Publications related to Chromosome conformation capture

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Hoboken2023

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

NATURE PORTFOLIO2022

Comparison of computational methods for the identification of topologically associating domains

Elisa Oricchio, Daniele Tavernari, Giovanni Ciriello

BackgroundChromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiati ...

BMC2018

Large scale genomic reorganization of topological domains at the HoxD locus

Denis Duboule, Marion Leleu, Lucille Delisle, Daniël Noordermeer, Pierre Raymond Fabre, Leonardo Beccari, Benjamin Howard Mormann

BACKGROUND: The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD g ...

BioMed Central2017

Principles of ChIP-seq Data Analysis Illustrated with Examples

Giovanna Ambrosini, Philipp Bucher, René Dreos

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single C ...

Copicentro Granada S L2014

Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method

Jacques Rougemont, Marion Leleu, Nele Gheldof, Daniël Noordermeer

Eukaryotic transcription is tightly regulated by transcriptional regulatory elements, even though these elements may be located far away from their target genes. It is now widely recognized that these regulatory elements can be brought in close proximity t ...

Springer Science+Business Media2011

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Chromosome conformation capture

Orchestrating chromosome conformation capture analysis with Bioconductor

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Comparison of computational methods for the identification of topologically associating domains

Large scale genomic reorganization of topological domains at the HoxD locus

Modeling and Engineering Proteins Thermostability

Principles of ChIP-seq Data Analysis Illustrated with Examples

Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method

Graph Chatbot

Chat with Graph Search

Orchestrating chromosome conformation capture analysis with Bioconductor

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Comparison of computational methods for the identification of topologically associating domains

Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Modeling and Engineering Proteins Thermostability

Principles of ChIP-seq Data Analysis Illustrated with Examples

Large scale genomic reorganization of topological domains at the HoxD locus