Computational methods for analysing multiscale 3D genome organization
Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …
characterization of the spatial organization and folding of the genome in the nucleus. In …
The 3D genome structure of single cells
The spatial organization of the genome in the cell nucleus is pivotal to cell function.
However, how the 3D genome organization and its dynamics influence cellular phenotypes …
However, how the 3D genome organization and its dynamics influence cellular phenotypes …
A fast, scalable and versatile tool for analysis of single-cell omics data
Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …
tissues. A major computational challenge in analyzing these datasets is to project the large …
Multiscale and integrative single-cell Hi-C analysis with Higashi
Abstract Single-cell Hi-C (scHi-C) can identify cell-to-cell variability of three-dimensional
(3D) chromatin organization, but the sparseness of measured interactions poses an analysis …
(3D) chromatin organization, but the sparseness of measured interactions poses an analysis …
dcHiC detects differential compartments across multiple Hi-C datasets
The compartmental organization of mammalian genomes and its changes play important
roles in distinct biological processes. Here, we introduce dcHiC, which utilizes a multivariate …
roles in distinct biological processes. Here, we introduce dcHiC, which utilizes a multivariate …
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
Loop-extrusion and phase-separation have been proposed as mechanisms that shape
chromosome spatial organization. It is unclear, however, how they perform relative to each …
chromosome spatial organization. It is unclear, however, how they perform relative to each …
High-content single-cell combinatorial indexing
RM Mulqueen, D Pokholok, BL O'Connell… - Nature …, 2021 - nature.com
Single-cell combinatorial indexing (sci) with transposase-based library construction
increases the throughput of single-cell genomics assays but produces sparse coverage in …
increases the throughput of single-cell genomics assays but produces sparse coverage in …
Single-cell Hi-C data analysis: safety in numbers
AA Galitsyna, MS Gelfand - Briefings in bioinformatics, 2021 - academic.oup.com
Over the past decade, genome-wide assays for chromatin interactions in single cells have
enabled the study of individual nuclei at unprecedented resolution and throughput. Current …
enabled the study of individual nuclei at unprecedented resolution and throughput. Current …
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi
Summary Single-cell Hi-C (scHi-C) technologies can probe three-dimensional (3D) genome
structures in individual cells. However, existing scHi-C analysis methods are hindered by the …
structures in individual cells. However, existing scHi-C analysis methods are hindered by the …
Large-scale DNA demethylation occurs in proliferating ovarian granulosa cells during mouse follicular development
T Kawai, JAS Richards, M Shimada - Communications Biology, 2021 - nature.com
During ovarian follicular development, granulosa cells proliferate and progressively
differentiate to support oocyte maturation and ovulation. To determine the underlying links …
differentiate to support oocyte maturation and ovulation. To determine the underlying links …