Published in BMC Bioinformatics on June 25, 2012
De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis. BMC Genomics (2015) 0.79
An alternative, arginase-independent pathway for arginine metabolism in Kluyveromyces lactis involves guanidinobutyrase as a key enzyme. Mol Microbiol (2014) 0.76
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science (2006) 21.03
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04
Cereal genome evolution. Grasses, line up and form a circle. Curr Biol (1995) 8.33
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics (2005) 7.29
The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86
A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One (2007) 5.62
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science (2005) 5.47
Polyploidy and angiosperm diversification. Am J Bot (2009) 4.41
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res (2008) 4.02
Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68
The genome of Theobroma cacao. Nat Genet (2010) 3.47
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res (2006) 3.41
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91
How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J (2008) 2.76
Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol (2010) 2.52
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet (2009) 2.32
Genomic duplication, fractionation and the origin of regulatory novelty. Genetics (2004) 2.22
The collapse of gene complement following whole genome duplication. BMC Genomics (2010) 1.98
The ABCs of MGR with DCJ. Evol Bioinform Online (2008) 1.41
The distribution of genomic distance between random genomes. J Comput Biol (2006) 1.27
On the PATHGROUPS approach to rapid small phylogeny. BMC Bioinformatics (2011) 1.17
Fractionation statistics. BMC Bioinformatics (2011) 1.09
A model for biased fractionation after whole genome duplication. BMC Genomics (2012) 1.08
Rearrangement phylogeny of genomes in contig form. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.94
Pathgroups, a dynamic data structure for genome reconstruction problems. Bioinformatics (2010) 0.93
Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants. J Comput Biol (2009) 0.90
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
Poisson adjacency distributions in genome comparison: multichromosomal, circular, signed and unsigned cases. Bioinformatics (2008) 1.63
Medians seek the corners, and other conjectures. BMC Bioinformatics (2012) 1.45
The ABCs of MGR with DCJ. Evol Bioinform Online (2008) 1.41
Genome halving with an outgroup. Evol Bioinform Online (2007) 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
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
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
Fractionation statistics. BMC Bioinformatics (2011) 1.09
Genome aliquoting with double cut and join. BMC Bioinformatics (2009) 1.07
Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinformatics (2010) 1.03
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
Descendants of whole genome duplication within gene order phylogeny. J Comput Biol (2008) 0.98
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
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
Common intervals and symmetric difference in a model-free phylogenomics, with an application to streptophyte evolution. J Comput Biol (2007) 0.91
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
Natural parameter values for generalized gene adjacency. J Comput Biol (2010) 0.90
Generalized gene adjacencies, graph bandwidth, and clusters in yeast evolution. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.87
Improving gene network inference by comparing expression time-series across species, developmental stages or tissues. J Bioinform Comput Biol (2004) 0.86
Genome aliquoting revisited. J Comput Biol (2011) 0.85
Removing noise and ambiguities from comparative maps in rearrangement analysis. IEEE/ACM Trans Comput Biol Bioinform (2007) 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
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
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
Practical aliquoting of flowering plant genomes. BMC Bioinformatics (2013) 0.77
Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events. BMC Genomics (2015) 0.75
Gene expression and fractionation resistance. BMC Genomics (2014) 0.75
Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants. BMC Genomics (2014) 0.75
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. BMC Bioinformatics (2012) 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
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