Results 81 to 90 of about 39,833,464 (257)

SnapHiC2: A computationally efficient loop caller for single cell Hi-C data

Computational and Structural Biotechnology Journal, 2022
Single cell Hi-C (scHi-C) technologies enable the study of chromatin spatial organization directly from complex tissues at single cell resolution.
Xiaoqi Li, Lindsay Lee, Armen Abnousi, Miao Yu, Weifang Liu, Le Huang, Yun Li, Ming Hu   +7 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

SPG4 and Dementia: Expanding the Clinical Spectrum

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Hereditary spastic paraplegia (HSP) is a group of disorders characterized by progressive spasticity and lower limb weakness, with mutations in SPG4/SPAST being the most common cause. Detailed studies and clinical and molecular comparisons across different populations are missing.
Emanuele Panza, Arun Meyyazhagan, Eliseo Picchi, Gustavo Ribas, Ingrid Faber, Ryosuke Miyamoto, Preethi Basavaraju, Paolo Eusebi, Haripriya Kuchi Bhotla, Mario Stasi, Fabrizio Gaudiello, Francesco Patti, Filippo Maria Santorelli, Marcondes Cavalcante França Jr, José Luiz Pedroso, Orlando Graziani Povoas Barsottini, Hélio Afonso Ghizoni Teive, Peter Henry St George‐Hyslop, Toshitaka Kawarai, Antonio Orlacchio   +19 more
wiley   +1 more source

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data

Genomics, Proteomics & Bioinformatics, 2018
Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome.
Riccardo Calandrelli, Qiuyang Wu, Jihong Guan, Sheng Zhong   +3 more
doaj   +1 more source

PHi-C: deciphering Hi-C data into polymer dynamics [PDF]

NAR Genomics and Bioinformatics, 2019
Computational modelling methods for Hi-C data have revealed averaged and static features of the 3D genome in cell nuclei. Here, we describe a 4D simulation method, PHi-C (Polymer dynamics deciphered from Hi-C data), that depicts dynamic 3D genome features through polymer modelling.
Soya Shinkai, Masaki Nakagawa, Takeshi Sugawara, Yuichi Togashi, Hiroshi Ochiai, Ryuichiro Nakato, Yuichi Taniguchi, Shuichi Onami   +7 more
openaire   +2 more sources

Clinical Impact of NOTCH3 Variant Location After First Stroke in CADASIL

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Despite its monogenic origin, Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy exhibits marked variability in clinical expression and severity. Variants in the NOTCH3 gene, within epidermal growth factor‐like repeat domains 1–6 or 7–34, are known to influence disease onset, but their impact ...
Léa Aguilhon, Hugues Chabriat, Dominique Hervé, Stéphanie Guey, Sophie Tezenas Du Montcel, Juliette Ortholand   +5 more
wiley   +1 more source

Application of Hi-C and other omics data analysis in human cancer and cell differentiation research

Computational and Structural Biotechnology Journal, 2021
With the development of 3C (chromosome conformation capture) and its derivative technology Hi-C (High-throughput chromosome conformation capture) research, the study of the spatial structure of the genomic sequence in the nucleus helps researchers ...
Haiyan Gong, Yi Yang, Sichen Zhang, Minghong Li, Xiaotong Zhang   +4 more
doaj   +1 more source

White Matter Microstructural Abnormalities in Neonatal Onset Genetic Epilepsy

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Recent evidence indicates that epilepsy is associated with abnormal white matter. If seizures alter white matter, then the impact upon network function, epileptogenesis, and cognition could be pronounced in neonates undergoing rapid developmental myelination. Neonates with epilepsy due to nonstructural genetic causes provide a unique
Amanda G. Sandoval Karamian, Tianjia Zhu, Hao Huang, Shavonne L. Massey, Mark P. Fitzgerald, Darshana Parikh, Arastoo Vossough, Ingo Helbig, Nicholas S. Abend   +8 more
wiley   +1 more source

FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

Genome Biology, 2020
Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats ...
Kai Kruse, Clemens B. Hug, Juan M. Vaquerizas   +2 more
doaj   +1 more source

Softshell turtle genome assemblies scaffolded with Hi-C data

, 2019
This dataset, associated with our prospected publication by Kadota et al., contains softshell turtle genome assemblies based on Hi-C scaffolding. See the file "Assembly_ID.xlsx" for details of the combinations of tissue, enzyme, scaffolding program and ...
Phyloinformatics Lab in RIKEN Kobe (4815111)
core   +1 more source