The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf
.
Filters
Evolution of gene neighborhoods within reconciled phylogenies
2012
Computer applications in the biosciences : CABIOS
Results: We define an 'adjacency phylogenetic tree' that describes the evolution of an adjacency, a neighborhood relation between two genes, by speciation, duplication or loss of one or both genes, and ...
We detect duplications involving several genes and compare the different modes of evolution between phyla and among lineages. ...
neighborhoods based on a model of evolution allowing gene duplications. ...
doi:10.1093/bioinformatics/bts374
pmid:22962456
pmcid:PMC3436801
fatcat:xcqjzszkp5cshbdgvsv5cu7mza
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
[article]
2015
bioRxiv
pre-print
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. ...
Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies ...
A reconciled gene tree is also a binary tree that describes the evolution of a set of genes, called a gene family, through the evolutionary mechanisms of speciation, gene duplication and gene loss, within ...
doi:10.1101/026310
fatcat:vhc5v2bzqjhy3jzvjrhsqrenjy
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
2015
BMC Bioinformatics
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. ...
Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies ...
They introduced the notion of adjacency forest, that models the evolution of gene adjacencies within a phylogeny, motivated by the reconstruction of the architecture of ancestral genomes, and described ...
doi:10.1186/1471-2105-16-s19-s6
pmid:26696141
pmcid:PMC4686788
fatcat:tivavlil7jbbzpaxxoclnqwvwa
Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach
[chapter]
2014
Lecture Notes in Computer Science
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. ...
Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies ...
They introduced the notion of adjacency forest, that models the evolution of gene adjacencies within a phylogeny, motivated by the reconstruction of the architecture of ancestral genomes, and described ...
doi:10.1007/978-3-319-12418-6_7
fatcat:vhb2c3zcqbhylcsv6jb476nwem
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies
2015
BMC Bioinformatics
It uses reconciled phylogenies, which integrate sequence and gene content evolution. ...
Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content ...
This work was performed using the computing facilities of the Computing Center LBBE/PRABI. This article has been published as part of BMC Bioinformatics Volume 16 Supplement 14, 2015 ...
doi:10.1186/1471-2105-16-s14-s5
pmid:26452018
pmcid:PMC4603630
fatcat:czhsgbbkwnc55aywrumwp5wila
Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies
[article]
2015
arXiv
pre-print
The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. ...
The DeCo algorithm, recently introduced by Bérard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. ...
the convex hull computations within DeClone. ...
arXiv:1503.05292v2
fatcat:ympjtt44rnbdxhennuqbjekcma
Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material
[chapter]
2015
Lecture Notes in Computer Science
The availability of many assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. ...
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. ...
the convex hull computations within DeClone. ...
doi:10.1007/978-3-319-19048-8_22
fatcat:qn2uhpyswvagdkrazir2fd4vhe
The quest for orthologs: finding the corresponding gene across genomes
2008
Trends in Genetics
(b) A reconciled gene tree (midpoint rooted) of mannose-binding lectin genes (experimentally verified) from mouse, rat and human. ...
(conserved gene neighborhoods) and functional (ontologies) origins. ...
doi:10.1016/j.tig.2008.08.009
pmid:18819722
fatcat:4w6qrixl7naw7aoqko73vruavq
Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications
2020
Molecular biology and evolution
Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event. ...
We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art ...
Acknowledgments We thank Pierre Vincens for the coordination of computing resources and all members of the GenoFish consortium for fruitful discussions. This work is funded by ANR GenoFish (Grant No. ...
doi:10.1093/molbev/msaa149
pmid:32556216
fatcat:lfyiprkzdnbsxgouylkgnlxic4
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
2012
BMC Bioinformatics
Gene tree -species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree. ...
These algorithms improve on the current solutions by a factor of n for searching SPR neighborhoods and n 2 for searching TBR neighborhoods, where n is the number of taxa in the given gene tree. ...
This work was conducted in parts with support from the Gene Tree Reconciliation Working Group at NIMBioS through NSF award EF-0832858, with additional support from the University of Tennessee. ...
doi:10.1186/1471-2105-13-s10-s11
pmid:22759416
pmcid:PMC3382437
fatcat:wfrpopwrqzh25f4es4nlbyno6a
Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles
2020
Science Advances
Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits. ...
The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear. ...
We built nucleotide-based ML phylogenies of cbsA and the genes from each neighborhood type and manually reconciled their evolutionary histories with the consensus species tree using a combination of parsimony-based ...
doi:10.1126/sciadv.abc4516
pmid:33188025
pmcid:PMC7673761
fatcat:kufzxglqu5f6bp2pnxzzzwr2me
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
2019
Bioinformatics
Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. ...
rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree-species tree reconciliations. ...
Acknowledgements We thank Vincent Daubin, Wandrille Duchemin, Nicolas Lartillot and Thibault Latrille for insightful discussions during the preparation of this manuscript. ...
doi:10.1093/bioinformatics/btz710
pmid:31566657
pmcid:PMC7031779
fatcat:wfyywcllkreblankienj7tiama
The Distant Siblings—A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis
2015
Genome Biology and Evolution
Although the majority of discord between species and gene history is explained by ancient duplications, this landscape has been altered by more recent duplications, as well as multiple horizontal gene ...
By reconciling the history of over 400 nonreducing polyketide synthases (NR-PKSs) with corresponding species history, we demonstrate that extant fungal NR-PKSs are clades of distant siblings, originating ...
The authors thank Morgan Price for access to FastTreeMP version with LG matrix support and Nicholas Lartillot for helpful advice regarding tests of PhyloBayes-MPI results. ...
doi:10.1093/gbe/evv204
pmid:26537223
pmcid:PMC5635595
fatcat:5vqyvoeud5hqpnztnq5nnr236y
Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles
[article]
2020
bioRxiv
pre-print
Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits. ...
The contrasting features of vascular and non-vascular diseases suggest distinct etiologies, but the basis for each remains unclear. ...
in cbsA's extant distribution. 435 436 We built nucleotide-based ML phylogenies of cbsA and the genes from each neighborhood type, 437 and manually reconciled their evolutionary histories with the consensus ...
doi:10.1101/2020.04.24.058529
fatcat:ppeybb4iy5dspma4p45m55l63m
Inferring Orthology and Paralogy
[chapter]
2012
Msphere
Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments. ...
We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. ...
Part of this chapter started as assignment for the graduate course "Reviews in Computational Biology" (263-5151-00L) at ETH Zurich. ...
doi:10.1007/978-1-61779-582-4_9
pmid:22407712
fatcat:52mxshbwvzffrllmaipbidh5ky
« Previous
Showing results 1 — 15 out of 283 results