{
  "abstract": "Single-strand DNA-specific Hi-C (ssHi-C) is a recently developed technique enabling the capture of chromatin interactions involving single-stranded DNA (ssDNA), an intermediate of various DNA metabolic processes. ssHi-C entails the restoration of restriction sites in ssDNA regions of interest upon introduction of designer, internally barcoded \"annealing oligonucleotides\" prior to the restriction digestion step of Hi-C. The design of these \"annealing oligonucleotides\", as well as the analysis of the resulting ssHi-C data presents specific challenges, such as (i) differentiating ssDNA from dsDNA-derived contacts, (ii) tracking probe-specific interactions, and (iii) calibrating the amount of ssDNA contacts across biological samples. Dedicated computational tools are therefore needed to facilitate the design of, and extract biological information from, ssHi-C experiments. We present ssHiCstuff, a Rust-and Python-based package for the design of key reagents for ssHi-C experiments and for the analysis of ssHi-C data. ssHiCstuff provides (i) an automated annealing oligonucleotides design module, (ii) an end-to-end analyses pipeline, and (iii) a graphical user interface. ssHiCstuff simplifies the high-resolution analysis of ssDNA interactions at genome-wide scale. A graphical user interface (GUI) implemented in Python is also available for biologists without coding skills.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "name": "Nicolas Mendiboure"
    },
    {
      "name": "Laurent Modolo"
    },
    {
      "name": "Stéphane Janczarski"
    },
    {
      "name": "Aurèle Piazza"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0psm8rpv9ffd0.bib",
  "cited_by": 0,
  "doi": "10.1093/bioinformatics/btag417",
  "fulltext_url": null,
  "id": "0psm8rpv9ffd0",
  "issns": [
    "1367-4803",
    "1367-4811"
  ],
  "landing_url": "https://hal.science/hal-05760171v1",
  "language": "en",
  "licence": "CC-BY-SA-4.0",
  "licence_label": "CC BY-SA 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-sa/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "0.sdv"
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    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
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  "openalex": "W7165541636",
  "pdf_url": "https://hal.science/hal-05760171/document",
  "pmcid": null,
  "pmid": null,
  "published": "2026-06-22",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/0psm8rpv9ffd0.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:39Z",
      "native_id": "hal-05760171",
      "source": "hal",
      "url": "https://hal.science/hal-05760171v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "hal:2.sdv.bbm.bm",
      "subfield": "molecular-biology"
    },
    {
      "field": "biochemistry",
      "origin": "hal:2.sdv.bbm.gtp",
      "subfield": "proteomics-metabolomics"
    },
    {
      "field": "biology",
      "origin": "hal:0.sdv",
      "subfield": "general"
    }
  ],
  "title": "ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments Authors",
  "title_text": "ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments Authors",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:39Z",
  "url": "https://research.draconitic.com/paper/0psm8rpv9ffd0",
  "venue": "Bioinformatics",
  "versions": []
}