Published in Mol Biol Evol on October 17, 2013
From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol (2014) 1.62
Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. Sci Rep (2016) 1.13
Transcriptomics of desiccation tolerance in the streptophyte green alga Klebsormidium reveal a land plant-like defense reaction. PLoS One (2014) 1.10
Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae. BMC Evol Biol (2014) 1.05
Nitrogen limitation and slow drying induce desiccation tolerance in conjugating green algae (Zygnematophyceae, Streptophyta) from polar habitats. PLoS One (2014) 0.92
Rooting the tree of life: the phylogenetic jury is still out. Philos Trans R Soc Lond B Biol Sci (2015) 0.91
Abiotic Stress Tolerance of Charophyte Green Algae: New Challenges for Omics Techniques. Front Plant Sci (2016) 0.82
Chloroplast Phylogenomic Inference of Green Algae Relationships. Sci Rep (2016) 0.80
Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there. BMC Biol (2014) 0.79
Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae. Front Plant Sci (2016) 0.78
Two new fern chloroplasts and decelerated evolution linked to the long generation time in tree ferns. Genome Biol Evol (2014) 0.78
Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models. Genome Biol Evol (2016) 0.77
The Origin of Land Plants: A Phylogenomic Perspective. Evol Bioinform Online (2015) 0.76
Estimating Bayesian Phylogenetic Information Content. Syst Biol (2016) 0.75
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A (2002) 5.48
The modern molecular clock. Nat Rev Genet (2003) 3.97
Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol (2004) 3.58
Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot (2011) 3.54
Evaluating hypotheses for the origin of eukaryotes. Bioessays (2007) 3.28
Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc Natl Acad Sci U S A (2009) 3.22
Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change. Proc Natl Acad Sci U S A (2008) 3.18
The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci U S A (2006) 3.10
Origin of land plants using the multispecies coalescent model. Trends Plant Sci (2013) 2.50
Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. Mol Biol Evol (2006) 2.48
Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol (2005) 2.46
The evolutionary root of flowering plants. Syst Biol (2012) 2.46
A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol (2004) 2.32
The biology of intron gain and loss. Trends Genet (2005) 2.07
Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life. Am J Bot (2009) 1.97
The root of the mammalian tree inferred from whole mitochondrial genomes. Mol Phylogenet Evol (2003) 1.89
A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am Nat (2009) 1.63
Favorable climate change response explains non-native species' success in Thoreau's woods. PLoS One (2010) 1.63
Phylogeny of the clusioid clade (Malpighiales): evidence from the plastid and mitochondrial genomes. Am J Bot (2011) 1.58
Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol (2006) 1.53
Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Mol Biol Evol (2006) 1.49
Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proc Natl Acad Sci U S A (2012) 1.48
Leaf out times of temperate woody plants are related to phylogeny, deciduousness, growth habit and wood anatomy. New Phytol (2014) 1.47
Spectronet: a package for computing spectra and median networks. Appl Bioinformatics (2002) 1.38
Evolutionary biology: relativity for molecular clocks. Nature (2005) 1.38
Comment on "Hexapod origins: monophyletic or paraphyletic?". Science (2003) 1.35
Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol Biol Evol (2002) 1.30
Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol (2007) 1.30
Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst Biol (2009) 1.30
Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations. Syst Biol (2006) 1.29
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria). Mol Biol Evol (2006) 1.28
Floral symmetry genes and the origin and maintenance of zygomorphy in a plant-pollinator mutualism. Proc Natl Acad Sci U S A (2010) 1.26
Coevolution of genomic intron number and splice sites. Trends Genet (2007) 1.26
Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous. Mol Biol Evol (2004) 1.24
Mitochondrial genomes and avian phylogeny: complex characters and resolvability without explosive radiations. Mol Biol Evol (2006) 1.22
Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol (2013) 1.22
A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics (2003) 1.20
Origin of introns by 'intronization' of exonic sequences. Trends Genet (2008) 1.20
Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol Phylogenet Evol (2006) 1.16
Toward resolving deep neoaves phylogeny: data, signal enhancement, and priors. Mol Biol Evol (2008) 1.15
Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics (2012) 1.14
Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet (2013) 1.12
Phylogeny and biogeography of the carnivorous plant family Sarraceniaceae. PLoS One (2012) 1.12
Molecular phylogenetics of Phyllanthaceae: evidence from plastid MATK and nuclear PHYC sequences. Am J Bot (2005) 1.10
Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years. J Med Virol (2006) 1.10
Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Mol Phylogenet Evol (2008) 1.09
Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation. Viruses (2011) 1.09
Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires. Gene (2002) 1.09
Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Mol Biol Evol (2007) 1.08
Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res (2006) 1.05
Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Res (2007) 1.03
Systematic error in seed plant phylogenomics. Genome Biol Evol (2011) 1.03
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes. Mol Biol Evol (2005) 1.03
Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. Mol Biol Evol (2007) 1.02
Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene (2003) 1.01
RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evol Biol (2007) 1.01
Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests. J Mol Evol (2009) 1.01
Bird evolution: testing the Metaves clade with six new mitochondrial genomes. BMC Evol Biol (2008) 1.01
Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Mol Biol Evol (2007) 1.00
The RNA infrastructure: dark matter of the eukaryotic cell? Trends Genet (2009) 1.00
Developmental origins of the world's largest flowers, Rafflesiaceae. Proc Natl Acad Sci U S A (2013) 0.99
Eukaryote evolution: engulfed by speculation. Nature (2007) 0.99
The place of Amborella within the radiation of angiosperms. Trends Plant Sci (2005) 0.98
On the incidence of intron loss and gain in paralogous gene families. Mol Biol Evol (2007) 0.98
Prokaryote and eukaryote evolvability. Biosystems (2003) 0.98
A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Mol Biol Evol (2007) 0.97
The problem of rooting rapid radiations. Mol Biol Evol (2007) 0.97
Record-breaking early flowering in the eastern United States. PLoS One (2013) 0.96
Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses. Mol Biol Evol (2006) 0.96
Advances in the floral structural characterization of the major subclades of Malpighiales, one of the largest orders of flowering plants. Ann Bot (2013) 0.95
Using ancestral sequences to uncover potential gene homologues. Appl Bioinformatics (2003) 0.94
High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. Genome Biol Evol (2009) 0.94
Treeness triangles: visualizing the loss of phylogenetic signal. Mol Biol Evol (2007) 0.94
Beyond phylogeny: pelecaniform and ciconiiform birds, and long-term niche stability. Mol Phylogenet Evol (2013) 0.92
The modern RNP world of eukaryotes. J Hered (2009) 0.92
Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes. Mol Biol Evol (2006) 0.91
Molecular phylogeny of the Herpestidae (Mammalia, Carnivora) with a special emphasis on the Asian Herpestes. Mol Phylogenet Evol (2009) 0.91
Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biol Evol (2010) 0.90
Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol Biol Evol (2007) 0.90
Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One (2013) 0.90
A bias in ML estimates of branch lengths in the presence of multiple signals. Mol Biol Evol (2007) 0.89
Intron length distributions and gene prediction. Nucleic Acids Res (2007) 0.89
Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice. Genome Biol Evol (2013) 0.88
Floral structure and development in Rafflesiaceae with emphasis on their exceptional gynoecia. Am J Bot (2014) 0.87
Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. PLoS One (2008) 0.87
Similar genetic mechanisms underlie the parallel evolution of floral phenotypes. PLoS One (2012) 0.85
Hepatitis E virus infection, Papua New Guinea, Fiji, and Kiribati, 2003-2005. Emerg Infect Dis (2014) 0.85
Origins of life: Common ancestry put to the test. Nature (2010) 0.85
Environmental bio-monitoring with high-throughput sequencing. Brief Bioinform (2013) 0.84
Infection frequency of hepatitis C virus and IL28B haplotypes in Papua New Guinea, Fiji, and Kiribati. PLoS One (2013) 0.83
Phylogenetic position of avian nocturnal and diurnal raptors. Genome Biol Evol (2014) 0.83
Divergent genetic mechanisms underlie reversals to radial floral symmetry from diverse zygomorphic flowered ancestors. Front Plant Sci (2013) 0.83