Generation and characterization of stable pig pregastrulation epiblast stem cell lines

M Zhi, J Zhang, Q Tang, D Yu, S Gao, D Gao, P Liu… - Cell Research, 2022 - nature.com
Pig epiblast-derived pluripotent stem cells are considered to have great potential and broad
prospects for human therapeutic model development and livestock breeding. Despite …

A survey on hyperlink prediction

C Chen, YY Liu - IEEE Transactions on Neural Networks and …, 2023 - ieeexplore.ieee.org
As a natural extension of link prediction on graphs, hyperlink prediction aims for the
inference of missing hyperlinks in hypergraphs, where a hyperlink can connect more than …

Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

D Li, C Ning, J Zhang, Y Wang, Q Tang, H Kui… - Nature …, 2022 - nature.com
Folliculogenesis is a complex biological process involving a central oocyte and its
surrounding somatic cells. Three-dimensional chromatin architecture is an important …

Deciphering multi-way interactions in the human genome

GA Dotson, C Chen, S Lindsly, A Cicalo… - Nature …, 2022 - nature.com
Chromatin architecture, a key regulator of gene expression, can be inferred using chromatin
contact data from chromosome conformation capture, or Hi-C. However, classical Hi-C does …

Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens

L Shen, X Bai, L Zhao, J Zhou, C Chang, X Li… - Nature …, 2024 - nature.com
Chickens are the most abundant agricultural animals globally, with controlling abdominal fat
deposition being a key objective in poultry breeding. While GWAS can identify genetic …

Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver

L Chen, J Li, R Yuan, Y Wang, J Zhang, Y Lin, L Wang… - Cell Discovery, 2022 - nature.com
Liver development is a complex process that is regulated by a series of signaling pathways.
Three-dimensional (3D) chromatin architecture plays an important role in transcriptional …

Reprogramming of 3D genome structure underlying HSPC development in zebrafish

M He, X Li, B Xu, Y Lu, J Lai, Y Ling, H Liu, Z An… - Stem Cell Research & …, 2024 - Springer
Background Development of hematopoietic stem and progenitor cells (HSPC) is a multi-
staged complex process that conserved between zebrafish and mammals. Understanding …

Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation

Y Zheng, L Zhang, L **, P Zhang, F Li, M Guo… - Journal of Biological …, 2022 - ASBMB
Spermatogonial stem cells (SSCs) are able to undergo both self-renewal and differentiation.
Unlike self-renewal, which replenishes the SSC and progenitor pool, differentiation is an …

Functional organization of the maternal and paternal human 4D nucleome

S Lindsly, W Jia, H Chen, S Liu, S Ronquist, C Chen… - IScience, 2021 - cell.com
Every human somatic cell inherits a maternal and a paternal genome, which work together
to give rise to cellular phenotypes. However, the allele-specific relationship between gene …

3D genomic alterations during development of skeletal muscle in chicken1

Z Xu, T Wang, W Zhu, M Yang, D Leng, Z Li… - Journal of Integrative …, 2024 - Elsevier
The development of skeletal muscle are complicated processes involving genes responsible
for proper muscle morphology, contractility, cell proliferation, differentiation, interactions …