{
  "abstract": "Three-dimensional genome organization plays a crucial regulatory role, but its evolutionary development across the tree of life remains unclear. Here, we present a protocol for identifying higher order genome architectures using HiArch. We describe steps for preprocessing Hi-C maps, applying NormDis normalization, and identifying global folding and checkerboard patterns. We then detail procedures for cross-sample comparison and statistical analysis. This protocol enables systematic and reproducible analysis of 3D genome organization across diverse species.\n\nFor complete information on the use and execution of this protocol, please refer to Che et al.1",
  "abstract_shown": true,
  "affiliations": [
    "School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China",
    "MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China",
    "Department of Gynecology and Obstetrics, Center for Mathematical Medical, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China",
    "Genome Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China",
    "Faculty of Science, Leiden University, Leiden, the Netherlands"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Mingxuan Li"
    },
    {
      "affs": [
        0,
        1,
        2,
        3,
        4
      ],
      "name": "Kai Ye"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2fthtgxxxhe2n.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104912",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13734862/",
  "id": "2fthtgxxxhe2n",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://doi.org/10.1016/j.xpro.2026.104912",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Protocol"
    ],
    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
    ]
  ],
  "openalex": "W7223840868",
  "pdf_url": null,
  "pmcid": "PMC13734862",
  "pmid": "42945209",
  "published": "2026-10-27",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/2fthtgxxxhe2n.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T12:20:40Z",
      "native_id": "PMC13734862",
      "source": "pmc",
      "url": "https://doi.org/10.1016/j.xpro.2026.104912"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Chromatin Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protocol to identify higher order architectures across multiple species using HiArch",
  "title_text": "Protocol to identify higher order architectures across multiple species using HiArch",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T12:20:40Z",
  "url": "https://research.draconitic.com/paper/2fthtgxxxhe2n",
  "venue": "STAR Protocols",
  "versions": []
}