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Gene regulatory network inference is crucial for understanding the complex molecular interactions in various genetic and environmental conditions. The rapid development of single-cell RNA sequencing (scRNA-seq) technologies unprecedentedly…

We introduce the Poisson Log-Normal Graphical Model for count data, and present a normality transformation for data arising from this distribution. The model and transformation are feasible for high-throughput microRNA (miRNA) sequencing…

Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…

Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…

Detecting differences in gene expression is an important part of single-cell RNA sequencing experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression…

In genomics studies, the investigation of the gene relationship often brings important biological insights. Currently, the large heterogeneous datasets impose new challenges for statisticians because gene relationships are often local. They…

Background: Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling at cellular resolution but is inherently affected by sparsity caused by dropout events, where expressed genes are recorded as zeros due to technical…

Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…

Background: Single-cell RNA sequencing (scRNA-seq) is a powerful profiling technique at the single-cell resolution. Appropriate analysis of scRNA-seq data can characterize molecular heterogeneity and shed light into the underlying cellular…

Gaussian graphical models are often used to infer gene networks based on microarray expression data. Many scientists, however, have begun using high-throughput sequencing technologies to measure gene expression. As the resulting…

Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…

The analysis of single-cell RNA sequencing (scRNA-seq) data often involves fitting a latent variable model to learn a low-dimensional representation for the cells. Validating such a model poses a major challenge. If we could sequence the…

RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…

Variable selection methods are required in practical statistical modeling, to identify and include only the most relevant predictors, and then improving model interpretability. Such variable selection methods are typically employed in…

In applications such as gene regulatory network analysis based on single-cell RNA sequencing data, samples often come from a mixture of different populations and each population has its own unique network. Available graphical models often…

Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…

We consider a method to jointly estimate sparse precision matrices and their underlying graph structures using dependent high-dimensional datasets. We present a penalized maximum likelihood estimator which encourages both sparsity and…

Ultra high-throughput sequencing of transcriptomes (RNA-Seq) is a widely used method for quantifying gene expression levels due to its low cost, high accuracy and wide dynamic range for detection. However, the nature of RNA-Seq makes it…

Recent advances in high-resolution sequencing have paved the way for population-scale analysis in single-cell RNA-sequencing (scRNA-seq) data. scRNA-seq data, in particular, have proven to be extremely powerful in profiling a variety of…

Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…