Published in BMC Bioinformatics on January 18, 2010
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Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst Biol (2012) 1.09
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Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. BMC Bioinformatics (2012) 0.88
Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithms Mol Biol (2013) 0.82
Consensus properties for the deep coalescence problem and their application for scalable tree search. BMC Bioinformatics (2012) 0.77
Clustering Genes of Common Evolutionary History. Mol Biol Evol (2016) 0.76
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Inferring phylogeny despite incomplete lineage sorting. Syst Biol (2006) 4.25
Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol (2007) 4.13
Discordance of species trees with their most likely gene trees. PLoS Genet (2006) 3.58
Bayesian estimation of concordance among gene trees. Mol Biol Evol (2006) 2.81
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Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A (2009) 2.25
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Species tree inference by minimizing deep coalescences. PLoS Comput Biol (2009) 1.84
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics (2008) 1.53
The Apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees. Mol Biol Evol (2008) 1.48
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol (2010) 1.36
Gene family evolution by duplication, speciation, and loss. J Comput Biol (2008) 1.09
Improved heuristics for minimum-flip supertree construction. Evol Bioinform Online (2007) 1.03
The gene-duplication problem: near-linear time algorithms for NNI-based local searches. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.90
An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem. IEEE/ACM Trans Comput Biol Bioinform (2008) 0.81
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci U S A (2010) 3.21
Prospects for building the tree of life from large sequence databases. Science (2004) 2.56
From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol (2014) 1.62
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics (2008) 1.53
Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications. IEEE/ACM Trans Comput Biol Bioinform (2015) 1.38
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol (2010) 1.36
The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol (2005) 1.22
Robinson-Foulds supertrees. Algorithms Mol Biol (2010) 1.21
Performance of flip supertree construction with a heuristic algorithm. Syst Biol (2004) 1.20
Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach. Am J Bot (2013) 1.18
Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol Biol Evol (2003) 1.16
iGTP: a software package for large-scale gene tree parsimony analysis. BMC Bioinformatics (2010) 1.11
Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst Biol (2012) 1.09
Covarion structure in plastid genome evolution: a new statistical test. Mol Biol Evol (2004) 1.09
Improved heuristics for minimum-flip supertree construction. Evol Bioinform Online (2007) 1.03
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics (2011) 1.02
Identifying optimal incomplete phylogenetic data sets from sequence databases. Mol Phylogenet Evol (2005) 1.02
Minimum-flip supertrees: complexity and algorithms. IEEE/ACM Trans Comput Biol Bioinform (2006) 0.98
Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Mol Biol Evol (2003) 0.98
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. BMC Bioinformatics (2012) 0.97
The multiple gene duplication problem revisited. Bioinformatics (2008) 0.94
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Surviving the K-T mass extinction: new perspectives of polyploidization in angiosperms. Proc Natl Acad Sci U S A (2009) 0.89
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. BMC Bioinformatics (2012) 0.88
Assessing parameter identifiability in phylogenetic models using data cloning. Syst Biol (2012) 0.87
An ILP solution for the gene duplication problem. BMC Bioinformatics (2011) 0.87
Triplet supertree heuristics for the tree of life. BMC Bioinformatics (2009) 0.87
Phylogenetic signal in matK vs. trnK: a case study in early diverging eudicots (angiosperms). Mol Phylogenet Evol (2008) 0.87
Recurrent evolution of dioecy in bryophytes. Evolution (2012) 0.83
The plexus model for the inference of ancestral multidomain proteins. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.82
An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem. IEEE/ACM Trans Comput Biol Bioinform (2008) 0.81
PhyloFinder: an intelligent search engine for phylogenetic tree databases. BMC Evol Biol (2008) 0.81
Unrooted tree reconciliation: a unified approach. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.80
Maximizing Deep Coalescence Cost. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.79
Exact solutions for species tree inference from discordant gene trees. J Bioinform Comput Biol (2013) 0.79
Fast local search for unrooted Robinson-Foulds supertrees. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.79
A scalable method for identifying frequent subtrees in sets of large phylogenetic trees. BMC Bioinformatics (2012) 0.79
Consensus properties for the deep coalescence problem and their application for scalable tree search. BMC Bioinformatics (2012) 0.77
Refining discordant gene trees. BMC Bioinformatics (2014) 0.76
Exploring biological interaction networks with tailored weighted quasi-bicliques. BMC Bioinformatics (2012) 0.75
DrML: probabilistic modeling of gene duplications. J Comput Biol (2013) 0.75
Explaining differences in the lifespan and replicative capacity of cells: a general model and comparative analysis of vertebrates. Proc Biol Sci (2012) 0.75
Guest editors' introduction to the Proceedings of the 9th International Symposium on Biomedical Research and Applications. BMC Bioinformatics (2014) 0.75
Unconstrained Diameters for Deep Coalescence. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.75
Maximizing Deep Coalescence Cost. IEEE/ACM Trans Comput Biol Bioinform (2013) 0.75
Computing Manhattan Path-Difference MedianTrees: a Practical Local Search Approach. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75
Scombroid fishes provide novel insights into the trait/rate associations of molecular evolution. J Mol Evol (2014) 0.75
Gene Tree Diameter for Deep Coalescence. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.75
Efficient Local Search for Euclidean Path-Difference Median Trees. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75
Bijective Diameters of Gene Tree Parsimony Costs. IEEE/ACM Trans Comput Biol Bioinform (2017) 0.75