Published in BMC Bioinformatics on December 24, 2009
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc (2013) 13.33
Comparing de novo assemblers for 454 transcriptome data. BMC Genomics (2010) 3.49
Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol (2011) 2.36
The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics (2011) 1.77
Pyrosequencing the transcriptome of the greenhouse whitefly, Trialeurodes vaporariorum reveals multiple transcripts encoding insecticide targets and detoxifying enzymes. BMC Genomics (2011) 1.53
Sugarcane giant borer transcriptome analysis and identification of genes related to digestion. PLoS One (2015) 1.42
Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach. PLoS One (2012) 1.37
A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC Genomics (2011) 1.28
ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence. BMC Genomics (2011) 1.26
High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species. BMC Plant Biol (2011) 1.20
Diversity of beetle genes encoding novel plant cell wall degrading enzymes. PLoS One (2010) 1.20
A sweet potato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics (2010) 1.17
Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Front Zool (2012) 1.17
Gene discovery in the horned beetle Onthophagus taurus. BMC Genomics (2010) 1.03
Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation. BMC Genomics (2012) 1.02
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genomics (2012) 1.01
Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon. BMC Genomics (2013) 1.00
The GMOD Drupal bioinformatic server framework. Bioinformatics (2010) 0.98
Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Res (2013) 0.96
Sequencing, De Novo assembly and annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata, Transcriptome. PLoS One (2014) 0.95
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genomics (2014) 0.93
SNP markers retrieval for a non-model species: a practical approach. BMC Res Notes (2012) 0.93
Transcriptome analysis in cotton boll weevil (Anthonomus grandis) and RNA interference in insect pests. PLoS One (2013) 0.90
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus). BMC Genomics (2013) 0.90
A comprehensive characterization of the caspase gene family in insects from the order Lepidoptera. BMC Genomics (2011) 0.89
The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus. BMC Genomics (2013) 0.86
Towards decrypting cryptobiosis--analyzing anhydrobiosis in the tardigrade Milnesium tardigradum using transcriptome sequencing. PLoS One (2014) 0.86
Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction. BMC Genomics (2013) 0.84
Potential value of nutrigenomics in Crohn's disease. Nat Rev Gastroenterol Hepatol (2012) 0.84
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. Database (Oxford) (2012) 0.82
Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development. BMC Genomics (2013) 0.81
CAPRG: sequence assembling pipeline for next generation sequencing of non-model organisms. PLoS One (2012) 0.81
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genomics (2014) 0.80
De novo transcriptome of the desert beetle Microdera punctipennis (Coleoptera: Tenebrionidae) using Illumina RNA-seq technology. Mol Biol Rep (2014) 0.80
First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao. PLoS One (2016) 0.78
Microsatellites for the marsh fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers. PLoS One (2013) 0.77
Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei. PLoS One (2015) 0.75
What's in the Gift? Towards a Molecular Dissection of Nuptial Feeding in a Cricket. PLoS One (2015) 0.75
The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects. F1000Res (2016) 0.75
4Pipe4 - A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information. BMC Bioinformatics (2016) 0.75
Transcriptome analysis of hexaploid hulless oat in response to salinity stress. PLoS One (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
dbSNP: the NCBI database of genetic variation. Nucleic Acids Res (2001) 76.97
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
CAP3: A DNA sequence assembly program. Genome Res (1999) 50.04
SSAHA: a fast search method for large DNA databases. Genome Res (2001) 48.64
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
dbEST--database for "expressed sequence tags". Nat Genet (1993) 41.10
The ENZYME database in 2000. Nucleic Acids Res (2000) 23.85
The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66
Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res (2005) 23.41
Next-generation sequencing transforms today's biology. Nat Methods (2007) 11.93
FlyBase: genes and gene models. Nucleic Acids Res (2005) 11.15
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res (2004) 10.40
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol (2008) 9.09
A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics (2007) 8.47
Comparison of DNA sequences with protein sequences. Genomics (1997) 7.76
Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet (2000) 6.11
Development, plasticity and evolution of butterfly eyespot patterns. Nature (1996) 5.15
The genome sequence of silkworm, Bombyx mori. DNA Res (2004) 4.27
VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res (2008) 3.73
VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res (2006) 2.94
The genetics and genomics of the silkworm, Bombyx mori. Annu Rev Entomol (2005) 2.92
The construction of an EST database for Bombyx mori and its application. Proc Natl Acad Sci U S A (2003) 2.56
SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res (2005) 2.50
Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci (2003) 2.35
PartiGene--constructing partial genomes. Bioinformatics (2004) 2.32
The molecular ecologist's guide to expressed sequence tags. Mol Ecol (2007) 2.23
Making sense of EST sequences by CLOBBing them. BMC Bioinformatics (2002) 2.08
prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics (2004) 2.07
Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques (2009) 1.95
Pyrosequencing the Manduca sexta larval midgut transcriptome: messages for digestion, detoxification and defence. Insect Mol Biol (2009) 1.65
ButterflyBase: a platform for lepidopteran genomics. Nucleic Acids Res (2007) 1.65
annot8r: GO, EC and KEGG annotation of EST datasets. BMC Bioinformatics (2008) 1.64
Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at the HmYb/Sb locus. Mol Ecol (2010) 1.56
Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera. Insect Biochem Mol Biol (2009) 1.55
A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome. PLoS Genet (2009) 1.51
Pyrosequence analysis of expressed sequence tags for Manduca sexta hemolymph proteins involved in immune responses. Insect Biochem Mol Biol (2008) 1.45
Genomic tools and cDNA derived markers for butterflies. Mol Ecol (2005) 1.38
ESTWeb: bioinformatics services for EST sequencing projects. Bioinformatics (2003) 1.37
BeetleBase: the model organism database for Tribolium castaneum. Nucleic Acids Res (2006) 1.33
Butterfly genomics eclosing. Heredity (Edinb) (2007) 1.15
SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics (2005) 1.05
The genome of Apis mellifera: dialog between linkage mapping and sequence assembly. Genome Biol (2007) 1.00
Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics (2007) 0.92
Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage. Bioinformatics (2004) 0.90
Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Mol Phylogenet Evol (2008) 0.90
Separation of sequences from host-pathogen interface using triplet nucleotide frequencies. Fungal Genet Biol (2007) 0.86
Evaluation of methods for extracting Xylella fastidiosa DNA from the glassy-winged sharpshooter. J Econ Entomol (2004) 0.83
Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One (2011) 2.68
Three cadherin alleles associated with resistance to Bacillus thuringiensis in pink bollworm. Proc Natl Acad Sci U S A (2003) 2.57
RNA interference in Lepidoptera: an overview of successful and unsuccessful studies and implications for experimental design. J Insect Physiol (2010) 2.47
An ABC transporter mutation is correlated with insect resistance to Bacillus thuringiensis Cry1Ac toxin. PLoS Genet (2010) 1.86
Allelic variation in a fatty-acyl reductase gene causes divergence in moth sex pheromones. Nature (2010) 1.79
Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in the Heliconius melpomene clade. PLoS Genet (2010) 1.73
Localization of Müllerian mimicry genes on a dense linkage map of Heliconius erato. Genetics (2006) 1.69
Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) and of its relationship to H. zea. BMC Evol Biol (2007) 1.68
Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics (2006) 1.66
Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in Heliconius erato. PLoS Genet (2010) 1.61
Parallel evolution of Bacillus thuringiensis toxin resistance in lepidoptera. Genetics (2011) 1.60
Evaluating the insecticide resistance potential of eight Drosophila melanogaster cytochrome P450 genes by transgenic over-expression. Insect Biochem Mol Biol (2007) 1.57
Invertebrates as a source of emerging human pathogens. Nat Rev Microbiol (2004) 1.45
Immune system responses and fitness costs associated with consumption of bacteria in larvae of Trichoplusia ni. BMC Biol (2007) 1.40
Shedding light on moths: shorter wavelengths attract noctuids more than geometrids. Biol Lett (2013) 1.39
Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens. BMC Genomics (2009) 1.33
Mis-spliced transcripts of nicotinic acetylcholine receptor alpha6 are associated with field evolved spinosad resistance in Plutella xylostella (L.). PLoS Genet (2010) 1.22
Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens. BMC Genomics (2010) 1.21
Diversity of beetle genes encoding novel plant cell wall degrading enzymes. PLoS One (2010) 1.20
Efficacy of genetically modified Bt toxins against insects with different genetic mechanisms of resistance. Nat Biotechnol (2011) 1.19
Rapid Virulence Annotation (RVA): identification of virulence factors using a bacterial genome library and multiple invertebrate hosts. Proc Natl Acad Sci U S A (2008) 1.18
Metabolism of imidacloprid and DDT by P450 CYP6G1 expressed in cell cultures of Nicotiana tabacum suggests detoxification of these insecticides in Cyp6g1-overexpressing strains of Drosophila melanogaster, leading to resistance. Pest Manag Sci (2008) 1.18
Mapping the larval midgut lumen proteome of Helicoverpa armigera, a generalist herbivorous insect. J Proteome Res (2008) 1.16
DDT resistance in flies carries no cost. Curr Biol (2005) 1.15
Toxicity of Bacillus thuringiensis insecticidal proteins for Helicoverpa armigera and Helicoverpa punctigera (Lepidoptera: Noctuidae), major pests of cotton. J Invertebr Pathol (2002) 1.15
Dietary-dependent trans-generational immune priming in an insect herbivore. Proc Biol Sci (2009) 1.13
Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes. BMC Evol Biol (2010) 1.11
Complexity and variability of gut commensal microbiota in polyphagous lepidopteran larvae. PLoS One (2012) 1.08
Immunity or digestion: glucanase activity in a glucan-binding protein family from Lepidoptera. J Biol Chem (2008) 1.05
Behavioral assays for studies of host plant choice and adaptation in herbivorous insects. Annu Rev Entomol (2013) 1.05
Resistance of Australian Helicoverpa armigera to fenvalerate is due to the chimeric P450 enzyme CYP337B3. Proc Natl Acad Sci U S A (2012) 1.03
Genetic basis of resistance to Cry1Ac and Cry2Aa in Heliothis virescens (Lepidoptera: Noctuidae). J Econ Entomol (2005) 1.03
Genetic mapping of Bt-toxin binding proteins in a Cry1A-toxin resistant strain of diamondback moth Plutella xylostella. Insect Biochem Mol Biol (2007) 1.02
Combining proteomics and transcriptome sequencing to identify active plant-cell-wall-degrading enzymes in a leaf beetle. BMC Genomics (2012) 1.02
The HevCaLP protein mediates binding specificity of the Cry1A class of Bacillus thuringiensis toxins in Heliothis virescens. Biochemistry (2004) 1.01
Over-expression of a cytochrome P450 is associated with resistance to pyriproxyfen in the greenhouse whitefly Trialeurodes vaporariorum. PLoS One (2012) 1.00
Colour pattern specification in the Mocker swallowtail Papilio dardanus: the transcription factor invected is a candidate for the mimicry locus H. Proc Biol Sci (2008) 0.99
Evolutionary origins of a novel host plant detoxification gene in butterflies. Mol Biol Evol (2008) 0.99
The GMOD Drupal bioinformatic server framework. Bioinformatics (2010) 0.98
A polymerase chain reaction screen of field populations of Heliothis virescens for a retrotransposon insertion conferring resistance to Bacillus thuringiensis toxin. J Econ Entomol (2007) 0.98
Study of the aminopeptidase N gene family in the lepidopterans Ostrinia nubilalis (Hübner) and Bombyx mori (L.): sequences, mapping and expression. Insect Biochem Mol Biol (2010) 0.97
Comparative analysis of the UDP-glycosyltransferase multigene family in insects. Insect Biochem Mol Biol (2011) 0.95
Effects of larval host plants on over-wintering physiological dynamics and survival of the cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). J Insect Physiol (2008) 0.95
Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen Burkholderia pseudomallei K96243. PLoS One (2010) 0.94
Crystallization of α- and β-carotene in the foregut of Spodoptera larvae feeding on a toxic food plant. Insect Biochem Mol Biol (2011) 0.93
Within-population variability in a moth sex pheromone blend: genetic basis and behavioural consequences. Proc Biol Sci (2014) 0.93
Pheromonal divergence between two strains of Spodoptera frugiperda. J Chem Ecol (2013) 0.92
Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis. Proc Natl Acad Sci U S A (2013) 0.92
Host plant flowering increases both adult oviposition preference and larval performance of a generalist herbivore. Environ Entomol (2010) 0.92
Sialome of a generalist lepidopteran herbivore: identification of transcripts and proteins from Helicoverpa armigera labial salivary glands. PLoS One (2011) 0.92
A comprehensive characterization of the caspase gene family in insects from the order Lepidoptera. BMC Genomics (2011) 0.89
Dissecting the insecticide-resistance- associated cytochrome P450 gene Cyp6g1. Pest Manag Sci (2008) 0.88
Sex linkage of CpGV resistance in a heterogeneous field strain of the codling moth Cydia pomonella (L.). J Invertebr Pathol (2009) 0.87
The phytohormone precursor OPDA is isomerized in the insect gut by a single, specific glutathione transferase. Proc Natl Acad Sci U S A (2009) 0.87
New plasmids and putative virulence factors from the draft genome of an Australian clinical isolate of Photorhabdus asymbiotica. FEMS Microbiol Lett (2010) 0.87
A host-plant specialist, Helicoverpa assulta, is more tolerant to capsaicin from Capsicum annuum than other noctuid species. J Insect Physiol (2011) 0.87
The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer. Proc Biol Sci (2013) 0.86
Bacterial feeding induces changes in immune-related gene expression and has trans-generational impacts in the cabbage looper (Trichoplusia ni). Front Zool (2009) 0.86
Trade-offs of host use between generalist and specialist Helicoverpa sibling species: adult oviposition and larval performance. Oecologia (2011) 0.86
Ostrinia revisited: Evidence for sex linkage in European Corn Borer Ostrinia nubilalis (Hubner) pheromone reception. BMC Evol Biol (2010) 0.86
Flavin-dependent monooxygenases as a detoxification mechanism in insects: new insights from the arctiids (lepidoptera). PLoS One (2010) 0.85
Host strain specific sex pheromone variation in Spodoptera frugiperda. Front Zool (2008) 0.84
Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera. BMC Genomics (2011) 0.84
Evaluation of the role of CYP6B cytochrome P450s in pyrethroid resistant Australian Helicoverpa armigera. Insect Mol Biol (2007) 0.84
Chromatographic and electrophoretic resolution of proteins and protein complexes from the larval midgut microvilli of Manduca sexta. Insect Biochem Mol Biol (2009) 0.84
Photorhabdus adhesion modification protein (Pam) binds extracellular polysaccharide and alters bacterial attachment. BMC Microbiol (2010) 0.84
Strong genetic differentiation and postglacial origin of populations in the marine midge Clunio marinus (Chironomidae, Diptera). Mol Ecol (2010) 0.84
Timing the tides: genetic control of diurnal and lunar emergence times is correlated in the marine midge Clunio marinus. BMC Genet (2011) 0.84
Genetic architecture of local adaptation in lunar and diurnal emergence times of the marine midge Clunio marinus (Chironomidae, Diptera). PLoS One (2012) 0.83
A serine proteinase homologue, SPH-3, plays a central role in insect immunity. J Immunol (2011) 0.82
OPDA isomerase GST16 is involved in phytohormone detoxification and insect development. FEBS J (2014) 0.82
Pdl1 is a putative lipase that enhances Photorhabdus toxin complex secretion. PLoS Pathog (2012) 0.81
Phylloplane location of glucosinolates in Barbarea spp. (Brassicaceae) and misleading assessment of host suitability by a specialist herbivore. New Phytol (2010) 0.80
Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore. BMC Evol Biol (2010) 0.80
Mutations in Dalpha1 or Dbeta2 nicotinic acetylcholine receptor subunits can confer resistance to neonicotinoids in Drosophila melanogaster. Insect Biochem Mol Biol (2008) 0.79
Allochronic separation versus mate choice: nonrandom patterns of mating between fall armyworm host strains. Am Nat (2011) 0.79
Metabolic detoxification of capsaicin by UDP-glycosyltransferase in three Helicoverpa species. Arch Insect Biochem Physiol (2011) 0.78
Can sulfur fertilisation improve the effectiveness of trap crops for diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae)? Pest Manag Sci (2010) 0.78
Insecticide resistance comes of age. Genome Biol (2014) 0.78
A robust phylogenetic framework for the bacterial genus Photorhabdus and its use in studying the evolution and maintenance of bioluminescence: a case for 16S, gyrB, and glnA. Mol Phylogenet Evol (2010) 0.77
Interaction of glucosinolate content of Arabidopsis thaliana mutant lines and feeding and oviposition by generalist and specialist lepidopterans. Phytochemistry (2012) 0.77
Comparative proteomic analysis of Helicoverpa armigera cells undergoing apoptosis. J Proteome Res (2011) 0.76
High-throughput sequencing of a single chromosome: a moth W chromosome. Chromosome Res (2013) 0.76
Isolation of 10 polymorphic microsatellite loci in the marine midge Clunio marinus (Chironomidae, Diptera) and their efficient characterization by heteroduplex analysis. Mol Ecol Resour (2008) 0.76
Karyotypes versus Genomes: The Nymphalid Butterflies Melitaea cinxia, Danaus plexippus, and D. chrysippus. Cytogenet Genome Res (2017) 0.75