Published in Bioinformatics on September 15, 2012
The inference of gene trees with species trees. Syst Biol (2014) 0.97
Gene tree correction guided by orthology. BMC Bioinformatics (2013) 0.94
Reconciliation of gene and species trees. Biomed Res Int (2014) 0.88
Linearization of ancestral multichromosomal genomes. BMC Bioinformatics (2012) 0.85
Lateral gene transfer, rearrangement, reconciliation. BMC Bioinformatics (2013) 0.85
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics (2015) 0.80
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies. BMC Bioinformatics (2015) 0.77
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. BMC Genomics (2015) 0.77
Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics (2015) 0.76
Efficient Gene Tree Correction Guided by Genome Evolution. PLoS One (2016) 0.75
Event inference in multidomain families with phylogenetic reconciliation. BMC Bioinformatics (2015) 0.75
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
Breakpoint graphs and ancestral genome reconstructions. Genome Res (2009) 2.78
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics (2006) 2.77
Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics (2010) 1.63
Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform (2011) 1.50
DUPCAR: reconstructing contiguous ancestral regions with duplications. J Comput Biol (2008) 1.50
Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res (2012) 1.44
Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc Natl Acad Sci U S A (2007) 1.18
On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinformatics (2011) 1.17
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput Biol (2008) 1.15
SCJ: a breakpoint-like distance that simplifies several rearrangement problems. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.07
Reconstructing the architecture of the ancestral amniote genome. Bioinformatics (2011) 1.05
Reconstructing ancestral gene content by coevolution. Genome Res (2009) 1.04
Yeast ancestral genome reconstructions: the possibilities of computational methods II. J Comput Biol (2010) 0.95
Parsimonious reconstruction of network evolution. Algorithms Mol Biol (2012) 0.92
Phylogeny-guided interaction mapping in seven eukaryotes. BMC Bioinformatics (2009) 0.89
Inferring the evolutionary history of gene clusters from phylogenetic and gene order data. Mol Biol Evol (2009) 0.88
A new, fast algorithm for detecting protein coevolution using maximum compatible cliques. Algorithms Mol Biol (2011) 0.87
Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol (2008) 5.31
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 5.06
From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol (2003) 4.47
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res (2006) 3.53
Evolutionary origins of genomic repertoires in bacteria. PLoS Biol (2005) 3.43
Examining bacterial species under the specter of gene transfer and exchange. Proc Natl Acad Sci U S A (2005) 2.28
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
Genome-scale coestimation of species and gene trees. Genome Res (2012) 1.82
Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci (2010) 1.66
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc Natl Acad Sci U S A (2012) 1.66
Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci (2008) 1.64
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55
Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform (2011) 1.50
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol Biol (2008) 1.41
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol (2010) 1.40
Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci U S A (2012) 1.40
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. BMC Genomics (2009) 1.31
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res (2009) 1.29
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics (2010) 1.24
Bio++: efficient extensible libraries and tools for computational molecular evolution. Mol Biol Evol (2013) 1.23
Precise detection of rearrangement breakpoints in mammalian chromosomes. BMC Bioinformatics (2008) 1.22
Efficient exploration of the space of reconciled gene trees. Syst Biol (2013) 1.20
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput Biol (2008) 1.15
Comparative genomics and the evolution of prokaryotes. Trends Microbiol (2007) 1.14
Genomes as documents of evolutionary history. Trends Ecol Evol (2009) 1.13
Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes. Genome Biol Evol (2009) 1.11
Lateral gene transfer from the dead. Syst Biol (2013) 1.10
Exploring the solution space of sorting by reversals, with experiments and an application to evolution. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.08
Reconstructing the architecture of the ancestral amniote genome. Bioinformatics (2011) 1.05
Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol Biol (2012) 1.01
Evolution under reversals: parsimony and conservation of common intervals. IEEE/ACM Trans Comput Biol Bioinform (2007) 1.00
ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics (2012) 0.99
Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol (2011) 0.98
Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. Mol Biol Evol (2003) 0.96
Yeast ancestral genome reconstructions: the possibilities of computational methods II. J Comput Biol (2010) 0.95
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event? BMC Evol Biol (2008) 0.94
Gene tree correction guided by orthology. BMC Bioinformatics (2013) 0.94
A Bayesian method for analyzing lateral gene transfer. Syst Biol (2014) 0.93
Cassis: detection of genomic rearrangement breakpoints. Bioinformatics (2010) 0.92
A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS One (2012) 0.92
FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinformatics (2013) 0.91
Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. PLoS One (2012) 0.89
Efficient selection of branch-specific models of sequence evolution. Mol Biol Evol (2012) 0.87
Moments of genome evolution by Double Cut-and-Join. BMC Bioinformatics (2015) 0.87
Bayesian sampling of genomic rearrangement scenarios via double cut and join. Bioinformatics (2010) 0.87
Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene. PLoS One (2011) 0.87
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol (2014) 0.86
Drift and genome complexity revisited. PLoS Genet (2011) 0.86
Linearization of ancestral multichromosomal genomes. BMC Bioinformatics (2012) 0.85
High-quality sequence clustering guided by network topology and multiple alignment likelihood. Bioinformatics (2012) 0.85
Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test. Mol Phylogenet Evol (2004) 0.85
Lateral gene transfer, rearrangement, reconciliation. BMC Bioinformatics (2013) 0.85
Mapping ancestral genomes with massive gene loss: a matrix sandwich problem. Bioinformatics (2011) 0.83
A bunch of fun-guys: the whole-genome view of yeast evolution. Trends Genet (2005) 0.79
An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution (2012) 0.79
Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes. J Comput Biol (2009) 0.78
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. BMC Genomics (2015) 0.77
TPMS: a set of utilities for querying collections of gene trees. BMC Bioinformatics (2013) 0.77
Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies. BMC Bioinformatics (2015) 0.77
Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria. BMC Genomics (2013) 0.77
The molecular signal for the adaptation to cold temperature during early life on Earth. Biol Lett (2013) 0.77
Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics (2015) 0.76
Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae. Pac Symp Biocomput (2010) 0.75
[Healing the tree of life with lateral gene transfers]. Med Sci (Paris) (2012) 0.75