Molecular quantitative trait loci

F Aguet, K Alasoo, YI Li, A Battle, HK Im… - Nature reviews …, 2023‏ - nature.com
Understanding functional effects of genetic variants is one of the key challenges in human
genetics, as much of disease-associated variation is located in non-coding regions with …

RNA sequencing data: hitchhiker's guide to expression analysis

K Van den Berge, KM Hembach… - Annual Review of …, 2019‏ - annualreviews.org
Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …

Cell-type-specific CAG repeat expansions and toxicity of mutant Huntingtin in human striatum and cerebellum

K Mätlik, M Baffuto, L Kus, AL Deshmukh, DA Davis… - Nature …, 2024‏ - nature.com
Brain region-specific degeneration and somatic expansions of the mutant Huntingtin (mHTT)
CAG tract are key features of Huntington's disease (HD). However, the relationships among …

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

MJ Gandal, P Zhang, E Hadjimichael, RL Walker… - Science, 2018‏ - science.org
INTRODUCTION Our understanding of the pathophysiology of psychiatric disorders,
including autism spectrum disorder (ASD), schizophrenia (SCZ), and bipolar disorder (BD) …

Salmon provides fast and bias-aware quantification of transcript expression

R Patro, G Duggal, MI Love, RA Irizarry, C Kingsford - Nature methods, 2017‏ - nature.com
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 …

A general and flexible method for signal extraction from single-cell RNA-seq data

D Risso, F Perraudeau, S Gribkova, S Dudoit… - Nature …, 2018‏ - nature.com
Single-cell RNA-sequencing (scRNA-seq) is a powerful high-throughput technique that
enables researchers to measure genome-wide transcription levels at the resolution of single …

Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease

C Pressl, K Mätlik, L Kus, P Darnell, JD Luo, MR Paul… - Neuron, 2024‏ - cell.com
The properties of the cell types that are selectively vulnerable in Huntington's disease (HD)
cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance …

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

C Soneson, MI Love, MD Robinson - F1000Research, 2016‏ - pmc.ncbi.nlm.nih.gov
High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the
transcriptome of cells. Many transcriptomic studies aim at comparing either abundance …

Immune induction strategies in metastatic triple-negative breast cancer to enhance the sensitivity to PD-1 blockade: the TONIC trial

L Voorwerk, M Slagter, HM Horlings, K Sikorska… - Nature medicine, 2019‏ - nature.com
The efficacy of programmed cell death protein 1 (PD-1) blockade in metastatic triple-
negative breast cancer ( TNBC) is low,,,–, highlighting a need for strategies that render the …

Missing data and technical variability in single-cell RNA-sequencing experiments

SC Hicks, FW Townes, M Teng, RA Irizarry - Biostatistics, 2018‏ - academic.oup.com
Until recently, high-throughput gene expression technology, such as RNA-Sequencing
(RNA-seq) required hundreds of thousands of cells to produce reliable measurements …