Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data

Z Li, S Portillo-Ledesma, T Schlick - Current Opinion in Cell Biology, 2023 - Elsevier
Chromosome conformation capture technologies that provide frequency information for
contacts between genomic regions have been crucial for increasing our understanding of …

Chromosome structure modeling tools and their evaluation in bacteria

T Liu, QT Qiu, KJ Hua, BG Ma - Briefings in Bioinformatics, 2024 - academic.oup.com
Abstract The three-dimensional (3D) structure of bacterial chromosomes is crucial for
understanding chromosome function. With the growing availability of high-throughput …

A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural …

G Shi, D Thirumalai - Nature Communications, 2023 - nature.com
The principles that govern the organization of genomes, which are needed for an
understanding of how chromosomes are packaged and function in eukaryotic cells, could be …

Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis

M Liu, W Wang, H Zhang, J Bi, B Zhang, T Shi… - International Journal of …, 2023 - mdpi.com
Ferroptosis is an iron-dependent form of cell death, which is reported to be associated with
glioma progression and drug sensitivity. Targeting ferroptosis is a potential therapeutic …

Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

Z Li, T Schlick - Nucleic acids research, 2024 - academic.oup.com
The structure and dynamics of the eukaryotic genome are intimately linked to gene
regulation and transcriptional activity. Many chromosome conformation capture experiments …

EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient

X Wang, WC Gu, J Li, BG Ma - Bioinformatics, 2023 - academic.oup.com
Motivation Reconstruction of 3D structure models is of great importance for the study of
chromosome function. Software tools for this task are highly needed. Results We present a …

Sensor network localization via Riemannian conjugate gradient and rank reduction: An extended version

Y Li, X Sun - arXiv preprint arXiv:2403.08442, 2024 - arxiv.org
This paper addresses the Sensor Network Localization (SNL) problem using received signal
strength. The SNL is formulated as an Euclidean Distance Matrix Completion (EDMC) …

The progression in developing genomic resources for crop improvement

P Ruperao, P Rangan, T Shah, V Thakur, S Kalia… - Life, 2023 - mdpi.com
Sequencing technologies have rapidly evolved over the past two decades, and new
technologies are being continually developed and commercialized. The emerging …

Evaluation of chromosome structure modelling tools in bacteria

T Liu, QT Qiu, KJ Hua, BG Ma - bioRxiv, 2023 - biorxiv.org
The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding
chromosome function. With the growing availability of high-throughput chromosome …

Grand Biological Universe: Genome space geometry unravels looking for a single metric is likely to be futile in evolution

N Sun, H Yu, R Ren, T Zhou, M Guan, L Zhao, SST Yau - bioRxiv, 2023 - biorxiv.org
Understanding the differences between genomic sequences of different lives is crucial for
biological classification and phylogeny. Here, we downloaded all the reliable sequences of …