[HTML][HTML] Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Long-read sequencing and novel long-range assays have revolutionized de novo genome
assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C …
assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C …
[HTML][HTML] The 3D architecture of the pepper genome and its relationship to function and evolution
The organization of chromatin into self-interacting domains is universal among eukaryotic
genomes, though how and why they form varies considerably. Here we report a …
genomes, though how and why they form varies considerably. Here we report a …
[HTML][HTML] Comparative 3D genome architecture in vertebrates
Background The three-dimensional (3D) architecture of the genome has a highly ordered
and hierarchical nature, which influences the regulation of essential nuclear processes at …
and hierarchical nature, which influences the regulation of essential nuclear processes at …
[HTML][HTML] Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D
Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable
profiling of long-range genomic interactions. However, data from these technologies are …
profiling of long-range genomic interactions. However, data from these technologies are …
[HTML][HTML] Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss
L Jin, D Wang, J Zhang, P Liu, Y Wang, Y Lin… - Nature …, 2023 - nature.com
Using an adult female miniature pig model with diet-induced weight gain/weight loss, we
investigated the regulatory mechanisms of three-dimensional (3D) genome architecture in …
investigated the regulatory mechanisms of three-dimensional (3D) genome architecture in …
[HTML][HTML] Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating'pigeon
Y Wang, X Wang, Y Luo, J Zhang, Y Lin, J Wu… - PLoS …, 2023 - journals.plos.org
Pigeons (Columba livia) are among a select few avian species that have developed a
specialized reproductive mode wherein the parents produce a 'milk'in their crop to feed …
specialized reproductive mode wherein the parents produce a 'milk'in their crop to feed …
Haplotype-resolved 3D chromatin architecture of the hybrid pig
Y Lin, J Li, Y Gu, L Jin, J Bai, J Zhang, Y Wang… - Genome …, 2024 - genome.cshlp.org
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to
imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three …
imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three …
Building Haplotype‐Resolved 3D Genome Maps of Chicken Skeletal Muscle
J Li, Y Lin, D Li, M He, H Kui, J Bai, Z Chen… - Advanced …, 2024 - Wiley Online Library
Haplotype‐resolved 3D chromatin architecture related to allelic differences in avian skeletal
muscle development has not been addressed so far, although chicken husbandry for meat …
muscle development has not been addressed so far, although chicken husbandry for meat …
[HTML][HTML] Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis
P Liu, D Li, J Zhang, M He, D Gao, Y Wang… - Journal of Biological …, 2023 - ASBMB
Elucidating the regulatory mechanisms of human adipose tissues (ATs) evolution is
essential for understanding human-specific metabolic regulation, but the functional …
essential for understanding human-specific metabolic regulation, but the functional …
R Tutorial: Detection of Differentially Interacting Chromatin Regions From Multiple Hi‐C Datasets
Abstract The three‐dimensional (3D) interactions of chromatin regulate cell‐type‐specific
gene expression, recombination, X‐chromosome inactivation, and many other genomic …
gene expression, recombination, X‐chromosome inactivation, and many other genomic …