Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data
Chromosome conformation capture technologies that provide frequency information for
contacts between genomic regions have been crucial for increasing our understanding of …
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 …
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 …
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 …
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
The structure and dynamics of the eukaryotic genome are intimately linked to gene
regulation and transcriptional activity. Many chromosome conformation capture experiments …
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 …
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) …
strength. The SNL is formulated as an Euclidean Distance Matrix Completion (EDMC) …
The progression in developing genomic resources for crop improvement
Sequencing technologies have rapidly evolved over the past two decades, and new
technologies are being continually developed and commercialized. The emerging …
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 …
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
Understanding the differences between genomic sequences of different lives is crucial for
biological classification and phylogeny. Here, we downloaded all the reliable sequences of …
biological classification and phylogeny. Here, we downloaded all the reliable sequences of …