RNA-Seq differential expression analysis: An extended review and a software tool
The correct identification of differentially expressed genes (DEGs) between specific
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
Toxicity testing in the 21st century: progress in the past decade and future perspectives
D Krewski, ME Andersen, MG Tyshenko… - Archives of …, 2020 - Springer
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 …
based on expanded application of high-throughput in vitro screening and in silico methods …
TPM, FPKM, or normalized counts? A comparative study of quantification measures for the analysis of RNA-seq data from the NCI patient-derived models repository
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 …
(RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter …
Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials
Y Zheng, Y Liu, J Yang, L Dong, R Zhang, S Tian… - Nature …, 2024 - nature.com
Abstract Characterization and integration of the genome, epigenome, transcriptome,
proteome and metabolome of different datasets is difficult owing to a lack of ground truth …
proteome and metabolome of different datasets is difficult owing to a lack of ground truth …
Blood molecular markers associated with COVID‐19 immunopathology and multi‐organ damage
YM Chen, Y Zheng, Y Yu, Y Wang, Q Huang… - The EMBO …, 2020 - embopress.org
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 …
adverse effects on the function of multiple organs. To understand host responses to COVID …
Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing
platforms remains an ongoing challenge. Here the Association of Biomolecular Resource …
platforms remains an ongoing challenge. Here the Association of Biomolecular Resource …
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Motivation: Next-generation sequencing technologies generate millions of short sequence
reads, which are usually aligned to a reference genome. In many applications, the key …
reads, which are usually aligned to a reference genome. In many applications, the key …
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts
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 …
seq experiments. The voom method estimates the mean-variance relationship of the log …
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
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 …
technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and …
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
Nature biotechnology, 2014 - nature.com
We present primary results from the Sequencing Quality Control (SEQC) project,
coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life …
coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life …