ArticleJournal of computational biology : a journal of computational molecular cell biology2008
DUPCAR: reconstructing contiguous ancestral regions with duplications.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 62 citations in OpenAlex.
- AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model.Evolutionary bioinformatics online · 2019Article
- On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella.BMC systems biology · 2018Article
- Article
- Ancestral Genome Reconstruction on Whole Genome Level.Current genomics · 2017Review
- Isometric gene tree reconciliation revisited.Algorithms for molecular biology : AMB · 2017Article
- Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.BMC bioinformatics · 2016Article
- Improved gene tree error correction in the presence of horizontal gene transfer.Bioinformatics (Oxford, England) · 2015Article
- Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.BMC bioinformatics · 2015Article
- Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.BMC bioinformatics · 2015Article
- Ancestral gene synteny reconstruction improves extant species scaffolding.BMC genomics · 2015Article
- MLGO: phylogeny reconstruction and ancestral inference from gene-order data.BMC bioinformatics · 2014Article
- Reconciliation of gene and species trees.BioMed research international · 2014Article
- Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Reference-assisted chromosome assembly.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Evolution of gene neighborhoods within reconciled phylogenies.Bioinformatics (Oxford, England) · 2012Article
- Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.Bioinformatics (Oxford, England) · 2012Article
- Linearization of ancestral multichromosomal genomes.BMC bioinformatics · 2012Article
- Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes.Genome biology and evolution · 2012Article
- Evolution of orthologous tandemly arrayed gene clusters.BMC bioinformatics · 2011Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tetraurelia.
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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.