Genome sequence of Aedes aegypti, a major arbovirus vector.

Malaria: progress, perils, and prospects for eradication. J Clin Invest (2008) 6.54

The Aedes aegypti toll pathway controls dengue virus infection. PLoS Pathog (2008) 4.81

Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res (2010) 4.18

Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes. Science (2007) 4.03

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73

Discovery of insect and human dengue virus host factors. Nature (2009) 3.49

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18

Dengue virus type 2 infections of Aedes aegypti are modulated by the mosquito's RNA interference pathway. PLoS Pathog (2009) 3.09

An evolutionary conserved function of the JAK-STAT pathway in anti-dengue defense. Proc Natl Acad Sci U S A (2009) 2.70

Ergatis: a web interface and scalable software system for bioinformatics workflows. Bioinformatics (2010) 2.69

Dengue Fever in mainland China. Am J Trop Med Hyg (2010) 2.47

Aedes aegypti uses RNA interference in defense against Sindbis virus infection. BMC Microbiol (2008) 2.33

Wolbachia induces reactive oxygen species (ROS)-dependent activation of the Toll pathway to control dengue virus in the mosquito Aedes aegypti. Proc Natl Acad Sci U S A (2011) 2.20

Considering transposable element diversification in de novo annotation approaches. PLoS One (2011) 2.11

Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics (2008) 2.09

Mitotic-chromosome-based physical mapping of the Culex quinquefasciatus genome. PLoS One (2015) 2.01

Exploring the molecular basis of insecticide resistance in the dengue vector Aedes aegypti: a case study in Martinique Island (French West Indies). BMC Genomics (2009) 1.98

Malaria control with transgenic mosquitoes. PLoS Med (2009) 1.83

Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense. BMC Microbiol (2011) 1.78

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements. Proc Natl Acad Sci U S A (2010) 1.74

Role of cytochrome P450s in insecticide resistance: impact on the control of mosquito-borne diseases and use of insecticides on Earth. Philos Trans R Soc Lond B Biol Sci (2013) 1.74

Low conservation of gene content in the Drosophila Y chromosome. Nature (2008) 1.72

Mosquito RNAi is the major innate immune pathway controlling arbovirus infection and transmission. Future Microbiol (2011) 1.72

Identity and transfer of male reproductive gland proteins of the dengue vector mosquito, Aedes aegypti: potential tools for control of female feeding and reproduction. Insect Biochem Mol Biol (2007) 1.69

Phenoloxidase activity acts as a mosquito innate immune response against infection with Semliki Forest virus. PLoS Pathog (2012) 1.69

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci U S A (2011) 1.65

Comparative genomics of small RNA regulatory pathway components in vector mosquitoes. BMC Genomics (2008) 1.58

Arbovirus-derived piRNAs exhibit a ping-pong signature in mosquito cells. PLoS One (2012) 1.58

Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens. Science (2010) 1.58

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc Natl Acad Sci U S A (2010) 1.55

Anopheles gambiae APL1 is a family of variable LRR proteins required for Rel1-mediated protection from the malaria parasite, Plasmodium berghei. PLoS One (2008) 1.55

Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet (2009) 1.53

The gap gene network. Cell Mol Life Sci (2010) 1.51

Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti. BMC Genomics (2009) 1.50

The birds and the bees and the flowers and the trees: lessons from genetic mapping of sex determination in plants and animals. Genetics (2010) 1.45

The α1,6-fucosyltransferase gene (fut8) from the Sf9 lepidopteran insect cell line: insights into fut8 evolution. PLoS One (2014) 1.43

Influence of urban landscapes on population dynamics in a short-distance migrant mosquito: evidence for the dengue vector Aedes aegypti. PLoS Negl Trop Dis (2010) 1.40

Implication of haematophagous arthropod salivary proteins in host-vector interactions. Parasit Vectors (2011) 1.39

Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol (2008) 1.36

Quantitative trait loci mapping of genome regions controlling permethrin resistance in the mosquito Aedes aegypti. Genetics (2008) 1.34

Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. Genome Biol Evol (2009) 1.31

Induction of a peptide with activity against a broad spectrum of pathogens in the Aedes aegypti salivary gland, following Infection with Dengue Virus. PLoS Pathog (2011) 1.30

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC Genomics (2011) 1.28

Genome engineering with CRISPR-Cas9 in the mosquito Aedes aegypti. Cell Rep (2015) 1.28

Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics (2010) 1.27

On the extent and origins of genic novelty in the phylum Nematoda. PLoS Negl Trop Dis (2008) 1.25

Chikungunya virus-vector interactions. Viruses (2014) 1.24

RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti. BMC Genomics (2011) 1.24

Molecular genetic analysis of midgut serine proteases in Aedes aegypti mosquitoes. Insect Biochem Mol Biol (2009) 1.24

Sindbis virus usurps the cellular HuR protein to stabilize its transcripts and promote productive infections in mammalian and mosquito cells. Cell Host Microbe (2010) 1.22

From Tucson to genomics and transgenics: the vector biology network and the emergence of modern vector biology. PLoS Negl Trop Dis (2009) 1.22

Alterations in the Aedes aegypti transcriptome during infection with West Nile, dengue and yellow fever viruses. PLoS Pathog (2011) 1.22

Dengue research opportunities in the Americas. J Infect Dis (2012) 1.22

Embryonic desiccation resistance in Aedes aegypti: presumptive role of the chitinized serosal cuticle. BMC Dev Biol (2008) 1.21

Genetic mapping of specific interactions between Aedes aegypti mosquitoes and dengue viruses. PLoS Genet (2013) 1.20

nanos gene control DNA mediates developmentally regulated transposition in the yellow fever mosquito Aedes aegypti. Proc Natl Acad Sci U S A (2007) 1.20

Juvenile hormone regulation of male accessory gland activity in the red flour beetle, Tribolium castaneum. Mech Dev (2009) 1.19

A transgenic sensor strain for monitoring the RNAi pathway in the yellow fever mosquito, Aedes aegypti. Insect Biochem Mol Biol (2008) 1.19

Transgene-mediated suppression of dengue viruses in the salivary glands of the yellow fever mosquito, Aedes aegypti. Insect Mol Biol (2010) 1.18

Complex modulation of the Aedes aegypti transcriptome in response to dengue virus infection. PLoS One (2012) 1.17

A review of FMRFamide- and RFamide-like peptides in metazoa. Invert Neurosci (2010) 1.17

A C-type lectin collaborates with a CD45 phosphatase homolog to facilitate West Nile virus infection of mosquitoes. Cell (2010) 1.17

The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Res (2013) 1.16

Genomic sequence around butterfly wing development genes: annotation and comparative analysis. PLoS One (2011) 1.15

Topological and functional characterization of an insect gustatory receptor. PLoS One (2011) 1.15

Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes. PLoS One (2008) 1.15

Global cross-talk of genes of the mosquito Aedes aegypti in response to dengue virus infection. PLoS Negl Trop Dis (2011) 1.14

Differential protein modulation in midguts of Aedes aegypti infected with chikungunya and dengue 2 viruses. PLoS One (2010) 1.14

Four-way regulation of mosquito yolk protein precursor genes by juvenile hormone-, ecdysone-, nutrient-, and insulin-like peptide signaling pathways. Front Physiol (2014) 1.14

Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in Haiti. BMC Genomics (2009) 1.13

Mosquito infection responses to developing filarial worms. PLoS Negl Trop Dis (2009) 1.12

What can you do with 0.1x genome coverage? A case study based on a genome survey of the scuttle fly Megaselia scalaris (Phoridae). BMC Genomics (2009) 1.12

The role of NF-kappaB factor REL2 in the Aedes aegypti immune response. Insect Biochem Mol Biol (2009) 1.12

Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res (2008) 1.12

An integrated linkage, chromosome, and genome map for the yellow fever mosquito Aedes aegypti. PLoS Negl Trop Dis (2013) 1.12

Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study. Genome Biol (2007) 1.11

aeGEPUCI: a database of gene expression in the dengue vector mosquito, Aedes aegypti. BMC Res Notes (2010) 1.10

The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector. G3 (Bethesda) (2013) 1.10

A set of ontologies to drive tools for the control of vector-borne diseases. J Biomed Inform (2010) 1.10

Silkworm expression system as a platform technology in life science. Appl Microbiol Biotechnol (2010) 1.09

High-quality genome (re)assembly using chromosomal contact data. Nat Commun (2014) 1.08

How insects survive the cold: molecular mechanisms-a review. J Comp Physiol B (2008) 1.08

The molecular evolution of four anti-malarial immune genes in the Anopheles gambiae species complex. BMC Evol Biol (2008) 1.08

Transcriptome analysis of the venom gland of the scorpion Scorpiops jendeki: implication for the evolution of the scorpion venom arsenal. BMC Genomics (2009) 1.08

Genomic organization and splicing evolution of the doublesex gene, a Drosophila regulator of sexual differentiation, in the dengue and yellow fever mosquito Aedes aegypti. BMC Evol Biol (2011) 1.06

Genome analysis of cytochrome P450s and their expression profiles in insecticide resistant mosquitoes, Culex quinquefasciatus. PLoS One (2011) 1.06

A dengue receptor as possible genetic marker of vector competence in Aedes aegypti. BMC Microbiol (2008) 1.06

Differential ammonia metabolism in Aedes aegypti fat body and midgut tissues. J Insect Physiol (2010) 1.06

Identification of early zygotic genes in the yellow fever mosquito Aedes aegypti and discovery of a motif involved in early zygotic genome activation. PLoS One (2012) 1.06

Annotation and expression profiling of apoptosis-related genes in the yellow fever mosquito, Aedes aegypti. Insect Biochem Mol Biol (2007) 1.05

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi. Genome Biol (2014) 1.05

Imaginal discs--a new source of chromosomes for genome mapping of the yellow fever mosquito Aedes aegypti. PLoS Negl Trop Dis (2011) 1.04

Patterned rhodopsin expression in R7 photoreceptors of mosquito retina: Implications for species-specific behavior. J Comp Neurol (2009) 1.04

Cell-to-cell spread of the RNA interference response suppresses Semliki Forest virus (SFV) infection of mosquito cell cultures and cannot be antagonized by SFV. J Virol (2009) 1.04

New Insights into Control of Arbovirus Replication and Spread by Insect RNA Interference Pathways. Insects (2012) 1.04

Transcriptome analysis of Aedes aegypti transgenic mosquitoes with altered immunity. PLoS Pathog (2011) 1.04

Mechanisms of pyrethroid resistance in the dengue mosquito vector, Aedes aegypti: target site insensitivity, penetration, and metabolism. PLoS Negl Trop Dis (2014) 1.04

Cloning and identification of an oxytocin/vasopressin-like receptor and its ligand from insects. Proc Natl Acad Sci U S A (2008) 1.03

Genome-wide RNAi screen identifies broadly-acting host factors that inhibit arbovirus infection. PLoS Pathog (2014) 1.03

Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies. BMC Genet (2009) 1.03

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43

Emerging flaviviruses: the spread and resurgence of Japanese encephalitis, West Nile and dengue viruses. Nat Med (2004) 8.54

Genetical genomics: the added value from segregation. Trends Genet (2001) 8.23

Genomic islands of speciation in Anopheles gambiae. PLoS Biol (2005) 5.03

Natural malaria infection in Anopheles gambiae is regulated by a single genomic control region. Science (2006) 4.38

An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol Biol Evol (2002) 4.22

The Anopheles gambiae detoxification chip: a highly specific microarray to study metabolic-based insecticide resistance in malaria vectors. Proc Natl Acad Sci U S A (2005) 3.09

Genome-wide analysis of gene expression in adult Anopheles gambiae. Insect Mol Biol (2006) 2.65

TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res (2004) 2.44

Target validation of G-protein coupled receptors. Drug Discov Today (2002) 2.26

Quantitative trait loci that control vector competence for dengue-2 virus in the mosquito Aedes aegypti. Genetics (2000) 2.20

Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution. Mol Phylogenet Evol (2006) 2.20

Structure, function and evolution of sex-determining systems in Dipteran insects. Development (2000) 2.19

Sindbis virus induces transport processes and alters expression of innate immunity pathway genes in the midgut of the disease vector, Aedes aegypti. Insect Biochem Mol Biol (2005) 1.98

Olfaction: mosquito receptor for human-sweat odorant. Nature (2004) 1.96

PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements. Genetics (2004) 1.79

Yellow fever: the recurring plague. Crit Rev Clin Lab Sci (2004) 1.78

Olfactory responses in a gustatory organ of the malaria vector mosquito Anopheles gambiae. Proc Natl Acad Sci U S A (2006) 1.77

Breakpoint structure reveals the unique origin of an interspecific chromosomal inversion (2La) in the Anopheles gambiae complex. Proc Natl Acad Sci U S A (2006) 1.75

Linkage map organization of expressed sequence tags and sequence tagged sites in the mosquito, Aedes aegypti. Insect Mol Biol (2002) 1.65

Description of the transcriptomes of immune response-activated hemocytes from the mosquito vectors Aedes aegypti and Armigeres subalbatus. Infect Immun (2004) 1.62

Retroelements containing introns in diverse invertebrate taxa. Nat Genet (2003) 1.53

Reemergence of an unusual disease: the chikungunya epidemic. Semin Pediatr Infect Dis (2006) 1.45

A molecular view of trypsin synthesis in the midgut of Aedes aegypti. J Insect Physiol (1999) 1.43

A toll receptor and a cytokine, Toll5A and Spz1C, are involved in toll antifungal immune signaling in the mosquito Aedes aegypti. J Biol Chem (2006) 1.43

Comparative genome analysis of the yellow fever mosquito Aedes aegypti with Drosophila melanogaster and the malaria vector mosquito Anopheles gambiae. J Hered (2004) 1.42

Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences. Mol Biol Evol (2004) 1.33

The Aedes aegypti genome: complexity and organization. Genet Res (1991) 1.32

Trypsin-modulating oostatic factor: a potential new larvicide for mosquito control. J Exp Biol (2003) 1.28

The four serotypes of dengue recognize the same putative receptors in Aedes aegypti midgut and Ae. albopictus cells. BMC Microbiol (2006) 1.25

Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae. Mol Biol Evol (2004) 1.16

Gambol and Tc1 are two distinct families of DD34E transposons: analysis of the Anopheles gambiae genome expands the diversity of the IS630-Tc1-mariner superfamily. Insect Mol Biol (2005) 1.02

Genetic and physical mapping in mosquitoes: molecular approaches. Annu Rev Entomol (2001) 0.98

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79

TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18

The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63

Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86

Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63

The Pfam protein families database. Nucleic Acids Res (2002) 51.34

Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45

Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63

Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23

The diploid genome sequence of an individual human. PLoS Biol (2007) 44.80

Patterns of somatic mutation in human cancer genomes. Nature (2007) 38.41

Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42

The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04

Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29

Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76

Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16

The human microbiome project. Nature (2007) 28.53

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17

Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 24.54

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58

Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04

High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97

ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2007) 22.53

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2008) 21.36

ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

International network of cancer genome projects. Nature (2010) 20.35

Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS (2008) 18.69

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44

A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature (2009) 18.39

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64

Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13

Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (2011) 15.45

Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90

Ensembl 2011. Nucleic Acids Res (2010) 14.68

The International Protein Index: an integrated database for proteomics experiments. Proteomics (2004) 14.67

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A (2005) 14.59

Ensembl 2012. Nucleic Acids Res (2011) 14.55

NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res (2003) 14.37

FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71

The TIGRFAMs database of protein families. Nucleic Acids Res (2003) 13.59

Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72

Ensembl 2014. Nucleic Acids Res (2013) 12.62

High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56

Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2009) 12.51