[HTML][HTML] Dynamic enhancer landscapes in human craniofacial development

SS Rajderkar, K Paraiso, ML Amaral, M Kosicki… - Nature …, 2024 - nature.com
The genetic basis of human facial variation and craniofacial birth defects remains poorly
understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal …

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Z Yao, H Liu, F Xie, S Fischer, AS Booeshaghi… - Biorxiv, 2020 - biorxiv.org
Single cell transcriptomics has transformed the characterization of brain cell identity by
providing quantitative molecular signatures for large, unbiased samples of brain cell …

[HTML][HTML] PeakVI: A deep generative model for single-cell chromatin accessibility analysis

T Ashuach, DA Reidenbach, A Gayoso, N Yosef - Cell reports methods, 2022 - cell.com
Single-cell ATAC sequencing (scATAC-seq) is a powerful and increasingly popular
technique to explore the regulatory landscape of heterogeneous cellular populations …

The role of single-cell genomics in human genetics

VKA Sreenivasan, S Balachandran… - Journal of medical …, 2022 - jmg.bmj.com
Single-cell sequencing is a powerful approach that can detect genetic alterations and their
phenotypic consequences in the context of human development, with cellular resolution …

Principled and interpretable alignability testing and integration of single-cell data

R Ma, ED Sun, D Donoho, J Zou - Proceedings of the …, 2024 - National Acad Sciences
Single-cell data integration can provide a comprehensive molecular view of cells, and many
algorithms have been developed to remove unwanted technical or biological variations and …

To transformers and beyond: large language models for the genome

ME Consens, C Dufault, M Wainberg, D Forster… - arXiv preprint arXiv …, 2023 - arxiv.org
In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool
for tackling complex computational challenges. This review focuses on the transformative …

[HTML][HTML] Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids

JH Kim, SJ Mun, JH Kim, MJ Son, SY Kim - Iscience, 2023 - cell.com
To gain deeper insights into transcriptomes and epigenomes of organoids, liver organoids
from two states (expandable and more differentiated) were subjected to single-cell RNA-seq …

Transcriptional and open chromatin analysis of bovine skeletal muscle development by single‐cell sequencing

C Cai, P Wan, H Wang, X Cai, J Wang, Z Chai… - Cell …, 2023 - Wiley Online Library
Skeletal muscle is a complex heterogeneous tissue and characterizing its cellular
heterogeneity and transcriptional and epigenetic signatures are important for understanding …

Single-cell analysis of cis-regulatory elements

AP Marand, RJ Schmitz - Current Opinion in Plant Biology, 2022 - Elsevier
Plant tissues and organs are composed of functionally discrete cell types that are all defined
by the same genome sequence. Cell-type variation in part arises from differential …

[HTML][HTML] Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system

LJ Campos, CM Arokiaraj, MR Chuapoco… - Current Research in …, 2023 - Elsevier
Modern neuroscience approaches including optogenetics, calcium imaging, and other
genetic manipulations have facilitated our ability to dissect specific circuits in rodent models …