[HTML][HTML] Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor …
The simultaneous measurement of three-dimensional (3D) genome structure and gene
expression of individual cells is critical for understanding a genome's structure–function …
expression of individual cells is critical for understanding a genome's structure–function …
[PDF][PDF] A machine-readable specification for genomics assays
AS Booeshaghi, X Chen, L Pachter - Bioinformatics, 2024 - academic.oup.com
Motivation Understanding the structure of sequenced fragments from genomics libraries is
essential for accurate read preprocessing. Currently, different assays and sequencing …
essential for accurate read preprocessing. Currently, different assays and sequencing …
Extruding transcription elongation loops observed in high-resolution single-cell 3D genomes
Inside human nuclei, genes are transcribed within a highly packed genome, whose
organization is facilitated by cohesin-mediated loop extrusion. However, whether cohesin …
organization is facilitated by cohesin-mediated loop extrusion. However, whether cohesin …
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice
The simultaneous measurement of three-dimensional (3D) genome structure and gene
expression of individual cells is critical for understanding genome's structure–function …
expression of individual cells is critical for understanding genome's structure–function …
Estimating and Assessing Differential Equation Models with Time-Course Data
Ordinary differential equation (ODE) models are widely used to describe chemical or
biological processes. This Article considers the estimation and assessment of such models …
biological processes. This Article considers the estimation and assessment of such models …
Assessing the multimodal tradeoff
Single-cell and single-nucleus genomics assays are becoming increasingly complex, with
multiple measurements of distinct modalities performed concurrently resulting in …
multiple measurements of distinct modalities performed concurrently resulting in …
Simultaneous single-cell chromatin architecture and gene expression sequencing by LiMCA
The concurrent measurement of chromatin organization and gene transcription within a
single cell provides a unique opportunity to investigate their intricate interplay. We introduce …
single cell provides a unique opportunity to investigate their intricate interplay. We introduce …
A single-cell 3D spatiotemporal multi-omics atlas from Drosophila embryogenesis to metamorphosis
M Wang, Q Hu, Z Tu, L Kong, J Yao, R Xiang, Z Chen… - bioRxiv, 2024 - biorxiv.org
The development of a multicellular organism is a highly intricate process tightly regulated by
numerous genes and pathways in both spatial and temporal manners. Here, we present …
numerous genes and pathways in both spatial and temporal manners. Here, we present …