ArticleCell systems2019
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organization.NAR genomics and bioinformatics · 2025Article
- Robust regression rescues poor phylogenetic decisions.BMC ecology and evolution · 2025Article
- Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence.bioRxiv : the preprint server for biology · 2025Article
- An integrative 3D-genome database for plants.Plant communications · 2025Article
- Divergent 3D genome organization in livers of cave and surface morphs ofbioRxiv : the preprint server for biology · 2025Article
- Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.Genome biology and evolution · 2024Article
- Strong association between genomic 3D structure and CRISPR cleavage efficiency.PLoS computational biology · 2024Article
- TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.Nature communications · 2023Article
- Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.bioRxiv : the preprint server for biology · 2023Article
- Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.Genome research · 2023Article
- The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs.Molecular biology and evolution · 2022Article
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- Article
- Conservation of chromatin conformation in carnivores.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization.Genome biology · 2021Article
- A TAD Skeptic: Is 3D Genome Topology Conserved?Trends in genetics : TIG · 2021Review
- Topologically associating domains and their role in the evolution of genome structure and function inGenome research · 2021Article
- Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability.American journal of human genetics · 2021Article
- CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction.Nature genetics · 2020Article
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5 authors.
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Abstract
Recent whole-genome mapping approaches for the chromatin interactome have offered new insights into 3D genome organization. However, our knowledge of the evolutionary patterns of 3D genome in mammals remains limited. In particular, there are no existing phylogenetic-model-based methods to analyze chromatin interactions as continuous features. Here, we develop phylogenetic hidden Markov random field (Phylo-HMRF) to identify evolutionary patterns of 3D genome based on multi-species Hi-C data by jointly utilizing spatial constraints among genomic loci and continuous-trait evolutionary models. We used Phylo-HMRF to uncover cross-species 3D genome patterns based on Hi-C data from the same cell type in four primate species (human, chimpanzee, bonobo, and gorilla). The identified evolutionary patterns of 3D genome correlate with features of genome structure and function. This work provides a new framework to analyze multi-species continuous genomic features with spatial constraints and has the potential to help reveal the evolutionary principles of 3D genome organization.
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