Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

PG Hendrickson, JA Doráis, EJ Grow, JL Whiddon… - Nature …, 2017 - nature.com
To better understand transcriptional regulation during human oogenesis and
preimplantation development, we defined stage-specific transcription, which highlighted the …

A test metric for assessing single-cell RNA-seq batch correction

M Büttner, Z Miao, FA Wolf, SA Teichmann, FJ Theis - Nature methods, 2019 - nature.com
Single-cell transcriptomics is a versatile tool for exploring heterogeneous cell populations,
but as with all genomics experiments, batch effects can hamper data integration and …

Biological sequence classification: A review on data and general methods

C Ao, S Jiao, Y Wang, L Yu, Q Zou - Research, 2022 - spj.science.org
With the rapid development of biotechnology, the number of biological sequences has
grown exponentially. The continuous expansion of biological sequence data promotes the …

Revealing the vectors of cellular identity with single-cell genomics

A Wagner, A Regev, N Yosef - Nature biotechnology, 2016 - nature.com
Single-cell genomics has now made it possible to create a comprehensive atlas of human
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

MA Eckersley-Maslin, C Alda-Catalinas… - … Reviews Molecular Cell …, 2018 - nature.com
A remarkable epigenetic remodelling process occurs shortly after fertilization, which restores
totipotency to the zygote. This involves global DNA demethylation, chromatin remodelling …

Single-cell messenger RNA sequencing reveals rare intestinal cell types

D Grün, A Lyubimova, L Kester, K Wiebrands, O Basak… - Nature, 2015 - nature.com
Understanding the development and function of an organ requires the characterization of all
of its cell types. Traditional methods for visualizing and isolating subpopulations of cells are …

[HTML][HTML] The technology and biology of single-cell RNA sequencing

AA Kolodziejczyk, JK Kim, V Svensson, JC Marioni… - Molecular cell, 2015 - cell.com
The differences between individual cells can have profound functional consequences, in
both unicellular and multicellular organisms. Recently developed single-cell mRNA …

Derivation of pluripotent stem cells with in vivo embryonic and extraembryonic potency

Y Yang, B Liu, J Xu, J Wang, J Wu, C Shi, Y Xu, J Dong… - Cell, 2017 - cell.com
Of all known cultured stem cell types, pluripotent stem cells (PSCs) sit atop the landscape of
developmental potency and are characterized by their ability to generate all cell types of an …

Classification of low quality cells from single-cell RNA-seq data

T Ilicic, JK Kim, AA Kolodziejczyk, FO Bagger… - Genome biology, 2016 - Springer
Single-cell RNA sequencing (scRNA-seq) has broad applications across biomedical
research. One of the key challenges is to ensure that only single, live cells are included in …

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

JA Dahl, I Jung, H Aanes, GD Greggains, A Manaf… - Nature, 2016 - nature.com
Maternal-to-zygotic transition (MZT) is essential for the formation of a new individual, but is
still poorly understood despite recent progress in analysis of gene expression and DNA …