Published in Genome Biol Evol on July 12, 2010
Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A (2014) 2.48
A functional phylogenomic view of the seed plants. PLoS Genet (2011) 1.44
Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biol Evol (2011) 1.31
What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evol Biol (2011) 0.96
Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads. Genome Biol Evol (2013) 0.94
Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One (2013) 0.90
Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants. Mol Biol Evol (2017) 0.76
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Novel tools for an old lineage: Population genomics for cycads. Commun Integr Biol (2011) 0.75
Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities. Front Genet (2016) 0.75
Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants. Genome Biol Evol (2017) 0.75
A Primary Sequence Analysis of the ARGONAUTE Protein Family in Plants. Front Plant Sci (2016) 0.75
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Signals of recent positive selection in a worldwide sample of human populations. Genome Res (2009) 8.38
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Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell (2006) 4.87
Evolution of hormone-receptor complexity by molecular exploitation. Science (2006) 4.65
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The nature of selection during plant domestication. Nature (2009) 4.06
Rates of molecular evolution are linked to life history in flowering plants. Science (2008) 4.06
Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature (2004) 3.92
DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol (2006) 3.90
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Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol (2006) 3.71
Rapid evolution of flowering time by an annual plant in response to a climate fluctuation. Proc Natl Acad Sci U S A (2007) 3.63
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci U S A (2007) 3.55
Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet (2007) 3.43
Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc Natl Acad Sci U S A (2009) 3.22
COP9: a new genetic locus involved in light-regulated development and gene expression in arabidopsis. Plant Cell (1992) 3.20
The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet (2006) 3.11
The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci U S A (2006) 3.10
Functional classification using phylogenomic inference. PLoS Comput Biol (2006) 2.88
Phylogenomics: intersection of evolution and genomics. Science (2003) 2.86
Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics (2004) 2.71
Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proc Natl Acad Sci U S A (2000) 2.58
Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol (2004) 2.57
Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst Biol (1997) 2.56
Genomic insights into positive selection. Trends Genet (2006) 2.53
Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science (2003) 2.49
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol (2007) 2.45
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics (2006) 2.39
Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol (2004) 2.34
Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. Evolution (2003) 2.33
Chloroplast research in the genomic age. Trends Genet (2003) 2.23
MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants. Proc Natl Acad Sci U S A (1999) 2.15
OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics (2006) 1.90
MicroRNA: past and present. Front Biosci (2007) 1.79
Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics (2007) 1.76
Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol (2006) 1.66
The COP9 signalosome: regulating plant development through the control of proteolysis. Annu Rev Plant Biol (2003) 1.53
Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol (2002) 1.51
The small interfering RNA production pathway is required for shoot meristem initiation in rice. Proc Natl Acad Sci U S A (2007) 1.46
The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev Biol (2005) 1.45
Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evol Biol (2007) 1.45
The chemical characteristic and distribution of brassinosteroids in plants. Phytochemistry (2003) 1.45
Evidence for FUS6 as a component of the nuclear-localized COP9 complex in Arabidopsis. Plant Cell (1996) 1.43
The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development. Plant Cell (2003) 1.43
Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms. BMC Evol Biol (2009) 1.42
Role of the MPN subunits in COP9 signalosome assembly and activity, and their regulatory interaction with Arabidopsis Cullin3-based E3 ligases. Plant Cell (2007) 1.40
Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling. Mol Phylogenet Evol (2008) 1.39
Bayesian estimation of positively selected sites. J Mol Evol (2004) 1.34
A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera. Proc Natl Acad Sci U S A (2008) 1.30
Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol (2009) 1.23
Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Am J Bot (2004) 1.18
Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids. BMC Evol Biol (2007) 1.16
Plant evolutionary genomics. Curr Opin Plant Biol (2002) 1.13
The evolution of gymnosperms redrawn by phytochrome genes: the Gnetatae appear at the base of the gymnosperms. J Mol Evol (2002) 1.13
Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Mol Biol Evol (2009) 1.08
The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One (2009) 1.06
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. BMC Bioinformatics (2008) 1.04
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data. Am J Bot (2008) 1.04
Novel phytohormones involved in long-range signaling. Curr Opin Plant Biol (2007) 1.00
Time to grow up: the temporal role of smallRNAs in plants. Curr Opin Plant Biol (2005) 0.98
An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene (2002) 0.98
The place of Amborella within the radiation of angiosperms. Trends Plant Sci (2005) 0.98
The COP9 signalosome: mediating between kinase signaling and protein degradation. Curr Protein Pept Sci (2004) 0.98
Comparative genomics as a tool for gene discovery. Curr Opin Biotechnol (2006) 0.98
Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics (2006) 0.92
Selection on nuclear genes in a Pinus phylogeny. Mol Biol Evol (2009) 0.87
Distinct MADS-box gene expression patterns in the reproductive cones of the gymnosperm Gnetum gnemon. Dev Genes Evol (2003) 0.80
Xylem hydraulic and photosynthetic function of Gnetum (Gnetales) species from Papua New Guinea. New Phytol (2007) 0.76
The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae. Insect Mol Biol (2003) 0.76
Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51
Comparative functional genomics of the fission yeasts. Science (2011) 6.00
The role of RNA interference in heterochromatic silencing. Nature (2004) 4.56
Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol (2003) 3.71
Resolution of a supertree/supermatrix paradox. Syst Biol (2002) 3.71
Choosing and using a plant DNA barcode. PLoS One (2011) 3.64
Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods (2005) 3.28
Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A (2008) 3.17
RNA interference guides histone modification during the S phase of chromosomal replication. Curr Biol (2008) 2.72
Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication. Mol Phylogenet Evol (2012) 2.65
Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature (2013) 2.58
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol (2007) 2.45
Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin. Cell (2008) 2.42
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci U S A (2014) 2.42
DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS One (2007) 2.38
Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A (2008) 2.17
Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods (2005) 2.10
ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize. Plant Cell (2006) 2.07
Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. Bioessays (2011) 2.04
Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 2.03
The Widespread Colonization Island of Actinobacillus actinomycetemcomitans. Nat Genet (2003) 1.92
Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr Biol (2013) 1.91
OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics (2006) 1.90
VirtualPlant: a software platform to support systems biology research. Plant Physiol (2009) 1.88
An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol (2002) 1.85
Morphology of Hydatellaceae, an anomalous aquatic family recently recognized as an early-divergent angiosperm lineage. Am J Bot (2007) 1.82
Combined support for wholesale taxic atavism in gavialine crocodylians. Syst Biol (2003) 1.82
Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics (2009) 1.80
A genome triplication associated with early diversification of the core eudicots. Genome Biol (2012) 1.80
Ontologies as integrative tools for plant science. Am J Bot (2012) 1.71
Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease. PLoS One (2008) 1.70
The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol (2012) 1.65
Two novel proteins, dos1 and dos2, interact with rik1 to regulate heterochromatic RNA interference and histone modification. Curr Biol (2005) 1.60
Falsifications and corroborations: Karl Popper's influence on systematics. Mol Phylogenet Evol (2005) 1.57
Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol (2005) 1.57
Nitrate signaling: adaptation to fluctuating environments. Curr Opin Plant Biol (2010) 1.57
Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol (2004) 1.53
Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. Proc Natl Acad Sci U S A (2011) 1.46
A functional phylogenomic view of the seed plants. PLoS Genet (2011) 1.44
Coordination of DNA replication and histone modification by the Rik1-Dos2 complex. Nature (2011) 1.44
Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol (2004) 1.44
Cycads: evolutionary innovations and the role of plant-derived neurotoxins. Trends Plant Sci (2003) 1.43
Commercial teas highlight plant DNA barcode identification successes and obstacles. Sci Rep (2011) 1.42
The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. Plant Physiol (2002) 1.39
Functions of the cytoplasmic RNA sensors RIG-I and MDA-5: key regulators of innate immunity. Pharmacol Ther (2009) 1.37
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome Res (2009) 1.36
Maize-targeted mutagenesis: A knockout resource for maize. Proc Natl Acad Sci U S A (2003) 1.35
Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97. J Virol (2008) 1.35
Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J Virol (2005) 1.34
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol (2010) 1.34
Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana. Mol Biol Evol (2002) 1.33
Relationships among characiform fishes inferred from analysis of nuclear and mitochondrial gene sequences. Mol Phylogenet Evol (2005) 1.31
Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol (2003) 1.29
Overexpression of the ASN1 gene enhances nitrogen status in seeds of Arabidopsis. Plant Physiol (2003) 1.28
ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol (2006) 1.24
In vitro assessment of chemokine receptor-ligand interactions mediating mouse eosinophil migration. J Leukoc Biol (2002) 1.23
The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi, Fungi. Mycol Res (2003) 1.20
Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration. Plant Physiol (2002) 1.19
Epigenetic interactions between transposons and genes: lessons from plants. Curr Opin Genet Dev (2008) 1.19
A framework integrating plant growth with hormones and nutrients. Trends Plant Sci (2011) 1.19
How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Syst Biol (2007) 1.16
Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot (2007) 1.16
Transcriptome-mining for single-copy nuclear markers in ferns. PLoS One (2013) 1.12
Lack of canonical E6 and E7 open reading frames in bird papillomaviruses: Fringilla coelebs papillomavirus and Psittacus erithacus timneh papillomavirus. J Virol (2002) 1.12
Systems biology for the virtual plant. Plant Physiol (2005) 1.11
Comparative ovule and megagametophyte development in Hydatellaceae and water lilies reveal a mosaic of features among the earliest angiosperms. Ann Bot (2008) 1.10
Genome of Drosophila suzukii, the spotted wing drosophila. G3 (Bethesda) (2013) 1.08
Relative quantitation of virus population size in mixed genotype infections using sequencing chromatograms. J Virol Methods (2007) 1.08
Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol (2003) 1.08
Genomic diversity and interspecies host infection of alpha12 Macaca fascicularis papillomaviruses (MfPVs). Virology (2009) 1.08
Transcriptome deep-sequencing and clustering of expressed isoforms from Favia corals. BMC Genomics (2013) 1.07
Evolution and taxonomic classification of alphapapillomavirus 7 complete genomes: HPV18, HPV39, HPV45, HPV59, HPV68 and HPV70. PLoS One (2013) 1.07
Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis. Plant Physiol (2003) 1.06
The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One (2009) 1.06
DNA barcoding: a new tool for palm taxonomists? Ann Bot (2011) 1.05
Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway. Plant J (2002) 1.04
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. BMC Bioinformatics (2008) 1.04
Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group. Mol Phylogenet Evol (2012) 1.03
Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis. Mol Phylogenet Evol (2010) 1.03
Next-generation phenomics for the Tree of Life. PLoS Curr (2013) 1.03
Testing dispersal hypotheses in foraging green sea turtles (Chelonia mydas) of Brazil. J Hered (2006) 1.02
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. BMC Syst Biol (2008) 1.02
Evidence, content and corroboration and the Tree of Life. Acta Biotheor (2008) 1.02