The correct identification of differentially expressed genes (DEGs) between specific
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …

Advances in the biological sciences have led to an ongoing paradigm shift in toxicity testing
based on expanded application of high-throughput in vitro screening and in silico methods …

Background In order to correctly decode phenotypic information from RNA-sequencing
(RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter …

Abstract Characterization and integration of the genome, epigenome, transcriptome,
proteome and metabolome of different datasets is difficult owing to a lack of ground truth …

COVID‐19 is characterized by dysregulated immune responses, metabolic dysfunction and
adverse effects on the function of multiple organs. To understand host responses to COVID …

Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing
platforms remains an ongoing challenge. Here the Association of Biomolecular Resource …

Motivation: Next-generation sequencing technologies generate millions of short sequence
reads, which are usually aligned to a reference genome. In many applications, the key …

New normal linear modeling strategies are presented for analyzing read counts from RNA-
seq experiments. The voom method estimates the mean-variance relationship of the log …

Read alignment is an ongoing challenge for the analysis of data from sequencing
technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and …

We present primary results from the Sequencing Quality Control (SEQC) project,
coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life …