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

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the resolution of individual cells, providing unprecedented insights into cellular heterogeneity and complex biological systems. This paper…

Many modern biological assays, including RNA sequencing, yield integer-valued counts that reflect the number of molecules detected. These measurements are often not at the desired resolution: while the unit of interest is typically a single…

Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data…

Recent experimental advances in biology allow researchers to obtain gene expression profiles at single-cell resolution over hundreds, or even thousands of cells at once. These single-cell measurements provide snapshots of the states of the…

Single-cell RNA sequencing (scRNA-seq) data simulation is limited by classical methods that rely on linear correlations, failing to capture the intrinsic, nonlinear dependencies. No existing simulator jointly models gene-gene and cell-cell…

In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…

Large language models (LLMs) have shown strong ability in generating rich representations across domains such as natural language processing and generation, computer vision, and multimodal learning. However, their application in biomedical…

Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…

Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…

Computational modeling of single-cell gene expression is crucial for understanding cellular processes, but generating realistic expression profiles remains a major challenge. This difficulty arises from the count nature of gene expression…

Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology…

Single-cell RNA sequencing (scRNA-seq) technologies have enabled the profiling of gene expression for a collection of cells across time during a dynamic biological process. Given that each time point provides only a static snapshot,…

Single-cell data analysis has the potential to revolutionize personalized medicine by characterizing disease-associated molecular changes at the single-cell level. Advanced single-cell multimodal assays can now simultaneously measure…

Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have…

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, enabling detailed molecular profiling at the individual cell level. However, integrating high-dimensional single-cell data into causal mediation…

Understanding cell identity and function through single-cell level sequencing data remains a key challenge in computational biology. We present a novel framework that leverages gene-specific textual annotations from the NCBI Gene database…

We introduce a novel gene regulatory network (GRN) inference method that integrates optimal transport (OT) with a deep-learning structural inference model. Advances in next-generation sequencing enable detailed yet destructive gene…

High-throughput sequencing is now regularly used for studies of the transcriptome (RNA-seq), particularly for comparisons among experimental conditions. For the time being, a limited number of biological replicates are typically considered…

Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…

Predicting phenotypes from gene expression data is a crucial task in biomedical research, enabling insights into disease mechanisms, drug responses, and personalized medicine. Traditional machine learning and deep learning rely on…