Published in Trends Genet on October 01, 2004
Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A (2005) 5.00
Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol (2007) 4.07
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res (2008) 4.02
The evolutionary significance of ancient genome duplications. Nat Rev Genet (2009) 3.95
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
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A (2011) 2.97
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91
Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 2.72
The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol (2006) 2.58
Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol (2008) 2.51
Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell (2006) 2.45
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci U S A (2007) 2.24
A genome-wide characterization of microRNA genes in maize. PLoS Genet (2009) 2.23
Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A (2012) 2.20
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol (2007) 2.17
Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol (2008) 2.14
Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci U S A (2010) 2.02
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A (2009) 1.94
Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell (2006) 1.92
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics (2006) 1.91
Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res (2008) 1.90
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci U S A (2006) 1.87
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol (2006) 1.85
PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol (2007) 1.74
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci U S A (2009) 1.71
Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proc Natl Acad Sci U S A (2012) 1.55
Arabidopsis intragenomic conserved noncoding sequence. Proc Natl Acad Sci U S A (2007) 1.52
Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci U S A (2009) 1.52
Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol (2007) 1.50
Cross genome comparisons of serine proteases in Arabidopsis and rice. BMC Genomics (2006) 1.48
Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol (2005) 1.44
Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biol Evol (2012) 1.36
Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiol (2006) 1.32
Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. Mol Genet Genomics (2009) 1.29
Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol (2009) 1.27
Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. Plant Cell (2011) 1.22
Paralogs in polyploids: one for all and all for one? Plant Cell (2005) 1.18
Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiol (2009) 1.18
External factors accelerate expression divergence between duplicate genes. Trends Genet (2007) 1.14
Green transcription factors: a chlamydomonas overview. Genetics (2008) 1.13
A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage. BMC Evol Biol (2006) 1.13
Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus. Genome Res (2011) 1.12
Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean. Plant Cell (2012) 1.08
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol (2011) 1.07
G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell (2007) 1.06
Phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate Hox clusters. BMC Evol Biol (2008) 1.05
Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors. Nucleic Acids Res (2010) 1.03
Unique genes in plants: specificities and conserved features throughout evolution. BMC Evol Biol (2008) 1.01
The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. BMC Genomics (2010) 0.99
Evolutionary and structural perspectives of plant cyclic nucleotide-gated cation channels. Front Plant Sci (2012) 0.98
Evolution by gene loss. Nat Rev Genet (2016) 0.96
Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants. Plant Physiol (2013) 0.95
Comparative evolution of photosynthetic genes in response to polyploid and nonpolyploid duplication. Plant Physiol (2011) 0.95
Escape from preferential retention following repeated whole genome duplications in plants. Front Plant Sci (2012) 0.94
Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species. BMC Plant Biol (2015) 0.93
Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae). BMC Evol Biol (2011) 0.93
Grass microRNA gene paleohistory unveils new insights into gene dosage balance in subgenome partitioning after whole-genome duplication. Plant Cell (2012) 0.92
Characterization of resistance gene analogues (RGAs) in apple (Malus × domestica Borkh.) and their evolutionary history of the Rosaceae family. PLoS One (2014) 0.91
A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean. Plant Physiol (2015) 0.90
Evolutionary dynamics of recently duplicated genes: Selective constraints on diverging paralogs in the Drosophila pseudoobscura genome. J Mol Evol (2009) 0.88
Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker. BMC Genomics (2014) 0.87
Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiol (2014) 0.87
Genome-wide identification, phylogeny, evolution and expression patterns of AP2/ERF genes and cytokinin response factors in Brassica rapa ssp. pekinensis. PLoS One (2013) 0.86
Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies. BMC Plant Biol (2014) 0.86
Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat. Plant Biotechnol J (2015) 0.84
Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms. Plant Cell (2016) 0.84
Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Front Plant Sci (2013) 0.83
Polyploidy-associated genome modifications during land plant evolution. Philos Trans R Soc Lond B Biol Sci (2014) 0.83
High time for a roll call: gene duplication and phylogenetic relationships of TCP-like genes in monocots. Ann Bot (2011) 0.83
Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses. BMC Genomics (2014) 0.82
Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. Mol Biol Evol (2013) 0.82
Extensive translational regulation of gene expression in an allopolyploid (Glycine dolichocarpa). Plant Cell (2014) 0.81
Functional bias in molecular evolution rate of Arabidopsis thaliana. BMC Evol Biol (2010) 0.81
Arabidopsis-rice-wheat gene orthologues for Na+ transport and transcript analysis in wheat-L. elongatum aneuploids under salt stress. Mol Genet Genomics (2006) 0.80
Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast. PLoS Genet (2016) 0.78
Evolution of Gene Duplication in Plants. Plant Physiol (2016) 0.78
Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. Biology (Basel) (2013) 0.78
Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana. Plant Physiol (2015) 0.77
Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications. Plant Signal Behav (2011) 0.77
Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates. Genome Biol Evol (2016) 0.76
Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana. BMC Genomics (2016) 0.76
Evolution Analysis of Simple Sequence Repeats in Plant Genome. PLoS One (2015) 0.76
Comparative Genomics of NAC Transcriptional Factors in Angiosperms: Implications for the Adaptation and Diversification of Flowering Plants. PLoS One (2015) 0.76
Conserved Non-Coding Sequences are Associated with Rates of mRNA Decay in Arabidopsis. Front Plant Sci (2013) 0.76
Identification and characterization of two wheat Glycogen Synthase Kinase 3/ SHAGGY-like kinases. BMC Plant Biol (2013) 0.76
Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae. J Mol Evol (2016) 0.76
Unraveling the evolution and regulation of the alternative oxidase gene family in plants. Dev Genes Evol (2015) 0.76
Evolutionary and Functional Analysis of Membrane-Bound NAC Transcription Factor Genes in Soybean. Plant Physiol (2016) 0.75
Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts. BMC Evol Biol (2017) 0.75
Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data. Genome Biol Evol (2016) 0.75
Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm. Front Plant Sci (2017) 0.75
Sequence, expression divergence, and complementation of homologous ALCATRAZ loci in Brassica napus. Planta (2009) 0.75
Identification of a novel protein with guanylyl cyclase activity in Arabidopsis thaliana. J Biol Chem (2002) 1.53
Nomenclature for members of the expansin superfamily of genes and proteins. Plant Mol Biol (2004) 1.51
Ca2+ signaling by plant Arabidopsis thaliana Pep peptides depends on AtPepR1, a receptor with guanylyl cyclase activity, and cGMP-activated Ca2+ channels. Proc Natl Acad Sci U S A (2010) 1.50
The Arabidopsis thaliana brassinosteroid receptor (AtBRI1) contains a domain that functions as a guanylyl cyclase in vitro. PLoS One (2007) 1.32
Salt and osmotic stress cause rapid increases in Arabidopsis thaliana cGMP levels. FEBS Lett (2004) 1.26
Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction. PLoS Genet (2005) 1.20
Xanthomonas axonopodis pv. citri uses a plant natriuretic peptide-like protein to modify host homeostasis. Proc Natl Acad Sci U S A (2008) 1.16
The Arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes. PLoS One (2010) 1.14
Engineering drought and salinity tolerance in plants: lessons from genome-wide expression profiling in Arabidopsis. Trends Biotechnol (2005) 1.11
AtPNP-A is a systemically mobile natriuretic peptide immunoanalogue with a role in Arabidopsis thaliana cell volume regulation. FEBS Lett (2004) 1.09
Co-expression and promoter content analyses assign a role in biotic and abiotic stress responses to plant natriuretic peptides. BMC Plant Biol (2008) 1.06
The phytosulfokine (PSK) receptor is capable of guanylate cyclase activity and enabling cyclic GMP-dependent signaling in plants. J Biol Chem (2011) 1.05
A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry. BMC Evol Biol (2004) 1.04
Ozone and nitric oxide induce cGMP-dependent and -independent transcription of defence genes in tobacco. New Phytol (2009) 1.03
A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana. BMC Syst Biol (2011) 1.02
A recombinant plant natriuretic peptide causes rapid and spatially differentiated K+, Na+ and H+ flux changes in Arabidopsis thaliana roots. Plant Cell Physiol (2004) 1.00
Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins. Cell Commun Signal (2013) 0.96
A eukaryotic-acquired gene by a biotrophic phytopathogen allows prolonged survival on the host by counteracting the shut-down of plant photosynthesis. PLoS One (2010) 0.90
A plant natriuretic peptide-like molecule of the pathogen Xanthomonas axonopodis pv. citri causes rapid changes in the proteome of its citrus host. BMC Plant Biol (2010) 0.89
NO release by nitric oxide donors in vitro and in planta. Plant Physiol Biochem (2008) 0.88
The hidden geometries of the Arabidopsis thaliana epidermis. PLoS One (2012) 0.87
A guide to the integrated application of on-line data mining tools for the inference of gene functions at the systems level. Biotechnol J (2008) 0.87
Gibberellic acid and cGMP-dependent transcriptional regulation in Arabidopsis thaliana. Plant Signal Behav (2010) 0.86
Deciphering cGMP signatures and cGMP-dependent pathways in plant defence. Plant Signal Behav (2009) 0.86
The Arabidopsis thaliana cysteine-rich receptor-like kinase CRK20 modulates host responses to Pseudomonas syringae pv. tomato DC3000 infection. J Plant Physiol (2011) 0.86
Plant nucleotide cyclases: an increasingly complex and growing family. Plant Signal Behav (2007) 0.86
Plant natriuretic peptides are apoplastic and paracrine stress response molecules. Plant Cell Physiol (2011) 0.85
Modulating host homeostasis as a strategy in the plant-pathogen arms race. Commun Integr Biol (2009) 0.84
Shedding light on the role of photosynthesis in pathogen colonization and host defense. Commun Integr Biol (2010) 0.84
The Arabidopsis thaliana proteome harbors undiscovered multi-domain molecules with functional guanylyl cyclase catalytic centers. Cell Commun Signal (2013) 0.84
Identification of a novel Arabidopsis thaliana nitric oxide-binding molecule with guanylate cyclase activity in vitro. FEBS Lett (2011) 0.84
Proteomic signatures implicate cAMP in light and temperature responses in Arabidopsis thaliana. J Proteomics (2013) 0.83
The type III protein secretion system contributes to Xanthomonas citri subsp. citri biofilm formation. BMC Microbiol (2014) 0.83
A red and far-red light receptor mutation confers resistance to the herbicide glyphosate. Plant J (2014) 0.82
Heritability in the efficiency of nonsense-mediated mRNA decay in humans. PLoS One (2010) 0.82
The Arabidopsis thaliana natriuretic peptide AtPNP-A is a systemic regulator of leaf dark respiration and signals via the phloem. J Plant Physiol (2011) 0.82
Unraveling plant responses to bacterial pathogens through proteomics. J Biomed Biotechnol (2011) 0.81
Moonlighting kinases with guanylate cyclase activity can tune regulatory signal networks. Plant Signal Behav (2012) 0.81
Insights into xanthomonas axonopodis pv. citri biofilm through proteomics. BMC Microbiol (2013) 0.80
Computational identification of candidate nucleotide cyclases in higher plants. Methods Mol Biol (2013) 0.79
Calcium is the switch in the moonlighting dual function of the ligand-activated receptor kinase phytosulfokine receptor 1. Cell Commun Signal (2014) 0.77
Noninvasive microelectrode ion flux estimation technique (MIFE) for the study of the regulation of root membrane transport by cyclic nucleotides. Methods Mol Biol (2013) 0.77
Phosphodiesterase activity is regulated by CC2D1A that is implicated in non-syndromic intellectual disability. Cell Commun Signal (2013) 0.76
cGMP in ozone and NO dependent responses. Plant Signal Behav (2008) 0.75
Plant natriuretic peptides: control of synthesis and systemic effects. Plant Signal Behav (2011) 0.75
Molecular methods for the study of signal transduction in plants. Methods Mol Biol (2013) 0.75