Published in Nucleic Acids Res on October 08, 2010
Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res (2011) 11.32
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res (2011) 5.34
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2013) 5.13
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. Theor Appl Genet (2013) 2.75
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res (2011) 2.45
Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell (2011) 1.88
PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Res (2011) 1.86
Ontologies as integrative tools for plant science. Am J Bot (2012) 1.71
The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol (2012) 1.65
The Sol Genomics Network (SGN)--from genotype to phenotype to breeding. Nucleic Acids Res (2014) 1.30
The banana genome hub. Database (Oxford) (2013) 1.29
Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol (2011) 1.28
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell (2012) 1.27
Tripal: a construction toolkit for online genome databases. Database (Oxford) (2011) 1.24
The Tomato Yellow Leaf Curl Virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA-dependent RNA polymerases. PLoS Genet (2013) 1.20
Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. Mol Genet Genomics (2012) 1.19
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. Database (Oxford) (2011) 1.16
TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections. Plant Cell Physiol (2011) 1.16
The grapevine gene nomenclature system. BMC Genomics (2014) 1.14
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. Nucleic Acids Res (2012) 1.11
Evolution of the land plant exocyst complexes. Front Plant Sci (2012) 1.04
Genetic basis and detection of unintended effects in genetically modified crop plants. Transgenic Res (2015) 1.04
Sterol side chain reductase 2 is a key enzyme in the biosynthesis of cholesterol, the common precursor of toxic steroidal glycoalkaloids in potato. Plant Cell (2014) 1.03
Genome-wide identification and expression analysis of aquaporins in tomato. PLoS One (2013) 1.01
Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity. Genome Biol (2013) 1.01
Identification of a BAHD acetyltransferase that produces protective acyl sugars in tomato trichomes. Proc Natl Acad Sci U S A (2012) 0.99
MetaBase--the wiki-database of biological databases. Nucleic Acids Res (2011) 0.98
Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta (2011) 0.96
A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One (2016) 0.96
Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiol (2012) 0.94
Characterization of the procera tomato mutant shows novel functions of the SlDELLA protein in the control of flower morphology, cell division and expansion, and the auxin-signaling pathway during fruit-set and development. Plant Physiol (2012) 0.91
Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties. BMC Genomics (2012) 0.90
The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense. BMC Plant Biol (2012) 0.90
Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant. BMC Plant Biol (2014) 0.90
The eIF4F and eIFiso4F Complexes of Plants: An Evolutionary Perspective. Comp Funct Genomics (2012) 0.90
The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res (2014) 0.89
Orchidstra: an integrated orchid functional genomics database. Plant Cell Physiol (2013) 0.89
The identification of two arabinosyltransferases from tomato reveals functional equivalency of xyloglucan side chain substituents. Plant Physiol (2013) 0.89
Fractionation, stability, and isolate-specificity of QTL for resistance to Phytophthora infestans in cultivated tomato (Solanum lycopersicum). G3 (Bethesda) (2012) 0.89
RNA trafficking in parasitic plant systems. Front Plant Sci (2012) 0.87
High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling. Theor Appl Genet (2015) 0.87
Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. Plant Cell Physiol (2014) 0.86
Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf. Plant J (2013) 0.86
Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. Plant Cell Physiol (2013) 0.86
Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles. BMC Plant Biol (2012) 0.86
Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites. G3 (Bethesda) (2013) 0.85
Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing. PLoS One (2014) 0.85
Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves. DNA Res (2014) 0.84
Tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research. PLoS One (2014) 0.84
De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters. PLoS One (2013) 0.83
An ontology approach to comparative phenomics in plants. Plant Methods (2015) 0.82
RNase J participates in a pentatricopeptide repeat protein-mediated 5' end maturation of chloroplast mRNAs. Nucleic Acids Res (2013) 0.82
Functional genomics of tomato in a post-genome-sequencing phase. Breed Sci (2013) 0.82
Over-expression of SlSHN1 gene improves drought tolerance by increasing cuticular wax accumulation in tomato. Int J Mol Sci (2014) 0.82
HsfA2 Controls the Activity of Developmentally and Stress-Regulated Heat Stress Protection Mechanisms in Tomato Male Reproductive Tissues. Plant Physiol (2016) 0.81
Updating the Micro-Tom TILLING platform. Breed Sci (2013) 0.81
Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives. PeerJ (2015) 0.81
The hypervariable amino-terminus of P1 protease modulates potyviral replication and host defense responses. PLoS Pathog (2014) 0.81
Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in Arabidopsis. Plant Physiol (2012) 0.81
Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing. Mol Breed (2015) 0.81
Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers. PLoS One (2012) 0.81
RNA sequencing analysis reveals transcriptomic variations in tobacco (Nicotiana tabacum) leaves affected by climate, soil, and tillage factors. Int J Mol Sci (2014) 0.81
gff2sequence, a new user friendly tool for the generation of genomic sequences. BioData Min (2013) 0.80
Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae). Genetics (2014) 0.80
Multiple QTL for horticultural traits and quantitative resistance to Phytophthora infestans linked on Solanum habrochaites chromosome 11. G3 (Bethesda) (2014) 0.79
Characterization of a flavonol 3-O-methyltransferase in the trichomes of the wild tomato species Solanum habrochaites. Planta (2012) 0.78
Genomics and bioinformatics resources for translational science in Rosaceae. Plant Biotechnol Rep (2013) 0.78
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. Int J Mol Sci (2013) 0.78
Expression of heterologous xyloglucan xylosyltransferases in Arabidopsis to investigate their role in determining xyloglucan xylosylation substitution patterns. Planta (2015) 0.78
MEGANTE: a web-based system for integrated plant genome annotation. Plant Cell Physiol (2013) 0.78
Galacturonosyltransferase 4 silencing alters pectin composition and carbon partitioning in tomato. J Exp Bot (2013) 0.78
An active ac/ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation. Plant Physiol (2013) 0.78
The tomato genome fleshed out. Nat Biotechnol (2012) 0.77
A Deluge of Complex Repeats: The Solanum Genome. PLoS One (2015) 0.77
Arbuscular mycorrhiza Symbiosis Induces a Major Transcriptional Reprogramming of the Potato SWEET Sugar Transporter Family. Front Plant Sci (2016) 0.77
RNA-sequencing Reveals Global Transcriptomic Changes in Nicotiana tabacum Responding to Topping and Treatment of Axillary-shoot Control Chemicals. Sci Rep (2015) 0.77
Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae. J Mol Evol (2016) 0.76
Development of a gene-centered ssr atlas as a resource for papaya (Carica papaya) marker-assisted selection and population genetic studies. PLoS One (2014) 0.76
Linking the potato genome to the conserved ortholog set (COS) markers. BMC Genet (2013) 0.76
Acylsugar Acylhydrolases: Carboxylesterase-Catalyzed Hydrolysis of Acylsugars in Tomato Trichomes. Plant Physiol (2016) 0.76
Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ (2016) 0.75
A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages. BMC Plant Biol (2015) 0.75
A DUF-246 family glycosyltransferase-like gene affects male fertility and the biosynthesis of pectic arabinogalactans. BMC Plant Biol (2016) 0.75
In silico prediction of proteins related to xyloglucan fucosyltransferases in Solanaceae genomes. Plant Signal Behav (2015) 0.75
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. Bioinform Biol Insights (2014) 0.75
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. Plant Physiol (2017) 0.75
Agroinfiltration contributes to VP1 recombinant protein degradation. Bioengineered (2016) 0.75
solGS: a web-based tool for genomic selection. BMC Bioinformatics (2014) 0.75
Alternative splicing in tomato pollen in response to heat stress. DNA Res (2016) 0.75
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. Database (Oxford) (2015) 0.75
A vicilin-like seed storage protein, PAP85, is involved in tobacco mosaic virus replication. J Virol (2013) 0.75
Indel Group in Genomes (IGG) Molecular Genetic Markers. Plant Physiol (2016) 0.75
Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes. BMC Genomics (2017) 0.75
Gr and hp-1 tomato mutants unveil unprecedented interactions between arbuscular mycorrhizal symbiosis and fruit ripening. Planta (2016) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics (2001) 28.35
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81
R/qtl: QTL mapping in experimental crosses. Bioinformatics (2003) 22.38
Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91
ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res (2003) 17.39
NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res (2008) 17.35
The Pathway Tools software. Bioinformatics (2002) 14.89
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res (2007) 14.24
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
High density molecular linkage maps of the tomato and potato genomes. Genetics (1992) 11.83
Single-molecule DNA sequencing of a viral genome. Science (2008) 11.66
The Protein Information Resource. Nucleic Acids Res (2003) 11.17
ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol (1999) 9.18
A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics (2007) 8.47
Archiving next generation sequencing data. Nucleic Acids Res (2009) 6.98
A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res (2010) 4.48
The Proteomics Identifications database: 2010 update. Nucleic Acids Res (2009) 4.47
Inferring evolutionary trees with PAUP*. Curr Protoc Bioinformatics (2003) 4.19
The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol (2005) 3.65
Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38
Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis. Proc Int Conf Intell Syst Mol Biol (1997) 2.64
Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol (2008) 2.30
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res (2008) 2.28
MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming. Comput Appl Biosci (1993) 1.97
A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res (2008) 1.82
A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol (2008) 1.34
A comparative analysis into the genetic bases of morphology in tomato varieties exhibiting elongated fruit shape. Theor Appl Genet (2008) 1.33
Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics. Plant Physiol (2010) 1.33
Morphological variation in tomato: a comprehensive study of quantitative trait loci controlling fruit shape and development. J Exp Bot (2007) 1.18
TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics (2010) 1.14
A microsatellite marker based linkage map of tobacco. Theor Appl Genet (2006) 1.06
Photolithographic synthesis of high-density oligonucleotide probe arrays. Nucleosides Nucleotides Nucleic Acids (2001) 1.01
Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res (2010) 0.98
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. Cell Mol Life Sci (2009) 0.95
AtEnsEMBL. Methods Mol Biol (2007) 0.86
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res (2003) 18.69
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2004) 10.71
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res (2009) 7.33
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res (2011) 5.34
Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol (2004) 5.17
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2013) 5.13
Gramene: a growing plant comparative genomics resource. Nucleic Acids Res (2007) 4.59
TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics (2002) 3.74
The SOL Genomics Network: a comparative resource for Solanaceae biology and beyond. Plant Physiol (2005) 3.65
Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. Plant Mol Biol (2002) 2.95
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics (2005) 2.48
The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet (2012) 2.33
Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nat Genet (2007) 2.31
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res (2008) 2.28
Overdominant quantitative trait loci for yield and fitness in tomato. Proc Natl Acad Sci U S A (2006) 2.19
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol (2006) 2.03
A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research. Mol Plant Microbe Interact (2012) 1.84
Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol (2010) 1.77
Rose scent: genomics approach to discovering novel floral fragrance-related genes. Plant Cell (2002) 1.76
Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69
PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res (2005) 1.67
The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol (2012) 1.65
Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. Plant J (2007) 1.58
Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am J Bot (2012) 1.55
A sequence-based map of Arabidopsis genes with mutant phenotypes. Plant Physiol (2003) 1.55
Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol (2005) 1.54
Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet (2005) 1.47
A dynamic interface for capsaicinoid systems biology. Plant Physiol (2009) 1.46
The SGN comparative map viewer. Bioinformatics (2008) 1.45
O-methyltransferases involved in the biosynthesis of volatile phenolic derivatives in rose petals. Plant Physiol (2002) 1.44
A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol (2008) 1.34
An alternative splice form of Mdm2 induces p53-independent cell growth and tumorigenesis. J Biol Chem (2003) 1.34
The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Res (2013) 1.28
Volatile ester formation in roses. Identification of an acetyl-coenzyme A. Geraniol/Citronellol acetyltransferase in developing rose petals. Plant Physiol (2003) 1.27
Gramene QTL database: development, content and applications. Database (Oxford) (2009) 1.25
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. Database (Oxford) (2011) 1.16
TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics (2010) 1.14
EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot. Plant Mol Biol (2006) 1.07
Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case. Proteomics (2012) 1.01
Analysis of ultra low genome conservation in Clostridium difficile. PLoS One (2010) 0.96
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. BMC Genomics (2012) 0.95
Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. BMC Plant Biol (2008) 0.91
Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. BMC Plant Biol (2014) 0.88
Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota). BMC Evol Biol (2012) 0.86
From manual curation to visualization of gene families and networks across Solanaceae plant species. Database (Oxford) (2013) 0.85
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database. BMC Bioinformatics (2010) 0.85
Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex. Genome (2014) 0.80
Flower proteome: changes in protein spectrum during the advanced stages of rose petal development. Planta (2005) 0.80
The tomato kinome and the tomato kinase library ORFeome: novel resources for the study of kinases and signal transduction in tomato and solanaceae species. Mol Plant Microbe Interact (2014) 0.79
Linking the potato genome to the conserved ortholog set (COS) markers. BMC Genet (2013) 0.76
solGS: a web-based tool for genomic selection. BMC Bioinformatics (2014) 0.75