ArticleBioinformatics (Oxford, England)2020
Serpentine: a flexible 2D binning method for differential Hi-C analysis.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.The EMBO journal · 2026Article
- Cooltools: Enabling high-resolution Hi-C analysis in Python.PLoS computational biology · 2024Article
- Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes.Nature structural & molecular biology · 2024Article
- Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome.Genome research · 2023Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria.Microbiome · 2023Article
- Article
- NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis.Nature communications · 2022Article
- Article
- Cohesin regulates homology search during recombinational DNA repair.Nature cell biology · 2021Article
- Sir3 mediates long-range chromosome interactions in budding yeast.Genome research · 2021Article
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5 authors.
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Abstract
motivationHi-C contact maps reflect the relative contact frequencies between pairs of genomic loci, quantified through deep sequencing. Differential analyses of these maps enable downstream biological interpretations. However, the multi-fractal nature of the chromatin polymer inside the cellular envelope results in contact frequency values spanning several orders of magnitude: contacts between loci pairs separated by large genomic distances are much sparser than closer pairs. The same is true for poorly covered regions, such as repeated sequences. Both distant and poorly covered regions translate into low signal-to-noise ratios. There is no clear consensus to address this limitation.
resultsWe present Serpentine, a fast, flexible procedure operating on raw data, which considers the contacts in each region of a contact map. Binning is performed only when necessary on noisy regions, preserving informative ones. This results in high-quality, low-noise contact maps that can be conveniently visualized for rigorous comparative analyses. AVAILABILITY AND IMPLEMENTATION: Serpentine is available on the PyPI repository and https://github.com/koszullab/serpentine; documentation and tutorials are provided at https://serpentine.readthedocs.io/en/latest/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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