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Peer-reviewedCC BY-NC-ND 4.0STAR Protocols

Protocol to identify higher order architectures across multiple species using HiArch

  • Mingxuan Li1,2
  • Kai Ye1,2,3,4,5
5 affiliations
  1. 1School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
  2. 2MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
  3. 3Department of Gynecology and Obstetrics, Center for Mathematical Medical, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
  4. 4Genome Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
  5. 5Faculty of Science, Leiden University, Leiden, the Netherlands
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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.

For complete information on the use and execution of this protocol, please refer to Che et al.1

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Cite

BibTeXRIS
BibTeX
@article{li2026protocol,
  title = {{Protocol to identify higher order architectures across multiple species using HiArch}},
  author = {Mingxuan Li and Kai Ye},
  journal = {STAR Protocols},
  year = {2026},
  month = oct,
  doi = {10.1016/j.xpro.2026.104912},
  url = {https://doi.org/10.1016/j.xpro.2026.104912},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - Protocol to identify higher order architectures across multiple species using HiArch
AU  - Mingxuan Li
AU  - Kai Ye
PY  - 2026
DA  - 2026/10/27
JO  - STAR Protocols
DO  - 10.1016/j.xpro.2026.104912
UR  - https://doi.org/10.1016/j.xpro.2026.104912
AB  - 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.  For complete information on the use and execution of this protocol, please refer to Che et al.1
SN  - 2666-1667
ER  -