Published in J Comput Biol on May 01, 2007
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput Biol (2008) 1.15
Using jackknife to assess the quality of gene order phylogenies. BMC Bioinformatics (2010) 0.84
Mapping ancestral genomes with massive gene loss: a matrix sandwich problem. Bioinformatics (2011) 0.83
ProCARs: Progressive Reconstruction of Ancestral Gene Orders. BMC Genomics (2015) 0.82
Polyploidy and angiosperm diversification. Am J Bot (2009) 4.41
Structural dynamics of eukaryotic chromosome evolution. Science (2003) 3.57
Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics (2009) 2.38
Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J Mol Biol (2003) 1.93
The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold. Structure (2006) 1.81
The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants. Mol Biol Evol (2006) 1.63
Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases. Bioinformatics (2008) 1.63
The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci U S A (2002) 1.56
The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol Biol Evol (2005) 1.46
The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids. Mol Biol Evol (2008) 1.46
The complete mitochondrial DNA sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants. Mol Biol Evol (2002) 1.45
Medians seek the corners, and other conjectures. BMC Bioinformatics (2012) 1.45
The ABCs of MGR with DCJ. Evol Bioinform Online (2008) 1.41
A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies. BMC Biol (2007) 1.36
Genome halving with an outgroup. Evol Bioinform Online (2007) 1.27
The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell (2003) 1.27
Stability of rearrangement measures in the comparison of genome sequences. J Comput Biol (2006) 1.24
The signal in the genomes. PLoS Comput Biol (2006) 1.18
Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry (2004) 1.18
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. Bioinformatics (2008) 1.17
On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinformatics (2011) 1.17
The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands. BMC Evol Biol (2006) 1.16
Phase change for the accuracy of the median value in estimating divergence time. BMC Bioinformatics (2013) 1.14
Tests for gene clustering. J Comput Biol (2003) 1.13
Genomic features in the breakpoint regions between syntenic blocks. Bioinformatics (2004) 1.12
Epidemiology and antifungal susceptibility of bloodstream Candida isolates in Quebec: Report on 453 cases between 2003 and 2005. Can J Infect Dis Med Microbiol (2008) 1.11
The exceptionally large chloroplast genome of the green alga Floydiella terrestris illuminates the evolutionary history of the Chlorophyceae. Genome Biol Evol (2010) 1.10
The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes. BMC Biol (2006) 1.09
Fractionation statistics. BMC Bioinformatics (2011) 1.09
Genome aliquoting with double cut and join. BMC Bioinformatics (2009) 1.07
Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae. BMC Evol Biol (2014) 1.05
Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum. Mol Genet Genomics (2006) 1.04
Genome evolution of a tertiary dinoflagellate plastid. PLoS One (2011) 1.03
Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinformatics (2010) 1.03
Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer. BMC Genomics (2008) 1.02
The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales. Mol Biol Evol (2009) 1.02
Gene loss under neighborhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. J Bioinform Comput Biol (2009) 1.00
Analysis of gene order evolution beyond single-copy genes. Methods Mol Biol (2012) 0.99
An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus. BMC Genomics (2007) 0.99
Descendants of whole genome duplication within gene order phylogeny. J Comput Biol (2008) 0.98
Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species. BMC Genomics (2014) 0.97
The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae. Curr Genet (2006) 0.96
Tracing the evolution of streptophyte algae and their mitochondrial genome. Genome Biol Evol (2013) 0.96
The statistical analysis of spatially clustered genes under the maximum gap criterion. J Comput Biol (2005) 0.94
Rearrangement phylogeny of genomes in contig form. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.94
The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae. BMC Genomics (2007) 0.94
Sets of medians in the non-geodesic pseudometric space of unsigned genomes with breakpoints. BMC Genomics (2014) 0.94
Genome halving with double cut and join. J Bioinform Comput Biol (2009) 0.94
Ancient eudicot hexaploidy meets ancestral eurosid gene order. BMC Genomics (2013) 0.92
Natural parameter values for generalized gene adjacency. J Comput Biol (2010) 0.90
The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral populus diploid. Comput Syst Bioinformatics Conf (2008) 0.90
Generalized gene adjacencies, graph bandwidth, and clusters in yeast evolution. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.87
The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales. Genome Biol Evol (2011) 0.86
Improving gene network inference by comparing expression time-series across species, developmental stages or tissues. J Bioinform Comput Biol (2004) 0.86
Removing noise and ambiguities from comparative maps in rearrangement analysis. IEEE/ACM Trans Comput Biol Bioinform (2007) 0.85
Genome aliquoting revisited. J Comput Biol (2011) 0.85
Reversal distance for partially ordered genomes. Bioinformatics (2005) 0.85
Structural vs. functional mechanisms of duplicate gene loss following whole genome doubling. BMC Bioinformatics (2015) 0.84
Near-medians that avoid the corners; a combinatorial probability approach. BMC Genomics (2014) 0.84
Genome fragmentation is not confined to the peridinin plastid in dinoflagellates. PLoS One (2012) 0.82
A consolidation algorithm for genomes fractionated after higher order polyploidization. BMC Bioinformatics (2012) 0.82
Genetic and molecular control of folate-homocysteine metabolism in mutant mice. Mamm Genome (2002) 0.82
The dynamics of functional classes of plant genes in rediploidized ancient polyploids. BMC Bioinformatics (2013) 0.81
Paths and cycles in breakpoint graph of random multichromosomal genomes. J Comput Biol (2007) 0.81
A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga Pycnococcus provasolii. J Mol Evol (2010) 0.79
Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution. BMC Bioinformatics (2012) 0.79
Listing all sorting reversals in quadratic time. Algorithms Mol Biol (2011) 0.78
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes. BMC Bioinformatics (2012) 0.77
Practical aliquoting of flowering plant genomes. BMC Bioinformatics (2013) 0.77
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. BMC Bioinformatics (2012) 0.75
Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants. BMC Genomics (2014) 0.75
Gene expression and fractionation resistance. BMC Genomics (2014) 0.75
Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events. BMC Genomics (2015) 0.75
Treatment of gram-positive peritonitis in peritoneal dialysis patients: cefazolin or vancomycin? Perit Dial Int (2004) 0.75
The Kernel of Maximum Agreement Subtrees. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.75
Evolutionary model for the statistical divergence of paralogous and orthologous gene pairs generated by whole genome duplication and speciation. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75
A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances. J Comput Biol (2010) 0.75
Listing all parsimonious reversal sequences: new algorithms and perspectives. J Comput Biol (2011) 0.75
Scaffold filling under the breakpoint and related distances. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.75