Related papers: A Unified Statistical Framework for Single Cell an…

Single-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for discovering and describing cell types in heterogeneous tissues, yet its measurement of expression often suffers from large systematic bias. A major source of this bias…

Molecular and genomic technological advancements have greatly enhanced our understanding of biological processes by allowing us to quantify key biological variables such as gene expression, protein levels, and microbiome compositions. These…

Motivation: Single-cell RNA sequencing (scRNA-seq) is a groundbreaking technology extensively utilized in biological research, facilitating the examination of gene expression at the individual cell level within a given tissue sample. While…

High-throughput RNA sequencing (RNA-seq) has emerged as a revolutionary and powerful technology for expression profiling. Most proposed methods for detecting differentially expressed (DE) genes from RNA-seq are based on statistics that…

Clustering analysis is fundamental in single-cell RNA sequencing (scRNA-seq) data analysis for elucidating cellular heterogeneity and diversity. Recent graph-based scRNA-seq clustering methods, particularly graph neural networks (GNNs),…

Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges.…

Bulk tissue RNA sequencing of heterogeneous samples provides averaged gene expression profiles, obscuring cell type-specific dynamics. To address this, we present a probabilistic hierarchical Bayesian model that deconvolves bulk RNA-seq…

In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression…

Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…

The advancement of single-cell RNA-sequencing (scRNA-seq) technologies allow us to study the individual level cell-type-specific gene expression networks by direct inference of genes' conditional independence structures. scRNA-seq data…

Bulk gene expression experiments relied on aggregations of thousands of cells to measure the average expression in an organism. Advances in microfluidic and droplet sequencing now permit expression profiling in single cells. This study of…

Single-cell RNA sequencing (scRNA-seq) technology has profiled hundreds of millions of human cells across organs, diseases, development and perturbations to date. However, the high-dimensional sparsity, batch effect noise, category…

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across…

Single-cell RNA sequencing has transformed biology by enabling the measurement of gene expression at cellular resolution, providing information for cell types, states, and disease contexts. Recently, single-cell foundation models have…

Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…

Single-cell RNA sequencing (scRNA-seq) is a relatively new technology that has stimulated enormous interest in statistics, data science, and computational biology due to the high dimensionality, complexity, and large scale associated with…

High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read count variability. These estimates are…

Single-cell transcriptomics techniques, such as scRNA-seq, attempt to characterize gene expression profiles in each cell of a heterogeneous sample individually. Due to growing amounts of data generated and the increasing complexity of the…

Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of…

Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…