James J. Cai

I'm a Professor in the Department of Veterinary Integrative Biosciences at Texas A&M University currently working on computational biology and bioinformatics with a focus on analyzing single-cell genomic data. My research uses machine learning and statistical approaches to study gene regulation and expression variation at the single-cell level.

My work focuses on developing computational methods and tools for analyzing large-scale genomic data, particularly single-cell RNA sequencing data. I'm interested in understanding how genes are regulated and how their expression varies between cells and in different conditions. Recently, I've developed several novel computational methods including scTenifoldKnk for performing virtual gene knockout experiments using single-cell data, and tools for analyzing cell-to-cell variability in gene expression.

Prior to joining Texas A&M, I was a postdoctoral researcher at Stanford University studying population genetics and molecular evolution. I've published extensively on topics including gene expression regulation, genetic variation, and development of computational tools for genomic analysis. My lab collaborates widely with experimental biologists to apply our computational approaches to important biological questions in development, disease, and evolution.

Publications

Extracellular vesicles from human‐induced pluripotent stem cell‐derived neural stem cells alleviate proinflammatory cascades within disease‐associated microglia in Alzheimer's disease

L. Madhu, Maheedhar Kodali, Raghavendra Upadhya, Shama Rao, Yogish Somayaji, Sahithi Attaluri, Bing Shuai, Maha Kirmani, Shreyan Gupta, Nathaniel Maness, Xiaolan Rao, James J. Cai, Ashok K. Shetty

Journal of Extracellular Vesicles 2024

ABS

Gene Function Revealed at the Moment of Stochastic Gene Silencing

Shreyan Gupta, James J. Cai

bioRxiv 2024

James J. Cai

Publications

Extracellular vesicles from human‐induced pluripotent stem cell‐derived neural stem cells alleviate proinflammatory cascades within disease‐associated microglia in Alzheimer's disease

Gene Function Revealed at the Moment of Stochastic Gene Silencing

Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis

Beyond Differential Expression: Embracing Cell-to-Cell Variability in Single-Cell Gene Expression Data Analysis

Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis.

Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli

Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells

Single-nucleus transcriptomics of epicardial adipose tissue from female pigs reveals effects of exercise training on resident innate and adaptive immune cells

Controlled noise: evidence of epigenetic regulation of single-cell expression variability

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

Intranasally Administered EVs from hiPSC-derived NSCs Alter the Transcriptomic Profile of Activated Microglia and Conserve Brain Function in an Alzheimer’s Model

Single-nucleus transcriptomics of epicardial adipose tissue from females reveals exercise control of innate and adaptive immune cells

FRI015 Single Nuclei Transcriptomics Of Epicardial Adipose Tissue From Female Pigs Reveals Differential Effects Of Endurance Exercise On Resident Innate And Adaptive Immune Cells

Suppression of FOXO1 attenuates inflamm‐aging and improves liver function during aging

Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet

Aryl Hydrocarbon Receptor (AhR) Signaling in Colonic Cells and Tumors

scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs.

A developmental program that regulates mammalian organ size offsets evolutionary distance

Hepatocyte Adenosine Kinase Promotes Excessive Fat Deposition and Liver Inflammation.

Gill transcriptome of the yellow peacock bass (Cichla ocellaris monoculus) exposed to contrasting physicochemical conditions

A Unified Bayesian Framework for Bi-overlapping-Clustering Multi-omics Data via Sparse Matrix Factorization

HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis

Quantum gene regulatory networks

Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice

Transcriptomic Profiling of Gene Expression Associated with Granulosa Cell Tumor Development in a Mouse Model

Gag‐like proteins: Novel mediators of prenatal alcohol exposure in neural development

Closing the Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient

The Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient

scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation

scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation

Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon

scTenifoldKnk: An Efficient Virtual Knockout Tool for Gene Function Predictions via Single-Cell Gene Regulatory Network Perturbation

rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database

Adipocyte Inducible 6-phosphofructo-2-kinase Suppresses Adipose Tissue Inflammation and Promotes Macrophage Anti-inflammatory Activation.

Adipose tissue inflammation and systemic insulin resistance in mice with diet-induced obesity is possibly associated with disruption of PFKFB3 in hematopoietic cells.

Adipose Tissue Inflammation and Systemic Insulin Resistance in Mice with Diet-induced Obesity Is Possibly Associated with Disruption of PFKFB3 in Hematopoietic Cells

In-Silico Knockout Experiments from Single-Cell Gene Regulatory Networks [R package scTenifoldKnk version 1.0.0]

Construct and Compare scGRN from Single-Cell Transcriptomic Data [R package scTenifoldNet version 1.2.4]

Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes

Correction: Expression profiling of disease progression in canine model of Duchenne muscular dystrophy

Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2

Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies

Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies

Overdispersed gene expression in schizophrenia

Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control

scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data

Single-Cell Expression Variability Implies Cell Function

Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder

Single cell expression variability in highly homogeneous populations of human cells is widespread, heritable, and implies cell function

Extent, Heritability, and Functional Relevance of Single Cell Expression Variability in Highly Homogeneous Populations of Human Cells

Single-cell RNA sequencing of a European and an African lymphoblastoid cell line

scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis

Osmoregulation in freshwaters: Gene expression in the gills of a Neotropical cichlid in contrasting pH and ionic environments

Overdispersed gene expression characterizes schizophrenic brains

Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei

Long noncoding RNA MALAT1 regulates generation of reactive oxygen species and the insulin responses in male mice

Expression profiling of disease progression in canine model of Duchenne muscular dystrophy

AEGS: identifying aberrantly expressed gene sets for differential variability analysis

Integrating multiple fitting regression and Bayes decision for cancer diagnosis with transcriptomic data from tumor-educated blood platelets.

Simulating variance heterogeneity in quantitative genome wide association studies

Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy

Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly.

Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis

Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action

Aberrant Gene Expression in Humans

Signature Gene Expression Reveals Novel Clues to the Molecular Mechanisms of Dimorphic Transition in Penicillium marneffei

Adaptive Human CDKAL1 Variants Underlie Hormonal Response Variations at the Enteroinsular Axis

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension

Morphotype Transition and Sexual Reproduction Are Genetically Associated in a Ubiquitous Environmental Pathogen

Population-level expression variability of mitochondrial DNA-encoded genes in humans

Additive, Epistatic, and Environmental Effects Through the Lens of Expression Variability QTL in a Twin Cohort

Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei

Microsatellite variation in the equine MHC.

Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection

Genetic Variants Contribute to Gene Expression Variability in Humans