ArticleCell systems2018
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- Complete sequencing of ape genomes.Nature · 2025Article
- Complete sequencing of ape genomes.bioRxiv : the preprint server for biology · 2024Article
- Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.Genome research · 2024Article
- Repli-seq Sample Preparation using Cell Sorting with Cell-Permeant Dyes.Current protocols · 2023Article
- Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits.Genome research · 2023Article
- Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss.Nature communications · 2023Article
- Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis.The Journal of biological chemistry · 2023Article
- The evolution of the human DNA replication timing program.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- SPIN reveals genome-wide landscape of nuclear compartmentalization.Genome biology · 2021Article
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Genomic methods for measuring DNA replication dynamics.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- Control of DNA replication timing in the 3D genome.Nature reviews. Molecular cell biology · 2019Review
- Ancestral reconstruction of protein interaction networks.PLoS computational biology · 2019Article
- Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.Cell systems · 2019Article
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Authors and funding
8 authors.
Funding
Abstract
A large amount of multi-species functional genomic data from high-throughput assays are becoming available to help understand the molecular mechanisms for phenotypic diversity across species. However, continuous-trait probabilistic models, which are key to such comparative analysis, remain under-explored. Here we develop a new model, called phylogenetic hidden Markov Gaussian processes (Phylo-HMGP), to simultaneously infer heterogeneous evolutionary states of functional genomic features in a genome-wide manner. Both simulation studies and real data application demonstrate the effectiveness of Phylo-HMGP. Importantly, we applied Phylo-HMGP to analyze a new cross-species DNA replication timing (RT) dataset from the same cell type in five primate species (human, chimpanzee, orangutan, gibbon, and green monkey). We demonstrate that our Phylo-HMGP model enables discovery of genomic regions with distinct evolutionary patterns of RT. Our method provides a generic framework for comparative analysis of multi-species continuous functional genomic signals to help reveal regions with conserved or lineage-specific regulatory roles.
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