Results 31 to 40 of about 39,833,464 (257)

Algorithmic considerations when analysing capture Hi-C data [version 2; peer review: 2 approved]

Wellcome Open Research, 2022
Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by ...
Linden Disney-Hogg, Richard Houlston, Ben Kinnersley   +2 more
doaj   +2 more sources

Significance in scale space for Hi-C data. [PDF]

Bioinformatics
Abstract Motivation Hi-C technology has been developed to profile genome-wide chromosome conformation. So far Hi-C data have been generated from a large compendium of different cell types and different tissue types. Among different chromatin conformation units, chromatin loops were found to play a key
Liu R, Zhang Z, Won H, Marron JS.
europepmc   +4 more sources

A Multigraph-Based Representation of Hi-C Data

Genes, 2022
Chromatin–chromatin interactions and three-dimensional (3D) spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts to environmental stimuli, the linear ...
Diána Makai, András Cseh, Adél Sepsi, Szabolcs Makai   +3 more
openaire   +3 more sources

Software tools for visualizing Hi-C data [PDF]

Genome Biology, 2016
Abstract Recently developed, high-throughput assays for measuring the three-dimensional configuration of DNA in the nucleus have provided unprecedented insights into the relationship between DNA 3D configuration and function. However, accurate interpretation of data from assays such as ChIA-PET and Hi-C is challenging because the data ...
Galip Gürkan Yardımcı, William Stafford Noble   +1 more
openaire   +2 more sources

Spectral and deep learning approaches to Hi-C data analysis [PDF]

, 2021
Hi-C matrices describe the genome-wide contact probability between chromatin loci. The comparison of Hi-C matrices is important both to assess the reproducibility in biological replicates and to find significant differences between non replicates from ...
Franzini, Stefano
core   +1 more source

Overcoming Artificial Structures in Resolution-Enhanced Hi-C Data by Signal Decomposition and Multi-Scale Attention. [PDF]

Adv Sci (Weinh)
Deep‐learning‐based signal enhancement is an effective way to recover high‐resolution details from a low‐resolution chromatin contact map. However, due to computational challenges, existing methods commonly divide up the contact map into small patches and create artificial discontinuities at patch boundaries.
Li Q, Li KY, Nicoletti C, Tsui SK, Puri PL, Cao Q, Yip KY.   +6 more
europepmc   +2 more sources

HI-FRIENDS participation in the SKA Data Challenge 2

, 2021
This repository contains the workflow used to find and characterize the HI sources in the data cube of the SKA Data Challenge 2. This is developed by the HI-FRIENDS team.
Darriba, Laura, Parra, Manuel, Kamphuis, Peter, Alberdi, Antonio, Garrido, Julian, School of Physics and Astronomy, Sabater, José, Márquez, Isabel, Józsa, Gyula, Sorgho, Amidou, Herranz, Diego, University of Arizona, Instituto de Astrofísica de Canarias, Jones, Michael, Francisco Gomez, Jose, Akhlaghi, Mohammad, Pandey-Pommier, Mamta, Kleiner, Dane, Moldon, Javier, Ruhr University Bochum, Cannon, John, Gomez, Jose Francisco, Verdes-Montenegro, Lourdes, Sanchez, Susana   +23 more
core   +2 more sources

Motif-Hi-C: A motif-based framework for rapid quality control of Hi-C data. [PDF]

aBIOTECH
Kong D, Wang Y, Tang Y, Tian Y, Yang S, Wang Y, Zhang Y, Kong S.   +7 more
europepmc   +2 more sources

MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data

BMC Genomics, 2020
Background Hi-C is a molecular biology technique to understand the genome spatial structure. However, data obtained from Hi-C experiments is biased. Therefore, several methods have been developed to model Hi-C data and identify significant interactions ...
Saman Khakmardan, Mohsen Rezvani, Ali Akbar Pouyan, Mansoor Fateh, Hamid Alinejad-Rokny   +4 more
doaj   +1 more source

Detecting community structures in Hi-C genomic data [PDF]

2016 Annual Conference on Information Science and Systems (CISS), 2016
Community detection (CD) algorithms are applied to Hi-C data to discover new communities of loci in the 3D conformation of human and mouse DNA. We find that CD has some distinct advantages over pre-existing methods: (1) it is capable of finding a variable number of communities, (2) it can detect communities of DNA loci either adjacent or distant in the
Irineo Cabreros, Emmanuel Abbe, Aristotelis Tsirigos   +2 more
openaire   +2 more sources