A chromosome-level assembly of the widely used Rockefeller strain of Aedes aegypti, the yellow fever mosquito

Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly

(2021) Mahul Chakraborty et al.   BMC BIOLOGY

Fitness costs of individual and combined pyrethroid resistance mechanisms, kdr and CYP-mediated detoxification, in Aedes aegypti

(2021) Letícia B. Smith et al.   PLoS Neglected Tropical Diseases

Levels of cross-resistance to pyrethroids conferred by the Vssc knockdown resistance allele 410L+1016I+1534C in Aedes aegypti

(2021) Juan J. Silva et al.   PLoS Neglected Tropical Diseases

Transcriptomic and proteomic analysis of pyrethroid resistance in the CKR strain of Aedes aegypti

(2021) Haina Sun et al.   PLoS Neglected Tropical Diseases

A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms

(2020) Nicolas Scalzitti et al.   BMC GENOMICS

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

CYP-mediated resistance and cross-resistance to pyrethroids and organophosphates in Aedes aegypti in the presence and absence of kdr

(2019) Letícia B. Smith et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

EnTAP: Bringing Faster and Smarter Functional Annotation to Non‐Model Eukaryotic Transcriptomes

(2019) Alexander J. Hart et al.   Molecular Ecology Resources

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

(2019) Mahul Chakraborty et al.   Nature Communications

Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti

(2019) Andrea Gloria-Soria et al.   PLoS Neglected Tropical Diseases

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Improved reference genome of Aedes aegypti informs arbovirus vector control

(2018) Benjamin J. Matthews et al.   NATURE

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

CYP-mediated permethrin resistance in Aedes aegypti and evidence for trans-regulation

(2018) Letícia B. Smith et al.   PLoS Neglected Tropical Diseases

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Voltage-sensitive sodium channel mutations S989P + V1016G in Aedes aegypti confer variable resistance to pyrethroids, DDT and oxadiazines

(2017) Letícia B Smith et al.   PEST MANAGEMENT SCIENCE

GeneValidator: identify problems with protein-coding gene predictions

(2016) Monica-Andreea Drăgan et al.   BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

An Integrated Linkage, Chromosome, and Genome Map for the Yellow Fever Mosquito Aedes aegypti

(2013) Vladimir A. Timoshevskiy et al.   PLoS Neglected Tropical Diseases

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Early History of Laboratory Breeding of Aedes aegypti (Diptera: Culicidae) Focusing on the Origins and Use of Selected Strains

(2010) Goro Kuno   JOURNAL OF MEDICAL ENTOMOLOGY