The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Y Wang, F Song, B Zhang, L Zhang, J Xu, D Kuang… - Genome biology, 2018 - Springer
Here, we introduce the 3D Genome Browser, http://3dgenome. org, which allows users to
conveniently explore both their own and over 300 publicly available chromatin interaction …

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome

NH Lazar, KA Nevonen, B O'Connell… - Genome …, 2018 - genome.cshlp.org
The relationship between evolutionary genome remodeling and the three-dimensional
structure of the genome remain largely unexplored. Here, we use the heavily rearranged …

Identification of copy number variations and translocations in cancer cells from Hi-C data

A Chakraborty, F Ay - Bioinformatics, 2018 - academic.oup.com
Motivation Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional
(3D) structure, which profoundly affects different cellular functions and outcomes including …

Allele-specific control of replication timing and genome organization during development

JC Rivera-Mulia, A Dimond, D Vera… - Genome …, 2018 - genome.cshlp.org
DNA replication occurs in a defined temporal order known as the replication-timing (RT)
program. RT is regulated during development in discrete chromosomal units, coordinated …

Optical map** reveals a higher level of genomic architecture of chained fusions in cancer

EKF Chan, DL Cameron, DC Petersen… - Genome …, 2018 - genome.cshlp.org
Genomic rearrangements are common in cancer, with demonstrated links to disease
progression and treatment response. These rearrangements can be complex, resulting in …

Three-dimensional genome organization in breast and gynecological cancers: how chromatin folding influences tumorigenic transcriptional programs

SI Nuñez-Olvera, J Puente-Rivera, R Ramos-Payán… - Cells, 2021 - mdpi.com
A growing body of research on the transcriptome and cancer genome has demonstrated that
many gynecological tumor-specific gene mutations are located in cis-regulatory elements …

A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships

R Lohia, N Fox, J Gillis - Genome biology, 2022 - Springer
Background Chromatin contacts are essential for gene-expression regulation; however,
obtaining a high-resolution genome-wide chromatin contact map is still prohibitively …

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

KK Yan, S Lou, M Gerstein - PLoS computational biology, 2017 - journals.plos.org
Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic
genomes are organized into structural units called topologically associating domains …

Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia

H Yang, H Zhang, Y Luan, T Liu, KG Roberts, M Qian… - bioRxiv, 2020 - biorxiv.org
Inherited non-coding genetic variants confer significant disease susceptibility in many
cancers. However, the molecular processes of by which germline variants contribute to …

The genomic false shuffle: epigenetic maintenance of topological domains in the rearranged gibbon genome

NH Lazar, KA Nevonen, B O'Connell, RE Green… - BioRxiv, 2017 - biorxiv.org
The relationship between evolutionary genome remodeling and the three-dimensional
structure of the genome remain largely unexplored. Here we use the heavily rearranged …