See the genome in 4D.

drag to rotate Human · chr11 · 4DNFILIM6FDL startend

PHi-D shares and visualizes PHi-C data to explore the dynamic 3D organization and physical properties of the genome.

PHi-C = Polymer dynamics simulation from Hi-C data. It turns a Hi-C contact matrix into a polymer model, transforming the same dataset into maps of dynamic physical properties, such as mean-square displacement (MSD) and loss tangent, and into a dynamic 3D genome structure.

In PHi-D, these dynamic properties can be mapped directly onto 3D genome structures. PHi-D is designed to integrate genomic annotations and experimental tracks, bringing genome structure, dynamics, and genomic information together in a unified view.

News

2026-10-08 The National Bioscience Database Center (NBDC) announces the release of PHi-D (English) (日本語)

2026-10-05 The official launch of PHi-D

Explore

Tools for the physical interpretation of Hi-C data.

Explore observed and reconstructed Hi-C contact maps, dynamic 3D genome structures, and genome-wide physical dynamics.

◌ Select an experiment, then a chromosome, to explore its contact map and 3D model.

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Normalized Contact Probability

Max (Normalized Contact Probability) Colormap

4D Genome Viewer

Simulation Step (ε) 1.0e-3

Strand Shape Smooth Width Beads Size

Color Color Fade 70%

Scene Depth Background Spin

Labels Labels Interval (beads) Hover

log₁₀ MSD(t)

Min (log₁₀ MSD) Max (log₁₀ MSD)

Colormap

log₁₀ tan δ(ω)

Min (log₁₀ tan δ) Max (log₁₀ tan δ)

Colormap

Overview

Diagnostic JSON output · ?diag prints view state, ?bench=1 runs the benchmark

About

Mission

Understanding how the genome moves and behaves as a physical, dynamic object — not just a static sequence — in the cell nucleus is essential to linking genome structure with gene expression and cellular function. PHi-D aims to make this dynamic view of the genome broadly accessible, by systematically transforming public Hi-C data into polymer physics models through PHi-C and sharing the resulting 4D genome information — structural dynamics, and physical properties — in a unified, browsable resource.

Development & Management

PHi-D is developed and maintained by Shinkai team at the RIKEN Center for Biosystems Dynamics Research (BDR). The underlying method, PHi-C, was developed by Soya Shinkai.

Future Vision

Beyond serving researchers, PHi-D is designed as a resource for AI as well as humans — a database for us and AI — building an accumulation of structure–dynamics–function relationships in a form usable both for direct exploration and as training data for future genome models.

For AI Assistants

AI assistants can search PHi-D directly through its MCP server. See PHi-D for AI Assistants for how to connect one.

Contact

Please address all questions and comments to phid-support@ml.riken.jp

Credits

Project Lead

Soya Shinkai

Project Supervision

Shuichi Onami

Software Engineers

Teruo Ishida

Hiroki Nakajima

Soya Hagiwara

Hiroya Itoga

Claude Code (Anthropic)

Codex (OpenAI)

Logo Design and
Web Design Supervision

Ryozo Shibasaki (button)

Special Thanks

Koji Kyoda

Onami Lab Members

Support

RIKEN

Funding

JST NBDC DICP (JPMJND2502)

JST CREST (JPMJCR23N3)

Releases

26.10.1 · 2026-10-23
- Improved the data selection steps and search
26.10.0 · 2026-10-05
- Official launch