ArticleGenome biology2016
HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 81 citations in OpenAlex.
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation.The EMBO journal · 2025Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- Novel AI-powered computational method using tensor decomposition for identification of common optimal bin sizes when integrating multiple Hi-C datasets.Scientific reports · 2025Article
- Reconstructing 3D chromosome structures from single-cell Hi-C data with SO(3)-equivariant graph neural networks.NAR genomics and bioinformatics · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- ARGV: 3D genome structure exploration using augmented reality.BMC bioinformatics · 2024Article
- Assessing chromatin relocalization in 3D using the patient rule induction method.Biostatistics (Oxford, England) · 2023Article
- ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction.Current issues in molecular biology · 2023Article
- Posterior inference of Hi-C contact frequency through sampling.Frontiers in bioinformatics · 2023Article
- ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data.BioData mining · 2022Article
- MODEL-BASED DISTANCE EMBEDDING WITH APPLICATIONS TO CHROMOSOMAL CONFORMATION BIOLOGY.The annals of applied statistics · 2022Article
- Can 3D diploid genome reconstruction from unphased Hi-C data be salvaged?NAR genomics and bioinformatics · 2022Article
- Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO.Nature communications · 2022Article
- Principal curve approaches for inferring 3D chromatin architecture.Biostatistics (Oxford, England) · 2022Article
- Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions.Frontiers in cell and developmental biology · 2022Review
- Article
- The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat.Ecology and evolution · 2021Article
- CBCR: A Curriculum Based Strategy For Chromosome Reconstruction.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Genome-wide 3C technologies (Hi-C) are being increasingly employed to study three-dimensional (3D) genome conformations. Existing computational approaches are unable to integrate accumulating data to facilitate studying 3D chromatin structure and function. We present HSA ( http://ouyanglab.jax.org/hsa/ ), a flexible tool that jointly analyzes multiple contact maps to infer 3D chromatin structure at the genome scale. HSA globally searches the latent structure underlying different cleavage footprints. Its robustness and accuracy outperform or rival existing tools on extensive simulations and orthogonal experiment validations. Applying HSA to recent in situ Hi-C data, we found the 3D chromatin structures are highly conserved across various human cell types.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.