# positions[].organizations[].parent[].label
College of Veterinary Medicine and Biomedical Sciences

# positions[].organizations[].parent[].label
School 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 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.

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
4009 Electronics, Sensors And Digital Hardware

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
Machine Learning And Artificial Intelligence

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
Nlr Family, Pyrin Domain-containing 3 Protein

# keywords[]
Human Induced Pluripotent Stem Cell‐derived Neural Stem Cells

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
Major Classification Is Biological Sciences

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
4009 Electronics, Sensors And Digital Hardware

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
Networking And Information Technology R&d (nitrd)

# keywords[]
Machine Learning And Artificial Intelligence

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3201 Cardiovascular Medicine And Haematology

# keywords[]
Nuclear Receptor Subfamily 4, Group A, Member 1

# keywords[]
Nuclear Receptor Subfamily 4, Group A, Member 2

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell - Human

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell - Human

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
2.6 Resources And Infrastructure (aetiology)

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell

# keywords[]
Alzheimer's Disease Including Alzheimer's Disease Related Dementias (ad/adrd)

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell - Human

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell

# keywords[]
Alzheimer's Disease Including Alzheimer's Disease Related Dementias (ad/adrd)

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
Stem Cell Research - Induced Pluripotent Stem Cell - Human

# educationAndTraining[].organization.label
University of Hong Kong - (Hong Kong, Hong Kong, China)

# educationAndTraining[].organization.label
Stanford University - (Stanford, California, United States)

# publications[].label
Population-level expression variability of mitochondrial DNA-encoded genes in humans.

# publications[].label
Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation.

# publications[].label
The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts.

# publications[].label
scTenifoldKnk: an efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation

# publications[].label
Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2

# publications[].label
Gene Function Revealed at the Moment of Stochastic Gene Silencing

# publications[].label
Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis

# publications[].label
Extent, Heritability, and Functional Relevance of Single Cell Expression Variability in Highly Homogeneous Populations of Human Cells

# publications[].label
Beyond Differential Expression: Embracing Cell-to-Cell Variability in Single-Cell Gene Expression Data Analysis

# publications[].label
scTenifoldNet: a machine learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from single-cell data

# publications[].label
Perceived and objective measures of the food store environment and the association with weight and diet among low-income women in North Carolina.

# publications[].label
Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer

# publications[].label
SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

# publications[].label
Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies

# publications[].publisher
Association for Computing Machinery (ACM)

# publications[].label
Pervasive hitchhiking at coding and regulatory sites in humans.

# publications[].label
Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis.

# publications[].label
Evolutionary Bioinformatics with a Scientific Computing Environment

# publications[].label
scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs.

# publications[].label
Overdispersed gene expression in schizophrenia.

# publications[].label
Digit regeneration in mice is stimulated by sequential treatment with FGF2 and BMP2

# publications[].label
A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly.

# publications[].label
Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action

# publications[].label
Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli.

# publications[].label
Aryl Hydrocarbon Receptor (AhR) Signaling in Colonic Cells and Tumors.

# publications[].label
Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei.

# publications[].label
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis.

# publications[].label
Hepatocyte Adenosine Kinase Promotes Excessive Fat Deposition and Liver Inflammation.

# publications[].label
Extracellular vesicles from human-induced pluripotent stem cell-derived neural stem cells alleviate proinflammatory cascades within disease-associated microglia in Alzheimer's disease.

# publications[].label
HFD feeding for seven months abolishes STING disruption-driven but not female sex-based protection against hepatic steatosis and inflammation in mice.

# publications[].label
Simulating variance heterogeneity in quantitative genome wide association studies.

# publications[].label
Draft genome sequence of Penicillium marneffei strain PM1.

# publications[].label
Transcriptomic signature, bioactivity and safety of a non-hepatotoxic analgesic generating AM404 in the midbrain PAG region.

# publications[].label
Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection.

# publications[].label
Widespread establishment and regulatory impact of Alu exons in human genes.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Functional diversification of the MADS-box gene family in fine-tuning the dimorphic transition of Talaromyces marneffei.

# publications[].label
Single-nucleus transcriptomics of epicardial adipose tissue from females reveals exercise control of innate and adaptive immune cells.

# publications[].label
Long noncoding RNA MALAT1 regulates generation of reactive oxygen species and the insulin responses in male mice.

# publications[].label
Exploring the Penicillium marneffei genome.

# publications[].label
Lanthanide transport, storage, and beyond: gene products and processes contributing to lanthanide and methanol metabolism in Methylorubrum extorquens AM1

# publications[].label
Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action.

# publications[].label
Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet

# publications[].label
scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data.

# publications[].label
Gene function revealed at the moment of sitochastic gene silencing.

# publications[].label
Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2

# publications[].label
AEGS: identifying aberrantly expressed gene sets for differential variability analysis.

# publications[].label
Single-cell RNA sequencing of a European and an African lymphoblastoid cell line.

# publications[].label
Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension.

# publications[].label
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control.

# publications[].label
scPOEM: robust co-embedding of peaks and genes revealing peak-gene regulation.

# publications[].label
Context-dependent robustness to 5' splice site polymorphisms in human populations.

# publications[].label
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control

# publications[].label
The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

# publications[].label
Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort.

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

# publications[].label
FRI015 Single Nuclei Transcriptomics Of Epicardial Adipose Tissue From Female Pigs Reveals Differential Effects Of Endurance Exercise On Resident Innate And Adaptive Immune Cells

# publications[].label
A SINGLE INTRANASAL DOSE OF HUMAN NSC-DERIVED EXTRACELLULAR VESICLES AFTER TBI INHIBITS PROINFLAMMATORY TRANSCRIPTOMIC SIGNATURES IN ASTROCYTES

# publications[].label
Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus.

# publications[].label
Single-nucleus transcriptomics of epicardial adipose tissue from female pigs reveals effects of exercise training on resident innate and adaptive immune cells.

# publications[].label
Expression of Prooncogenic Nuclear Receptor 4A (NR4A)-Regulated Genes 1-Integrin and G9a Inhibited by Dual NR4A1/2 Ligands.

# publications[].label
Single-Cell RNA Sequencing Reveals Extensive Heterogeneity and Unique Gene Trajectories in Non-Transformed and Transformed Human Lung Epithelial Cells: Insights into the Role of LncRNAs in Tumor Heterogeneity

# publications[].label
Single-Cell Expression Variability Implies Cell Function.

# publications[].label
Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes.

# publications[].label
Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy.

# publications[].label
scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation.

# publications[].label
MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution.

# publications[].label
The lncRNA RZE1 Controls Cryptococcal Morphological Transition.

# publications[].label
The Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient.

# publications[].label
Genotype-Phenotype Distinctions in Spastic Paraplegia 4 Reveal HDAC6 as a Therapeutic Target.

# publications[].label
Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon.

# publications[].publisher
American Association for Cancer Research (AACR)

# publications[].label
Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development.

# publications[].label
Suppression of FOXO1 attenuates inflamm-aging and improves liver function during aging.

# publications[].label
A developmental program that regulates mammalian organ size offsets evolutionary distance

# publications[].label
Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei.

# publications[].label
Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei (vol 580, pg 3409, 2006)

# publications[].label
Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks.

# publications[].label
Osmoregulation in freshwaters: Gene expression in the gills of a Neotropical cichlid in contrasting pH and ionic environments

# publications[].label
Diverse splicing patterns of exonized Alu elements in human tissues

# publications[].label
Gill transcriptome of the yellow peacock bass (Cichla ocellaris monoculus) exposed to contrasting physicochemical conditions

# publications[].label
Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes 2011;60:726734

# publications[].label
HIV-2/SIV Vpx antagonises NF-B activation by targeting p65

# publications[].label
Aging shapes the population-mean and dispersion of gene expression in human brains

# publications[].label
Exploring cell-to-cell variability and functional insights through differentially variable gene analysis.

# publications[].label
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis

# publications[].label
Expression profiling of disease progression in canine model of Duchenne muscular dystrophy.

# publications[].label
Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells.

# publications[].label
Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis.

# publications[].label
Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia.

# publications[].label
Controlled Noise: Evidence of Epigenetic Regulation of Single-Cell Expression Variability

# publications[].label
Genetic variants contribute to gene expression variability in humans.

# publications[].label
Morphotype transition and sexual reproduction are genetically associated in a ubiquitous environmental pathogen.

# publications[].label
Extent, heritability, and functional relevance of single cell expression variability in highly homogeneous populations of human cells

# publications[].label
High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei.

# publications[].label
Hyaline cartilage differentiation of fibroblasts in regeneration and regenerative medicine.

# publications[].label
Role of RSPO3 in Estrogen-mediated Sex Differences in Body Fat Distribution: A Single-cell Data-driven Study

# publications[].label
A Unified Bayesian Framework for Bi-overlapping-Clustering Multi-omics Data via Sparse Matrix Factorization.

# publications[].label
Single-cell RNA sequencing of a European and an African lymphoblastoid cell line

# publications[].label
Order-based structure learning without score equivalence

# publications[].label
Microsatellite variation in the equine MHC.

# publications[].label
Similarly strong purifying selection acts on human disease genes of all evolutionary ages.

# publications[].label
scTenifoldKnk: An Efficient Virtual Knockout Tool for Gene Function Predictions via Single-Cell Gene Regulatory Network Perturbation

# publications[].label
Closing the Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient

# publications[].label
HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis.

# publications[].label
Diverse splicing patterns of exonized Alu elements in human tissues.

# publications[].label
Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains.

# publications[].label
Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota.

# publications[].label
Adaptive selection of an incretin gene in Eurasian populations.

# publications[].label
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database

# publications[].label
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database

# publications[].label
Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei.

# publications[].label
Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis

# publications[].label
Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis.

# publications[].label
Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice.

# publications[].label
Transcriptomic Profiling of Gene Expression Associated with Granulosa Cell Tumor Development in a Mouse Model.

# publications[].label
Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei.

# publications[].label
Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder.

# publications[].label
PGEToolbox: A Matlab toolbox for population genetics and evolution.

# publications[].label
Correction:Expression profiling of disease progression in canine model of Duchenne muscular dystrophy.

# publications[].label
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.

# publications[].label
Controlled Noise: Evidence of epigenetic regulation of Single-Cell expression variability.

# publications[].label
Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis.

# publications[].label
MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

# publications[].label
Intranasally Administered EVs from hiPSC-derived NSCs Alter the Transcriptomic Profile of Activated Microglia and Conserve Brain Function in an Alzheimer's Model.

# publications[].label
Aerobic exercise decreases the number and transcript expression of inflammatory M1 macrophages and CD8+ T cells in the epicardial adipose tissue of female pigs.

# publications[].label
Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet.

# publications[].label
scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation.

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

# publications[].label
Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes.

# publications[].label
Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies.

# publications[].label
Extracellular Vesicles from hiPSC-derived NSCs Protect Human Neurons against A-42 Oligomers Induced Neurodegeneration, Mitochondrial Dysfunction and Tau Phosphorylation.

# publications[].label
Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes.

# researcherOn[].label
Discovery Of Host Cell Candidate Proteins Critical To The Attachment By Cryptosporidium Sporozoites

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# researcherOn[].awardedBy.preferredLabel
DHHS-NIH-National Institute of Allergy and Infectious Diseases

# researcherOn[].label
MADS-box transcriptional regulation of dimorphic transition in Penicillium marneffei

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# researcherOn[].label
Inferring Single-Cell Regulatory Networks in Neurons Derived from Veterans Afflicted with GWI

# researcherOn[].awardedBy.label
United States Department of Defense - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Host Genetic Determinants of Diversity in Viral-Induced Neuropathology

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# researcherOn[].awardedBy.preferredLabel
DHHS-NIH-National Institute of Neurological Disorders and Stroke

# streetAddress
MS 4458; Veterinary Integrative Biosciences; 4458 TAMU

# organizations[]
College of Veterinary Medicine and Biomedical Sciences

# organizations[]
School of Veterinary Medicine and Biomedical Sciences

# schools[]
College of Veterinary Medicine and Biomedical Sciences

# schools[]
School of Veterinary Medicine and Biomedical Sciences

# inTheNews[].label
$1.19 million grant will leverage single-cell sequencing technology

# inTheNews[].label
CVMBS GRADUATE STUDENT RECEIVES FELLOWSHIP TO STUDY GENETIC DRIVERS OF BREAST CANCER IN NORWAY

# etdChairOf[].label
Osorio Hurtado, Daniel C. (2021-05). Single-Cell Gene Expression Variability: Functional Assessment and Applications in Functional Genomics. Doctoral Dissertation.

# etdChairOf[].label
Chen, Jingshu (2020-05). Regulation of Oxidative Stress Pathway by LNCRNA Malat1 as a Linchpin Connecting Malat1 Pleiotropic Functions with Multiple Diseases. Doctoral Dissertation.

# etdChairOf[].label
Xu, Lahong (2022-08). Characterization of the Localized Immune Responses at the Single Cell Resolution in Arabidopsis Roots. Doctoral Dissertation.

# etdChairOf[].label
Wang, Gang (2016-05). Effects of Genetic Variants on Gene Expression Variability. Doctoral Dissertation.

# etdChairOf[].label
Osorio Hurtado, Daniel C. (2021-03). Single-Cell Gene Expression Variability: Functional Assessment and Applications in Functional Genomics. Doctoral Dissertation.