Structure determination of genomic domains by satisfaction of spatial restraints
D Baù, MA Marti-Renom - Chromosome research, 2011 - Springer
Abstract The three-dimensional (3D) architecture of a genome is non-random and known to
facilitate the spatial colocalization of regulatory elements with the genes they regulate …
facilitate the spatial colocalization of regulatory elements with the genes they regulate …
Genome structure determination via 3C-based data integration by the Integrative Modeling Platform
D Bau, MA Marti-Renom - Methods, 2012 - Elsevier
The three-dimensional (3D) architecture of a genome determines the spatial localization of
regulatory elements and the genes they regulate. Thus, elucidating the 3D structure of a …
regulatory elements and the genes they regulate. Thus, elucidating the 3D structure of a …
Integrative studies of 3D genome organization and chromatin structure
M Di Stefano, G Cavalli - Current Opinion in Structural Biology, 2022 - Elsevier
The structural organization of the genome is emerging as a crucial regulator of the cell state,
affecting gene transcription, DNA replication, and repair. Over the last twenty years …
affecting gene transcription, DNA replication, and repair. Over the last twenty years …
Bridging the resolution gap in structural modeling of 3D genome organization
MA Marti-Renom, LA Mirny - PLoS computational biology, 2011 - journals.plos.org
Over the last decade, and especially after the advent of fluorescent in situ hybridization
imaging and chromosome conformation capture methods, the availability of experimental …
imaging and chromosome conformation capture methods, the availability of experimental …
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
Abstract The three-dimensional (3D) organization of chromosomes can be probed using
methods like Capture-C. However, it is unclear how such population-level data relate to the …
methods like Capture-C. However, it is unclear how such population-level data relate to the …
Computational methods for analyzing and modeling genome structure and organization
D Lin, G Bonora, GG Yardımcı… - … : Systems Biology and …, 2019 - Wiley Online Library
Recent advances in chromosome conformation capture technologies have led to the
discovery of previously unappreciated structural features of chromatin. Computational …
discovery of previously unappreciated structural features of chromatin. Computational …
Uncovering the principles of genome folding by 3D chromatin modeling
A Yildirim, L Boninsegna… - Cold Spring Harbor …, 2022 - cshperspectives.cshlp.org
Our understanding of how genomic DNA is tightly packed inside the nucleus, yet is still
accessible for vital cellular processes, has grown dramatically over recent years with …
accessible for vital cellular processes, has grown dramatically over recent years with …
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 …
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations
A multitude of sequencing-based and microscopy technologies provide the means to
unravel the relationship between the three-dimensional organization of genomes and key …
unravel the relationship between the three-dimensional organization of genomes and key …
[HTML][HTML] Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture
SJ Tjalsma, W de Laat - Current Opinion in Genetics & Development, 2021 - Elsevier
Recent years have seen a vast expansion of knowledge on three-dimensional (3D) genome
organization. The majority of studies on chromosome topology consists of pairwise …
organization. The majority of studies on chromosome topology consists of pairwise …