Published in Bioinformatics on July 01, 2011
A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinformatics (2012) 1.03
A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication. BMC Genomics (2014) 0.97
Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biol Evol (2012) 0.92
Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. Genome Biol Evol (2015) 0.85
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res (2008) 7.35
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics (2010) 2.86
Breakpoint graphs and ancestral genome reconstructions. Genome Res (2009) 2.78
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A (2009) 1.71
Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci (2010) 1.66
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics (2010) 1.63
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55
DUPCAR: reconstructing contiguous ancestral regions with duplications. J Comput Biol (2008) 1.50
Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? Genome Res (2006) 1.38
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput Biol (2008) 1.15
Recovering genome rearrangements in the mammalian phylogeny. Genome Res (2009) 1.14
Yeast ancestral genome reconstructions: the possibilities of computational methods II. J Comput Biol (2010) 0.95
Common intervals and symmetric difference in a model-free phylogenomics, with an application to streptophyte evolution. J Comput Biol (2007) 0.91
A unified approach for reconstructing ancient gene clusters. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.89
Minimal conflicting sets for the consecutive ones property in ancestral genome reconstruction. J Comput Biol (2010) 0.81
The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree. J Comput Biol (2011) 0.80
A physical map of the 1-gigabase bread wheat chromosome 3B. Science (2008) 3.21
Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell (2005) 2.40
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
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55
The 'inner circle' of the cereal genomes. Curr Opin Plant Biol (2008) 1.55
FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring. Genomics Proteomics Bioinformatics (2007) 1.49
Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci U S A (2012) 1.40
Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics (2006) 1.31
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. BMC Genomics (2009) 1.31
Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J (2013) 1.26
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics (2010) 1.24
Precise detection of rearrangement breakpoints in mammalian chromosomes. BMC Bioinformatics (2008) 1.22
An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework. IEEE/ACM Trans Comput Biol Bioinform (2011) 1.20
Efficient exploration of the space of reconciled gene trees. Syst Biol (2013) 1.20
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics (2010) 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
Space of gene/species trees reconciliations and parsimonious models. J Comput Biol (2009) 1.15
Structure and expression analysis of rice paleo duplications. Nucleic Acids Res (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
Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics (2012) 1.07
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol (2011) 1.07
Reconstructing the architecture of the ancestral amniote genome. Bioinformatics (2011) 1.05
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
Yeast ancestral genome reconstructions: the possibilities of computational methods II. J Comput Biol (2010) 0.95
Gene tree correction guided by orthology. BMC Bioinformatics (2013) 0.94
Cassis: detection of genomic rearrangement breakpoints. Bioinformatics (2010) 0.92
Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication. Plant Cell (2012) 0.92
Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biol Evol (2012) 0.92
FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinformatics (2013) 0.91
Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses. BMC Genomics (2012) 0.89
Bayesian sampling of genomic rearrangement scenarios via double cut and join. Bioinformatics (2010) 0.87
Moments of genome evolution by Double Cut-and-Join. BMC Bioinformatics (2015) 0.87
Linearization of ancestral multichromosomal genomes. BMC Bioinformatics (2012) 0.85
Perfect sorting by reversals is not always difficult. IEEE/ACM Trans Comput Biol Bioinform (2007) 0.85
Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species. J Mol Evol (2008) 0.85
Lateral gene transfer, rearrangement, reconciliation. BMC Bioinformatics (2013) 0.85
Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics (2007) 0.84
Comparing genomes with duplications: a computational complexity point of view. IEEE/ACM Trans Comput Biol Bioinform (2007) 0.82
Branch-and-bound approach for parsimonious inference of a species tree from a set of gene family trees. Adv Exp Med Biol (2011) 0.81
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics (2015) 0.80
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. BMC Bioinformatics (2011) 0.80
Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes. J Comput Biol (2009) 0.78
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
Gene Tree Construction and Correction using SuperTree and Reconciliation. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75
A 2-approximation for the minimum duplication speciation problem. J Comput Biol (2011) 0.75
The SCJ Small Parsimony Problem for Weighted Gene Adjacencies. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75
The BRaliBase dent-a tale of benchmark design and interpretation. Brief Bioinform (2017) 0.75
Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae. Pac Symp Biocomput (2010) 0.75
Algorithms and complexity results for genome mapping problems. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75