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 ...
Read More »Do I Need to Validate My RNA-Seq Results With qPCR?
Despite RNA-Seq being the capstone technology for gene expression profiling, qPCR remains the go-to technique for validation. To this day, qPCR validation of microarray data is commonplace, and many see it as necessary, given that microarrays involve hybridization to a glass ...
Read More »Correcting for RNA quality in differential expression analysis
RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. Researchers at the Johns Hopkins School of Medicine demonstrate here that statistical adjustment using existing quality measures largely fails to ...
Read More »Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data
In differential expression analysis of RNA-sequencing (RNA-seq) read count data for two sample groups, it is known that highly expressed genes (or longer genes) are more likely to be differentially expressed which is called read count bias (or gene length ...
Read More »Gene length and detection bias in single cell RNA sequencing protocols
Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, ...
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