Results 21 to 30 of about 18,851,748 (235)

Hi-C maps, 3D communities, and domains.

, 2023
(a) Hi-C maps where the red-to-blue pixel colors are a proxy for short-to-long 3D distances. The squares decorating the map’s diagonals represent GenLouvain-derived 3D communities for three γ values (0.5, 0.6, and 0.7).
Dolores Bernenko (16528426), Ludvig Lizana (2440240), Sang Hoon Lee (211083), Per Stenberg (36562)   +3 more
core   +1 more source

Energetics of Hi-C EUV brightenings [PDF]

Astronomy & Astrophysics, 2018
We study the thermal structure and energetics of the point-like extreme ultraviolet (EUV) brightenings within a system of fan loops observed in the active region AR 11520. These brightenings were simultaneously observed on 2012 July 11 by the High-resolution Coronal (Hi-C) imager and the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics ...
Srividya Subramanian, Vinay L. Kashyap, Durgesh Tripathi, Maria S. Madjarska, John G. Doyle   +4 more
openaire   +3 more sources

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization [PDF]

Nucleic Acids Research, 2020
AbstractThe Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data.
Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A. Grüning   +6 more
openaire   +5 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  

Hi-C interaction map on GM12878 HiC data.

, 2022
Heatmap showing the raw read count of interactions at 5k bins of chr21 (36000kb to 39500kb) (same region as S10 Fig in the cLoops paper [43] on the GM12878 Hi-C dataset in Rao et al. [5]. The heatmap is colored based on the log of read count. Significant
Hamid Alinejad-Rokny (518381), Ehsan Ramezani Sarbandi (12937223), Rassa Ghavami Modegh (12937220), Alistair R. R. Forrest (11469502), Hamid R. Rabiee (5264216), Kin Tung Tam (12937226), Narges Rezaie (11991104)   +6 more
core   +1 more source

De novo assembly of a chromosome-level reference genome of the ornamental butterfly Sericinus montelus based on nanopore sequencing and Hi-C analysis

Frontiers in Genetics, 2023
Sericinus montelus (Lepidoptera, Papilionidae, Parnassiinae) is a high-value ornamental swallowtail butterfly species widely distributed in Northern and Central China, Japan, Korea, and Russia.
Jingjing Li, Jingjing Li, Haiyan Wang, Jianqing Zhu, Qi Yang, Yang Luan, Leming Shi, Leming Shi, José Arturo Molina-Mora, Yuanting Zheng   +9 more
doaj   +1 more source

The statistical summaries of significant interactions identified by MaxHiC, GOTHiC, CHiCAGO, Fit-Hi-C, Fit-Hi-C2, and HiCDC+ on the Mifsud GM12878 capture Hi-C library at fragments 5kb and 10kb.

, 2022
As the table shows, the average read count of significant interactions identified by MaxHiC are much higher than those identified by CHiCAGO, GOTHiC, Fit-Hi-C, Fit-HiC2 and HiCDC+. (XLSX)
Hamid Alinejad-Rokny (518381), Ehsan Ramezani Sarbandi (12937223), Rassa Ghavami Modegh (12937220), Alistair R. R. Forrest (11469502), Hamid R. Rabiee (5264216), Kin Tung Tam (12937226), Narges Rezaie (11991104)   +6 more
core   +1 more source

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Genome Biology, 2020
Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed instaGRAAL, a complete ...
Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho, Romain Koszul   +12 more
doaj   +1 more source

Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions

BMC Biology, 2023
Background Long-range interactions between promoters and cis-regulatory elements, such as enhancers, play critical roles in gene regulation. However, the role of three-dimensional (3D) chromatin structure in orchestrating changes in transcriptional ...
Miao Wang, Bing He, Yueling Hao, Divyaa Srinivasan, Jatin Shrinet, Peter Fraser   +5 more
doaj   +1 more source

Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries

Вавиловский журнал генетики и селекции, 2023
The genome-wide variant of the chromatin conformation capture technique (Hi-C) is a powerful tool for revealing patterns of genome spatial organization, as well as for understanding the effects of their disturbance on disease development. In addition, Hi-
M. M. Gridina, E. Vesna, M. E. Minzhenkova, N. V. Shilova, O. P. Ryzhkova, L. P. Nazarenko, E. O. Belyaeva, I. N. Lebedev, V. S. Fishman   +8 more
doaj   +1 more source