Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility
Induced pluripotent stem cell (iPSC) technologies have provided in vitro models of
inaccessible human cell types, yielding new insights into disease mechanisms especially for …
inaccessible human cell types, yielding new insights into disease mechanisms especially for …
[HTML][HTML] Translating RNA sequencing into clinical diagnostics: opportunities and challenges
SA Byron, KR Van Keuren-Jensen… - Nature Reviews …, 2016 - nature.com
With the emergence of RNA sequencing (RNA-seq) technologies, RNA-based biomolecules
hold expanded promise for their diagnostic, prognostic and therapeutic applicability in …
hold expanded promise for their diagnostic, prognostic and therapeutic applicability in …
A compendium of uniformly processed human gene expression and splicing quantitative trait loci
N Kerimov, JD Hayhurst, K Peikova, JR Manning… - Nature …, 2021 - nature.com
Many gene expression quantitative trait locus (eQTL) studies have published their summary
statistics, which can be used to gain insight into complex human traits by downstream …
statistics, which can be used to gain insight into complex human traits by downstream …
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
The human reference genome represents only a small number of individuals, which limits its
usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for …
usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for …
Salmon provides fast and bias-aware quantification of transcript expression
We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA–
seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich …
seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich …
scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
Single-cell RNA sequencing has enabled the characterization of highly specific cell types in
many tissues, as well as both primary and stem cell-derived cell lines. An important facet of …
many tissues, as well as both primary and stem cell-derived cell lines. An important facet of …
RNA sequencing and analysis
KR Kukurba, SB Montgomery - Cold Spring Harbor Protocols, 2015 - cshprotocols.cshlp.org
RNA sequencing (RNA-Seq) uses the capabilities of high-throughput sequencing methods
to provide insight into the transcriptome of a cell. Compared to previous Sanger sequencing …
to provide insight into the transcriptome of a cell. Compared to previous Sanger sequencing …
Normalization of RNA-seq data using factor analysis of control genes or samples
Normalization of RNA-sequencing (RNA-seq) data has proven essential to ensure accurate
inference of expression levels. Here, we show that usual normalization approaches mostly …
inference of expression levels. Here, we show that usual normalization approaches mostly …
The role of regulatory variation in complex traits and disease
FW Albert, L Kruglyak - Nature Reviews Genetics, 2015 - nature.com
We are in a phase of unprecedented progress in identifying genetic loci that cause variation
in traits ranging from growth and fitness in simple organisms to disease in humans …
in traits ranging from growth and fitness in simple organisms to disease in humans …
Ballgown bridges the gap between transcriptome assembly and expression analysis
To the Editor: Analysis of raw reads from RNA sequencing (RNA-seq) makes it possible to
reconstruct complete gene structures, including multiple splice variants, without relying on …
reconstruct complete gene structures, including multiple splice variants, without relying on …