Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition and state, which can otherwise only be estimated by applying deconvolution methods to bulk RNA-Seq estimates. However, it has not yet become a widely used tool ...
Read More »On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiment
In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have...
Read More »Statistical analysis of differential transcript usage following Salmon quantification
Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Researchers at the University of North Carolina at Chapel Hill have developed a simple workflow...
Read More »SAVER – gene expression recovery for single-cell RNA sequencing
In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable...
Read More »Gene expression distribution deconvolution in single-cell RNA sequencing
Single-cell RNA sequencing (scRNA-seq) enables the quantification of each gene’s expression distribution across cells, thus allowing the assessment of the...
Read More »Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs
Genome-wide association studies have identified hundreds of risk loci for autoimmune disease, yet only a minority (~25%) share genetic effects with changes to gene expression (eQTLs) in immune cells. RNA-Seq based quantification at whole-gene resolution, where abundance is estimated by ...
Read More »A statistical framework for applying RNA profiling to chemical hazard detection
Use of ‘omics technologies in environmental science is expanding. However, application is mostly restricted to characterizing molecular steps leading from toxicant interaction with molecular receptors to apical endpoints in laboratory species. Use in environmental decision-making is limited, due to difficulty ...
Read More »Reproducible Bioinformatics Project
Reproducible research is a key component of the scientific method and represents the ability of repeating an experiment in any place with any person. A study can be truly reproducible when it satisfies at least the following three criteria. – ...
Read More »Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data
The amounts and types of available multimodal tumor data are rapidly increasing, and their integration is critical for fully understanding the underlying cancer biology and personalizing treatment. However, the development of methods for effectively integrating multimodal data in a principled ...
Read More »A comprehensive simulation study on classification of RNA-Seq data
RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as ...
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