Published in BMC Evol Biol on February 12, 2010
De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res (2011) 4.06
Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol (2011) 2.36
Circadian control of global gene expression patterns. Annu Rev Genet (2010) 1.85
MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol (2013) 1.48
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana. BMC Evol Biol (2011) 1.30
Life at the extreme: lessons from the genome. Genome Biol (2012) 1.14
A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana. J Exp Bot (2011) 1.12
Taxonomically restricted genes are associated with the evolution of sociality in the honey bee. BMC Genomics (2011) 1.06
Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. BMC Genomics (2013) 0.97
Evolution of the class IV HD-zip gene family in streptophytes. Mol Biol Evol (2013) 0.85
Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana. PLoS One (2013) 0.85
RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha. PLoS One (2014) 0.83
Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on guanine-cytosine content and the breadth of expression. Plant Physiol (2013) 0.81
Large-Scale Transcriptome Analysis in Faba Bean (Vicia faba L.) under Ascochyta fabae Infection. PLoS One (2015) 0.78
Pyrosequencing data reveals tissue-specific expression of lineage-specific transcripts in chickpea. Plant Signal Behav (2011) 0.78
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. Plant Biotechnol J (2017) 0.77
Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis). BMC Genomics (2015) 0.77
On the Origin of De Novo Genes in Arabidopsis thaliana Populations. Genome Biol Evol (2016) 0.75
Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity. BMC Genomics (2016) 0.75
Data in support of genome-wide identification of lineage-specific genes within Caenorhabditis elegans. Data Brief (2015) 0.75
GFam: a platform for automatic annotation of gene families. Nucleic Acids Res (2012) 0.75
Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution. Genome Biol Evol (2016) 0.75
ORFanFinder: automated identification of taxonomically restricted orphan genes. Bioinformatics (2016) 0.75
A database for orphan genes in Poaceae. Exp Ther Med (2017) 0.75
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
Profile hidden Markov models. Bioinformatics (1998) 56.04
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res (2003) 38.75
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol (2000) 22.77
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
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res (2007) 14.24
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (2007) 9.85
The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res (2006) 8.26
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res (2003) 5.73
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science (2001) 5.32
Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol (2004) 5.17
The male determinant of self-incompatibility in Brassica. Science (1999) 5.03
DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics (2004) 3.74
The S receptor kinase determines self-incompatibility in Brassica stigma. Nature (2000) 2.96
Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci U S A (2006) 2.84
Inverse relationship between evolutionary rate and age of mammalian genes. Mol Biol Evol (2004) 2.79
Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol (2005) 2.60
An evolutionary analysis of orphan genes in Drosophila. Genome Res (2003) 2.52
The pollen determinant of self-incompatibility in Brassica campestris. Proc Natl Acad Sci U S A (2000) 2.50
Self-incompatibility in the genus Arabidopsis: characterization of the S locus in the outcrossing A. lyrata and its autogamous relative A. thaliana. Plant Cell (2001) 2.30
Comparative plant genomics resources at PlantGDB. Plant Physiol (2005) 2.19
Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol (2008) 2.14
Genomic organization of the S locus: Identification and characterization of genes in SLG/SRK region of S(9) haplotype of Brassica campestris (syn. rapa). Genetics (1999) 2.12
Gene transfer in the evolution of parasite nucleotide biosynthesis. Proc Natl Acad Sci U S A (2004) 2.05
Generation of self-incompatible Arabidopsis thaliana by transfer of two S locus genes from A. lyrata. Science (2002) 1.89
The source of laterally transferred genes in bacterial genomes. Genome Biol (2003) 1.87
Computational identification and characterization of novel genes from legumes. Plant Physiol (2004) 1.67
Analysis of singleton ORFans in fully sequenced microbial genomes. Proteins (2003) 1.61
An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice. Gene (2004) 1.56
Species specificity in pollen-pistil interactions. Annu Rev Genet (2004) 1.49
Intron gain and loss in segmentally duplicated genes in rice. Genome Biol (2006) 1.48
GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res (2007) 1.43
Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol (2006) 1.33
The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes. Genetics (2001) 1.32
Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis. Plant Physiol (2002) 1.27
Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics (2005) 1.25
Pollen-stigma interaction in Brassica. III. Hydration of the pollen grains. J Cell Sci (1985) 1.24
Cell-cell signaling in the self-incompatibility response. Curr Opin Plant Biol (2000) 1.23
Assaying gene content in Arabidopsis. Proc Natl Acad Sci U S A (2002) 1.23
Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity. Plant Physiol (2008) 1.20
Characterization of paralogous protein families in rice. BMC Plant Biol (2008) 1.19
Two large Arabidopsis thaliana gene families are homologous to the Brassica gene superfamily that encodes pollen coat proteins and the male component of the self-incompatibility response. Plant Mol Biol (2001) 1.19
Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol (2007) 1.19
PARC6, a novel chloroplast division factor, influences FtsZ assembly and is required for recruitment of PDV1 during chloroplast division in Arabidopsis. Plant J (2009) 1.16
Birth and death of orphan genes in Rickettsia. Mol Biol Evol (2003) 1.15
Self-incompatibility in the Brassicaceae: receptor-ligand signaling and cell-to-cell communication. Plant Cell (2002) 1.10
Isolation and characterization of pollen coat proteins of Brassica campestris that interact with S locus-related glycoprotein 1 involved in pollen-stigma adhesion. Proc Natl Acad Sci U S A (2000) 1.05
Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus. Genomics (2009) 1.00
A small family of chloroplast atypical thioredoxins. Plant Physiol (2008) 0.98
Significant comparative characteristics between orphan and nonorphan genes in the rice (Oryza sativa L.) genome. Comp Funct Genomics (2007) 0.95
Comparison of the genome structure of the self-incompatibility (S) locus in interspecific pairs of S haplotypes. Genetics (2006) 0.95
Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. BMC Genomics (2008) 0.94
Diversification of ftsZ during early land plant evolution. J Mol Evol (2004) 0.84
The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res (2006) 8.26
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
Role of duplicate genes in genetic robustness against null mutations. Nature (2003) 7.81
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A (2009) 4.65
The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res (2004) 4.31
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27
The institute for genomic research Osa1 rice genome annotation database. Plant Physiol (2005) 3.96
The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci U S A (2002) 3.82
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
Sequencing of a rice centromere uncovers active genes. Nat Genet (2004) 3.66
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res (2003) 3.12
Genome-wide atlas of transcription during maize development. Plant J (2011) 3.07
High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics (2003) 3.02
Type 1 capsule genes of Staphylococcus aureus are carried in a staphylococcal cassette chromosome genetic element. J Bacteriol (2002) 2.76
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. Genome Res (2007) 2.72
Expression divergence between duplicate genes. Trends Genet (2005) 2.69
The TIGR Plant Transcript Assemblies database. Nucleic Acids Res (2006) 2.62
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol (2010) 2.44
Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight. Proc Natl Acad Sci U S A (2003) 2.43
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics (2006) 2.41
Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell (2002) 2.40
Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol (2005) 2.38
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol (2010) 2.36
Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A (2002) 2.27
Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One (2012) 2.26
Induced gene expression in human brain after the split from chimpanzee. Trends Genet (2003) 2.19
Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol (2008) 2.14
Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One (2012) 2.09
Multiple models for Rosaceae genomics. Plant Physiol (2008) 2.08
Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet (2008) 1.99
A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics (2004) 1.94
Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiol (2009) 1.94
Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics (2003) 1.92
Comparative analyses of potato expressed sequence tag libraries. Plant Physiol (2003) 1.84
Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc Natl Acad Sci U S A (2002) 1.81
Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci (2002) 1.77
Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One (2012) 1.75
Two-component systems and their co-option for eukaryotic signal transduction. Curr Biol (2011) 1.74
Microarray expression profiling resources for plant genomics. Trends Plant Sci (2005) 1.65
Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs. Genome Res (2008) 1.63
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics (2008) 1.62
Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol (2006) 1.61
A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family. Plant Physiol (2003) 1.60
Integration of two diploid potato linkage maps with the potato genome sequence. PLoS One (2012) 1.60
Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PLoS One (2012) 1.57
Evolution of alternative splicing after gene duplication. Genome Res (2005) 1.55
Repeatless and repeat-based centromeres in potato: implications for centromere evolution. Plant Cell (2012) 1.54
Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One (2008) 1.53
Diversity in conserved genes in tomato. BMC Genomics (2007) 1.52
Identification of important regions for ethylene binding and signaling in the transmembrane domain of the ETR1 ethylene receptor of Arabidopsis. Plant Cell (2006) 1.50
Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics (2007) 1.49
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res (2005) 1.48
Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics (2011) 1.48
Intron gain and loss in segmentally duplicated genes in rice. Genome Biol (2006) 1.48
Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica. Genome Biol (2004) 1.48
MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol (2013) 1.48
Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One (2013) 1.40
How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution? Trends Genet (2004) 1.38
Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell (2005) 1.37
Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. Plant Cell (2007) 1.36
Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biol (2006) 1.36
Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics (2013) 1.32
Two-component signaling elements and histidyl-aspartyl phosphorelays. Arabidopsis Book (2008) 1.32
The rice kinase database. A phylogenomic database for the rice kinome. Plant Physiol (2006) 1.31
Genomic transition to pathogenicity in chytrid fungi. PLoS Pathog (2011) 1.31
Insights into the maize pan-genome and pan-transcriptome. Plant Cell (2014) 1.30
Advances in plant genome sequencing. Plant J (2012) 1.28
Carotenoid cleavage dioxygenase4 is a negative regulator of β-carotene content in Arabidopsis seeds. Plant Cell (2013) 1.27
Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J (2012) 1.27
The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell (2009) 1.27
Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell (2006) 1.27
Molecular identification and characterization of the tomato flagellin receptor LeFLS2, an orthologue of Arabidopsis FLS2 exhibiting characteristically different perception specificities. Plant Mol Biol (2007) 1.26
Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genet (2012) 1.25
Gene coexpression network analysis as a source of functional annotation for rice genes. PLoS One (2011) 1.25
Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins. Fungal Genet Biol (2007) 1.25
Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics (2005) 1.25
Gene expression profiling of potato responses to cold, heat, and salt stress. Funct Integr Genomics (2005) 1.23
Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res (2002) 1.23
Characterization of genes involved in cytokinin signaling and metabolism from rice. Plant Physiol (2012) 1.23
Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2011) 1.21
Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evol Biol (2011) 1.20
Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PLoS One (2011) 1.19
Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A. Mol Plant Microbe Interact (2006) 1.19