[HTML][HTML] Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities

D Jiang, CR Armour, C Hu, M Mei, C Tian… - Frontiers in …, 2019 - frontiersin.org
The advent of large-scale microbiome studies affords newfound analytical opportunities to
understand how these communities of microbes operate and relate to their environment …

Light-sheet microscopy and its potential for understanding developmental processes

Y Wan, K McDole, PJ Keller - Annual review of cell and …, 2019 - annualreviews.org
The ability to visualize and quantitatively measure dynamic biological processes in vivo and
at high spatiotemporal resolution is of fundamental importance to experimental …

Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell

A Ayyaz, S Kumar, B Sangiorgi, B Ghoshal, J Gosio… - Nature, 2019 - nature.com
The turnover of the intestinal epithelium is driven by multipotent LGR5+ crypt-base columnar
cells (CBCs) located at the bottom of crypt zones. However, CBCs are lost following injury …

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 …

M3Drop: dropout-based feature selection for scRNASeq

TS Andrews, M Hemberg - Bioinformatics, 2019 - academic.oup.com
Motivation Most genomes contain thousands of genes, but for most functional responses,
only a subset of those genes are relevant. To facilitate many single-cell RNASeq …

Key role for CTCF in establishing chromatin structure in human embryos

X Chen, Y Ke, K Wu, H Zhao, Y Sun, L Gao, Z Liu… - Nature, 2019 - nature.com
In the interphase of the cell cycle, chromatin is arranged in a hierarchical structure within the
nucleus,, which has an important role in regulating gene expression,,–. However, the …

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program

M Eckersley-Maslin, C Alda-Catalinas… - Genes & …, 2019 - genesdev.cshlp.org
The molecular regulation of zygotic genome activation (ZGA) in mammals remains an
exciting area of research. Primed mouse embryonic stem cells contain a rare subset of “2C …

[HTML][HTML] Mechanosensing and mechanoregulation of endothelial cell functions

Y Fang, D Wu, KG Birukov - Comprehensive physiology, 2019 - ncbi.nlm.nih.gov
Vascular endothelial cells (ECs) form a semiselective barrier for macromolecules and cell
elements regulated by dynamic interactions between cytoskeletal elements and cell …

[HTML][HTML] Single-cell reconstruction of follicular remodeling in the human adult ovary

X Fan, M Bialecka, I Moustakas, E Lam… - Nature …, 2019 - nature.com
The ovary is perhaps the most dynamic organ in the human body, only rivaled by the uterus.
The molecular mechanisms that regulate follicular growth and regression, ensuring ovarian …

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

Y Lin, S Ghazanfar, KYX Wang… - Proceedings of the …, 2019 - National Acad Sciences
Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq)
data promises further biological insights that cannot be uncovered with individual datasets …