Linking environmental risk factors with epigenetic mechanisms in Parkinson's disease

M Tsalenchuk, SM Gentleman, SJ Marzi - npj Parkinson's Disease, 2023 - nature.com
Sporadic Parkinson's disease (PD) is a progressive neurodegenerative disease, with a
complex risk structure thought to be influenced by interactions between genetic variants and …

Benchmarking computational doublet-detection methods for single-cell RNA sequencing data

NM Xi, JJ Li - Cell systems, 2021 - cell.com
In single-cell RNA sequencing (scRNA-seq), doublets form when two cells are encapsulated
into one reaction volume. The existence of doublets, which appear to be—but are not—real …

SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references

M Dong, A Thennavan, E Urrutia, Y Li… - Briefings in …, 2021 - academic.oup.com
Recent advances in single-cell RNA sequencing (scRNA-seq) enable characterization of
transcriptomic profiles with single-cell resolution and circumvent averaging artifacts …

Amniogenesis occurs in two independent waves in primates

M Rostovskaya, S Andrews, W Reik, PJ Rugg-Gunn - Cell Stem Cell, 2022 - cell.com
In primates, the amnion emerges through cavitation of the epiblast during implantation,
whereas in other species it does so later at gastrulation by the folding of the ectoderm. How …

Cancer transcriptome profiling at the juncture of clinical translation

M Cieślik, AM Chinnaiyan - Nature Reviews Genetics, 2018 - nature.com
Methodological breakthroughs over the past four decades have repeatedly revolutionized
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …

Transcriptomic comparison of human and mouse brain microvessels

HW Song, KL Foreman, BD Gastfriend, JS Kuo… - Scientific reports, 2020 - nature.com
The brain vasculature maintains brain homeostasis by tightly regulating ionic, molecular,
and cellular transport between the blood and the brain parenchyma. These blood–brain …

[HTML][HTML] DoubletDecon: deconvoluting doublets from single-cell RNA-sequencing data

EAK DePasquale, DJ Schnell, PJ Van Camp… - Cell reports, 2019 - cell.com
Methods for single-cell RNA sequencing (scRNA-seq) have greatly advanced in recent
years. While droplet-and well-based methods have increased the capture frequency of cells …

Accurate estimation of cell-type composition from gene expression data

D Tsoucas, R Dong, H Chen, Q Zhu, G Guo… - Nature …, 2019 - nature.com
The rapid development of single-cell transcriptomic technologies has helped uncover the
cellular heterogeneity within cell populations. However, bulk RNA-seq continues to be the …

[PDF][PDF] Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human pre-implantation epiblast

GG Stirparo, T Boroviak, G Guo, J Nichols… - …, 2018 - journals.biologists.com
Single-cell profiling techniques create opportunities to delineate cell fate progression in
mammalian development. Recent studies have provided transcriptome data from human pre …

scds: computational annotation of doublets in single-cell RNA sequencing data

AS Bais, D Kostka - Bioinformatics, 2020 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) technologies enable the study of
transcriptional heterogeneity at the resolution of individual cells and have an increasing …