Single-cell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is either strongly non-zero or non-detectable. We propose a two-part, generalized linear model for such bimodal data that parameterizes both of these features. We argue that the cellular detection rate, the fraction of genes expressed in a cell, should be adjusted for as a source of nuisance variation. Our model provides gene set enrichment analysis tailored to single-cell data. It provides insights into how networks of co-expressed genes evolve across an experimental treatment. MAST is available at https://github.com/RGLab/MAST .
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
Profound enhancement of the IL-12/IL-18 pathway of IFN-gamma secretion in human CD8+ memory T cell subsets via IL-15
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells
Bystander-activated memory CD8 T cells control early pathogen load in an innate-like, NKG2D-dependent manner
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms
SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation
Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development
Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells
ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data
Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data
Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data
Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes
Controlled Human Malaria Infection Leads to Long-Lasting Changes in Innate and Innate-like Lymphocyte Populations
Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics
clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data
Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes
Optimal Gene Filtering for Single-Cell data (OGFSC)-a gene filtering algorithm for single-cell RNA-seq data
A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers
Single-cell RNA-Seq of follicular lymphoma reveals malignant B-cell types and coexpression of T-cell immune checkpoints.
Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing
Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome
A divergent population of autoantigen-responsive CD4+ T cells in infants prior to β cell autoimmunity
Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease
scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data
Detection of differentially expressed genes in discrete single-cell RNA sequencing data using a hurdle model with correlated random effects
ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
Evaluating genetic causes of azoospermia: What can we learn from a complex cellular structure and single-cell transcriptomics of the human testis?
Understanding the complexity of retina and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospective
The human tissue-resident CCR5+ T cell compartment maintains protective and functional properties during inflammation
netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis
Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer's disease
Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response
Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection
Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth
Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium
Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection.
Single cell RNA sequencing identifies an early monocyte gene signature in acute respiratory distress syndrome
Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories
Identification and characterization of cellular heterogeneity within the developing renal interstitium
Integrated Skin Transcriptomics and Serum Multiplex Assays Reveal Novel Mechanisms of Wound Healing in Diabetic Foot Ulcers
TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data.
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
A statistical approach for identifying differential distributions in single-cell RNA-seq experiments
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data
CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type
SREBP1 drives Keratin-80-dependent cytoskeletal changes and invasive behavior in endocrine-resistant ERα breast cancer
Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development
Mono- and multi-nucleated ventricular cardiomyocytes constitute a transcriptionally homogenous cell population
Single-cell RNA sequencing identifies senescent cerebromicrovascular endothelial cells in the aged mouse brain
Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses
Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes
Enhanced Phenotype Definition for Precision Isolation of Precursor Exhausted Tumor-Infiltrating CD8 T Cells
Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies.
Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.
Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature
T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers.
Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19
Metabolic plasticity of HIV-specific CD8+ T cells is associated with enhanced antiviral potential and natural control of HIV-1 infection
Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
High-Resolution Transcriptomic Profiling of the Heart During Chronic Stress Reveals Cellular Drivers of Cardiac Fibrosis and Hypertrophy
Single Cell RNA-seq Data Analysis Reveals the Potential Risk of SARS-CoV-2 Infection Among Different Respiratory System Conditions
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes
Beyond Enumeration: Functional and Computational Analysis of Circulating Tumor Cells to Investigate Cancer Metastasis
Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm
DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis.
Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8+ T cell responses
Systematic expression analysis of ligand-receptor pairs reveals important cell-to-cell interactions inside glioma
Single Cell Profiling Reveals PTEN Overexpression in Influenza-Specific B cells in Aging HIV-infected individuals on Anti-retroviral Therapy
CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation
Chronic Immune Activation in Systemic Lupus Erythematosus and the Autoimmune PTPN22 Trp620 Risk Allele Drive the Expansion of FOXP3+ Regulatory T Cells and PD-1 Expression
Single-Cell Transcriptome Data Clustering via Multinomial Modeling and Adaptive Fuzzy K-Means Algorithm
Integration and reanalysis of transcriptomics and methylomics data derived from blood and testis tissue of men with 47,XXY Klinefelter syndrome indicates the primary involvement of Sertoli cells in the testicular pathogenesis
Prdm8 regulates pMN progenitor specification for motor neuron and oligodendrocyte fates by modulating Shh signaling response
DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data
Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles
Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway
Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement
bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation
Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy
Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq.
Differential Impacts on Host Transcription by ROP and GRA Effectors from the Intracellular Parasite Toxoplasma gondii
VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies
DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy
Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity
M1hot tumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer.
Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq.
Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis.
DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning
Identification of differentially expressed genes in lung adenocarcinoma cells using single-cell RNA sequencing not detected using traditional RNA sequencing and microarray
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA sequencing data quality control
Limited proliferation capacity of aortic intima resident macrophages requires monocyte recruitment for atherosclerotic plaque progression
Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Mesenchymal stem cells alleviate LPS-induced acute lung injury by inhibiting the proinflammatory function of Ly6C+ CD8+ T cells
SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation
Gli1+ mesenchymal stromal cells form a pathological niche to promote airway progenitor metaplasia in the fibrotic lung
Staphylococcus epidermidis Boosts Innate Immune Response by Activation of Gamma Delta T Cells and Induction of Perforin-2 in Human Skin
Single-Cell Transcriptomics of Engineered Cardiac Tissues From Patient-Specific Induced Pluripotent Stem Cell-Derived Cardiomyocytes Reveals Abnormal Developmental Trajectory and Intrinsic Contractile Defects in Hypoplastic Right Heart Syndrome.
Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19
Emergence of non-canonical parvalbumin-containing interneurons in hippocampus of a murine model of Type I lissencephaly
muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data
Distinct inflammatory profiles distinguish COVID-19 from influenza with limited contributions from cytokine storm
Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade
Constitutive activation of cellular immunity underlies the evolution of resistance to infection in Drosophila
Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
A comparison of methods accounting for batch effects in differential expression analysis of UMI count based single cell RNA sequencing
Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging.
Control of the Anterior Pituitary Cell Lineage Regulator POU1F1 by the Stem Cell Determinant Musashi.
Adipose tissue inflammation and systemic insulin resistance in mice with diet-induced obesity is possibly associated with disruption of PFKFB3 in hematopoietic cells.
Whole-body senescent cell clearance alleviates age-related brain inflammation and cognitive impairment in mice.
Baricitinib treatment resolves lower-airway macrophage inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques.
Single-Cell RNA Sequencing Reveals Heterogeneity of Vascular Cells in Early Stage Murine Abdominal Aortic Aneurysm.
Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells.
Dissecting the Invasion-Associated Long Non-coding RNAs Using Single-Cell RNA-Seq Data of Glioblastoma.
Transcriptional Diversity and Niche-Specific Distribution of Leukocyte Populations during Staphylococcus aureus Craniotomy-Associated Biofilm Infection.
Increased APOE ε4 expression is associated with the difference in Alzheimer's disease risk from diverse ancestral backgrounds.
Binary Fate Choice between Closely Related Interneuronal Types Is Determined by a Fezf1-Dependent Postmitotic Transcriptional Switch
JOINT for large-scale single-cell RNA-sequencing analysis via soft-clustering and parallel computing
Single-cell molecular profiling of all three components of the HPA axis reveals adrenal ABCB1 as a regulator of stress adaptation.
Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
Single-cell transcriptional analysis reveals developmental stage-dependent changes in retinal progenitors in the murine early optic vesicle.
Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.
Identification of Novel Population-Specific Cell Subsets in Chinese Ulcerative Colitis Patients Using Single-Cell RNA Sequencing.
Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation.
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Chromatin Regulation and Circadian Clocks
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