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Molecular quantitative trait loci
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 …
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 …
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 …
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) …
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 …
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 …
enables researchers to measure genome-wide transcription levels at the resolution of single …
Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease
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 …
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 …
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 …
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 …
(RNA-seq) required hundreds of thousands of cells to produce reliable measurements …