An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data
O Oluwadare, M Highsmith, J Cheng - Biological procedures online, 2019 - Springer
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and
genome structures have proliferated. This has been primarily due to the development of high …
genome structures have proliferated. This has been primarily due to the development of high …
[HTML][HTML] Application of Hi-C and other omics data analysis in human cancer and cell differentiation research
With the development of 3C (chromosome conformation capture) and its derivative
technology Hi-C (High-throughput chromosome conformation capture) research, the study of …
technology Hi-C (High-throughput chromosome conformation capture) research, the study of …
A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data
O Oluwadare, Y Zhang, J Cheng - BMC genomics, 2018 - Springer
Background The development of chromosomal conformation capture techniques,
particularly, the Hi-C technique, has made the analysis and study of the spatial conformation …
particularly, the Hi-C technique, has made the analysis and study of the spatial conformation …
GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data
O Oluwadare, M Highsmith, D Turner… - BMC molecular and cell …, 2020 - Springer
Advances in the study of chromosome conformation capture technologies, such as Hi-C
technique-capable of capturing chromosomal interactions in a genome-wide scale-have led …
technique-capable of capturing chromosomal interactions in a genome-wide scale-have led …
DciA helicase operators exhibit diversity across bacterial phyla
HC Blaine, JT Burke, J Ravi, CL Stallings - Journal of bacteriology, 2022 - Am Soc Microbiol
ABSTRACT A fundamental requirement for life is the replication of an organism's DNA.
Studies in Escherichia coli and Bacillus subtilis have set the paradigm for DNA replication in …
Studies in Escherichia coli and Bacillus subtilis have set the paradigm for DNA replication in …
3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?
The genome is organized in a hierarchical fashion within the nucleus in interphase. This
nonrandom folding of the chromatin fiber is thought to play important roles in the processing …
nonrandom folding of the chromatin fiber is thought to play important roles in the processing …
NeRV-3D-DC: a nonlinear dimensionality reduction visualization method for 3D chromosome structure reconstruction with high resolution Hi-C data
Chromosome structure plays an essential role in exploring the relationship between
chromosome structure and gene transcription. In recent years, High-resolution Hi-C data …
chromosome structure and gene transcription. In recent years, High-resolution Hi-C data …
A 3-D Chromosome Structure Reconstruction Method With High Resolution Hi-C Data Using Nonlinear Dimensionality Reduction and Divide-and-Conquer Strategy
Chromosomes are fundamental components of genetic material, and their structural
characteristics play an essential role in the regulation of gene expression. The advent of …
characteristics play an essential role in the regulation of gene expression. The advent of …
Estimation of the spatial chromatin structure based on a multiresolution bead-chain model
We present a method to infer 3D chromatin configurations from Chromosome Conformation
Capture data. Quite a few methods have been proposed to estimate the structure of the …
Capture data. Quite a few methods have been proposed to estimate the structure of the …
ChromeBat: A bio-inspired approach to 3D genome reconstruction
With the advent of Next Generation Sequencing and the Hi-C experiment, high quality
genome-wide contact data are becoming increasingly available. These data represents an …
genome-wide contact data are becoming increasingly available. These data represents an …