
Woo, P., Chong, K., Tse, H., Cai, J. J., Lau, C., Zhou, A. C., Lau, S., & Yuen, K.
(2006).
Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei. FEBS Letters.
580(14), 3409-3416.
-
Cai, J. J., Woo, P., Lau, S., Smith, D. K., & Yuen, K.
(2006).
Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. Journal of Molecular Evolution.
63(1), 1-11.
-
Woo, P., Lau, S., Chu, C., Chan, K., Tsoi, H., Huang, Y. i., ... Yuen, K.
(2005).
Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. Journal of Virology.
79(2), 884-895.
-
Woo, P., Zhen, H., Cai, J. J., Yu, J., Lau, S., Wang, J., ... Yuen, K.
(2003).
The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Letters.
555(3), 469-477.
-
Yuen, K., Pascal, G., Wong, S., Glaser, P., Woo, P., Kunst, F., ... Danchin, A.
(2003).
Exploring the Penicillium marneffei genome. Archives of Microbiology.
179(5), 339-353.
-
Brinkmeyer-Langford, C. L., Guan, J., Ji, G., & Cai, J. J.
Aging shapes the population-mean and dispersion of gene expression in human brains
-
Safe, S., Han, H., Jayaraman, A., Davidson, L. A., Allred, C. D., Ivanov, I., ... Chapkin, R. S.
Aryl Hydrocarbon Receptor (AhR) Signaling in Colonic Cells and Tumors
-
Tanaka, J., Kondo, Y., Sakurai, M., Sawada, A., Hwang, Y., Miura, A., ... Mori, M.
Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells. 5(06-18),
-
Cai, J. J., Smith, D. K., Xia, X., & Yuen, K.
MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics.
6(1), 64-64.
-
Lau, S., Lo, G., Chow, F., Fan, R., Cai, J. J., Yuen, K., & Woo, P.
Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei. 10.1128/mbio.00947-10.1128/mbio.00918.
-
Huang, G., Osorio, D., Guan, J., Ji, G., & Cai, J. J.
Overdispersed gene expression characterizes schizophrenic brains
-
Bazan, H. A., Bhattacharjee, S., Reid, M. M., Jun, B., Polk, C., Strain, M., ... Bazan, N. G.
Transcriptomic signature, bioactivity and safety of a non-hepatotoxic analgesic generating AM404 in the midbrain PAG region. Scientific Reports.
14(1), 11103.
-
Osorio, D., Zhong, Y., Li, G., Xu, Q., Yang, Y., Tian, Y., ... Cai, J. J.
scTenifoldKnk: an efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation
-
Yan, X., Li, C., Liu, K., Zhang, T., Xu, Q., Li, X., ... Zhang, X.
(2024).
Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis. 10(7), 1126-1143.
-
chapter
-
Cai, J. J., & Osorio, D.
(2021).
Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2. Lecture Notes in Computer Science.
Computational Advances in Bio and Medical Sciences.
(pp. 88-94).
Springer Nature.
-
Cai, J. J.
Evolutionary Bioinformatics with a Scientific Computing Environment. Yang, N. S. (Eds.),
Systems and Computational Biology - Bioinformatics and Computational Modeling.
IntechOpen.
-
Cai, J. J., & Osorio, D.
(2021).
Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2. Lecture Notes in Computer Science.
Computational Advances in Bio and Medical Sciences.
(pp. 88-94).
Springer Nature.
-
conference paper
-
Al Kawam, A., Alshawaqfeh, M., Cai, J., Serpedin, E., & Datta, A.
(2017).
Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies. 762-763.
-
Shetty, A., Kodali, M., Rao, S., Madhu, L. N., & Cai, J.
A SINGLE INTRANASAL DOSE OF HUMAN NSC-DERIVED EXTRACELLULAR VESICLES AFTER TBI INHIBITS PROINFLAMMATORY TRANSCRIPTOMIC SIGNATURES IN ASTROCYTES. JOURNAL OF NEUROTRAUMA.
A92-A92.
-
Al Kawam, A., Alshawaqfeh, M., Cai, J., Serpedin, E., & Datta, A.
(2017).
Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies. 762-763.
-
institutional repository document
-
Zhong, Y., Cui, S., Yang, Y., & Cai, J. J.
(2024).
Controlled Noise: Evidence of Epigenetic Regulation of Single-Cell Expression Variability
-
Ahmad, I., Gupta, S., Faulkner, P., Mullens, D., Thomas, M., Sytha, S. P., ... Newell-Fugate, A. E.
(2023).
Single-nucleus transcriptomics of epicardial adipose tissue from females reveals exercise control of innate and adaptive immune cells
-
Yang, Y., Lin, Y., Li, G., Zhong, Y., Xu, Q., & Cai, J. J.
(2023).
Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet
-
Shimamura, Y., Tanaka, J., Kakiuchi, M., Sarmah, H., Miura, A., Hwang, Y., ... Mori, M.
(2022).
A developmental program that regulates mammalian organ size offsets evolutionary distance
-
Cai, J., & Roman-Vicharra, C.
(2022).
Quantum gene regulatory networks
-
Osorio, D., Zhong, Y., Li, G., Xu, Q., Yang, Y., Hillhouse, A., ... Cai, J. J.
(2021).
scTenifoldKnk: An Efficient Virtual Knockout Tool for Gene Function Predictions via Single-Cell Gene Regulatory Network Perturbation
-
Cai, J. J., & Hurtado, D.
(2020).
Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2
-
Osorio, D., Yu, X., Zhong, Y., Li, G., Yu, P., Serpedin, E., Huang, J., & Cai, J. J.
(2019).
Extent, Heritability, and Functional Relevance of Single Cell Expression Variability in Highly Homogeneous Populations of Human Cells
-
Gatlin, V., Gupta, S., Romero, S., Chapkin, R. S., & Cai, J. J.
Beyond Differential Expression: Embracing Cell-to-Cell Variability in Single-Cell Gene Expression Data Analysis
-
Gupta, S., & Cai, J. J.
Gene Function Revealed at the Moment of Stochastic Gene Silencing
-
Ferrer, P., Upadhyay, S., Cai, J. J., & Clement, T. M.
Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported by In Vivo Characterizations and AI Facilitated In Silico Mechanistic Modeling with Implications for Epigenetic Regulation in Spermiogenesis
-
Roman-Vicharra, C., & Cai, J. J.
Quantum gene regulatory networks
-
Zhong, Y., Cui, S., Yang, Y., & Cai, J. J.
(2024).
Controlled Noise: Evidence of Epigenetic Regulation of Single-Cell Expression Variability
Research
principal investigator on
- Inferring Single-Cell Regulatory Networks in Neurons Derived from Veterans Afflicted with GWI awarded by United States Department of Defense - (Washington D.C., District of Columbia, United States) 2021 - 2024
- MADS-box transcriptional regulation of dimorphic transition in Penicillium marneffei awarded by National Institutes of Health - (Bethesda, Maryland, United States) 2016 - 2019
investigator on
- Host Genetic Determinants of Diversity in Viral-Induced Neuropathology awarded by National Institutes of Health - (Bethesda, Maryland, United States) 2017 - 2022
- Discovery Of Host Cell Candidate Proteins Critical To The Attachment By Cryptosporidium Sporozoites awarded by National Institutes of Health - (Bethesda, Maryland, United States) 2018 - 2020
Teaching
teaching activities
- BIMS491 Hnr-research Instructor
- BIOT684 Directed Prof Internship Instructor
- BIOT684 Directed Prof Internship Instructor
- BIOT685 Directed Studies Instructor
- ECEN684 Professional Internship Instructor
- ECEN691 Research Instructor
- VIBS485 Directed Studies Instructor
- VIBS613 Evolutionary Bioinfo Instructor
- VIBS675 Sngl Cell Data Analysis Via Ml Instructor
- VIBS684 Professional Internship Instructor
- VIBS685 Directed Studies Instructor
- VIBS689 Sptp: Scrnaseq Via Ml Instructor
- VIBS689 Sptp: Single Cell Analyses Instructor
- VIBS689 Sptp: Single Cell Data Instructor
- VIBS689 Sptp: Single Cell Data & Ml Instructor
- VIBS689 Sptp: Single Cell Data Ana &ml Instructor
- VIBS689 Sptp: Single-cell Analy Via Ml Instructor
- VIBS691 Research Instructor
- VIBS691 Research Instructor
Works By Students
chaired theses and dissertations
-
Chen, Jingshu (2020-03). Regulation of Oxidative Stress Pathway by LNCRNA Malat1 as a Linchpin Connecting Malat1 Pleiotropic Functions with Multiple Diseases.
-
Osorio Hurtado, Daniel C. (2021-03). Single-Cell Gene Expression Variability: Functional Assessment and Applications in Functional Genomics.
-
Osorio Hurtado, Daniel C. (2021-03). Single-Cell Gene Expression Variability: Functional Assessment and Applications in Functional Genomics.
-
Wang, Gang (2016-05). Effects of Genetic Variants on Gene Expression Variability.
-
Xu, Lahong (2022-06). Characterization of the Localized Immune Responses at the Single Cell Resolution in Arabidopsis Roots.
Background
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
Contact
first name
- James
has last name
- Cai
mailing address
-
MS 4458
Veterinary Integrative Biosciences
4458 TAMU
College Station, Texas 77843
USA
Other
In the News
- jcai@tamu.edu