ArticlePLoS computational biology2016
Inference of Ancestral Recombination Graphs through Topological Data Analysis.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 75 citations in OpenAlex.
- Topo-CNN: Retinal Image Analysis with Topological Deep Learning.Journal of imaging informatics in medicine · 2026Article
- Node persistence from topological data analysis reveals changes in brain functional connectivity.Patterns (New York, N.Y.) · 2026Article
- HOG-CNN: Integrating Histogram of Oriented Gradients with Convolutional Neural Networks for Retinal Image Classification.Journal of imaging informatics in medicine · 2026Article
- Finding maximum common contractions between phylogenetic networks.Algorithms for molecular biology : AMB · 2025Article
- Topological data analysis captures horizontal gene transfer in antimicrobial resistance gene families among clinically relevant bacteria.Frontiers in microbiology · 2025Article
- Article
- A general and efficient representation of ancestral recombination graphs.bioRxiv : the preprint server for biology · 2024Article
- Global and Local Ancestry and its Importance: A Review.Current genomics · 2024Review
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Methodologies for Microbial Ancestral Sequence Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Global Patterns of Recombination across Human Viruses.Molecular biology and evolution · 2021Article
- Noise robustness of persistent homology on greyscale images, across filtrations and signatures.PloS one · 2021Article
- Identification of relevant genetic alterations in cancer using topological data analysis.Nature communications · 2020Article
- The shape of things to come: Topological data analysis and biology, from molecules to organisms.Developmental dynamics : an official publication of the American Association of Anatomists · 2020Review
- Topological data analysis to model the shape of immune responses during co-infections.Communications in nonlinear science & numerical simulation · 2020Article
- High-fidelity phenotyping: richness and freedom from bias.Journal of the American Medical Informatics Association : JAMIA · 2018Article
- Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.Nature biotechnology · 2017Article
- Topological methods for genomics: present and future directions.Current opinion in systems biology · 2017Article
- A roadmap for the computation of persistent homology.EPJ data science · 2017Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands.
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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.