Publications associées à Chromosome conformation capture

Orchestrating chromosome conformation capture analysis with Bioconductor

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

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

Daniele Tavernari, Giovanni Ciriello

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 ...

Wiley2023

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

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, Marie-Pierre Zufferey, 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 ...

2018

Large scale genomic reorganization of topological domains at the HoxD locus

Denis Duboule, Marion Leleu, Daniël Noordermeer, Lucille Delisle, 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 ...

2017

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