De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

RNA Interference in Insects: Protecting Beneficials and Controlling Pests

(2019) Elise Vogel et al.   Frontiers in Physiology

Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies

(2019) Keyur Talsania et al.   Genes

Genome-wide divergence among invasive populations of Aedes aegypti in California

(2019) Yoosook Lee et al.   BMC GENOMICS

Insect genomes: progress and challenges

(2019) Fei Li et al.   INSECT MOLECULAR BIOLOGY

Identification of Y‐chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralog common to many Bactrocera pest species

(2019) Amanda Choo et al.   INSECT MOLECULAR BIOLOGY

Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests

(2019) Angela Meccariello et al.   SCIENCE

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

(2018) Jérémy Berthelier et al.   BMC GENOMICS

Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae

(2018) David Weetman et al.   Scientific Reports

Population structure of a vector of human diseases: Aedes aegypti in its ancestral range, Africa

(2018) Panayiota Kotsakiozi et al.   Ecology and Evolution

Clustering gene expression time series data using an infinite Gaussian process mixture model

(2018) Ian C. McDowell et al.   PLoS Computational Biology

The genomics of insecticide resistance: insights from recent studies in African malaria vectors

(2018) Chris S Clarkson et al.   Current Opinion in Insect Science

A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes

(2018) Kyros Kyrou et al.   NATURE BIOTECHNOLOGY

Computational tools to unmask transposable elements

(2018) Patricia Goerner-Potvin et al.   NATURE REVIEWS GENETICS

De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture

(2018) Shivani Mahajan et al.   PLOS BIOLOGY

Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome

(2018) Ching-Ho Chang et al.   GENETICS

Improved reference genome of Aedes aegypti informs arbovirus vector control

(2018) Benjamin J. Matthews et al.   NATURE

Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences

(2018) Chris-Andre Leimeister et al.   GigaScience

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

New advances in sequence assembly

(2017) Adam M. Phillippy   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Massive horizontal transfer of transposable elements in insects

(2017) Jean Peccoud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Y and W Chromosome Assemblies: Approaches and Discoveries

(2017) Marta Tomaszkiewicz et al.   TRENDS IN GENETICS

A Genomic Perspective on the Generation and Maintenance of Genetic Diversity in Herbivorous Insects

(2016) Andrew D. Gloss et al.   Annual Review of Ecology Evolution and Systematics

Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

(2016) Camille Sessegolo et al.   Biology Letters

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

(2016) Marta Tomaszkiewicz et al.   GENOME RESEARCH

Haplotypes drop by drop

(2016) Jacob O Kitzman   NATURE BIOTECHNOLOGY

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

(2016) Nick D.L. Owens et al.   Cell Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genomics of adaptation to host-plants in herbivorous insects

(2015) J.-C. Simon et al.   Briefings in Functional Genomics

Successful test launch for nanopore sequencing

(2015) Nicholas J Loman et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Birth of a new gene on the Y chromosome ofDrosophila melanogaster

(2015) Antonio Bernardo Carvalho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome

(2015) F. J. Krsticevic et al.   G3-Genes Genomes Genetics

Best practices in insect genome sequencing: what works and what doesn’t

(2015) Stephen Richards et al.   Current Opinion in Insect Science

Impact of transposable elements on insect genomes and biology

(2015) Florian Maumus et al.   Current Opinion in Insect Science

The Bactrocera oleae genome: localization of nine genes on the polytene chromosomes of the olive fruit fly (Diptera: Tephritidae)

(2015) Elena Drosopoulou et al.   GENOME

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

jvenn: an interactive Venn diagram viewer

(2014) Philippe Bardou et al.   BMC BIOINFORMATICS

The molecular biology of the olive fly comes of age

(2014) Efthimia Sagri et al.   BMC GENETICS

Olive fly transcriptomics analysis implicates energy metabolism genes in spinosad resistance

(2014) Efthimia Sagri et al.   BMC GENOMICS

The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

(2014) Monica Poelchau et al.   NUCLEIC ACIDS RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

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

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

Embryonic development of the olive fruit fly, Bactrocera oleae Rossi (Diptera: Tephritidae), in vivo

(2014) Hanife GENÇ   TURKISH JOURNAL OF ZOOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Six novel Y chromosome genes in Anopheles mosquitoes discovered by independently sequencing males and females

(2013) Andrew Brantley Hall et al.   BMC GENOMICS

Efficient identification of Y chromosome sequences in the human andDrosophilagenomes

(2013) Antonio Bernardo Carvalho et al.   GENOME RESEARCH

Genetic changes during laboratory domestication of an olive fly SIT strain

(2013) N. E. Zygouridis et al.   JOURNAL OF APPLIED ENTOMOLOGY

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration

(2013) Doris Bachtrog   NATURE REVIEWS GENETICS

Analysis of the Olive Fruit Fly Bactrocera oleae Transcriptome and Phylogenetic Classification of the Major Detoxification Gene Families

(2013) Nena Pavlidi et al.   PLoS One

Molecular Characterization and Chromosomal Distribution of a Species-Specific Transcribed Centromeric Satellite Repeat from the Olive Fruit Fly, Bactrocera oleae

(2013) Konstantina T. Tsoumani et al.   PLoS One

Sex chromosomes and associated rDNA form a heterochromatic network in the polytene nuclei of Bactrocera oleae (Diptera: Tephritidae)

(2012) Elena Drosopoulou et al.   GENETICA

Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

(2012) Jennifer F. Hughes et al.   NATURE

Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research

(2012) Meiping Zhang et al.   Nature Protocols

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

(2012) A. Boc et al.   NUCLEIC ACIDS RESEARCH

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Revisiting the evolution of ecological specialization, with emphasis on insect–plant interactions

(2011) M. L. Forister et al.   ECOLOGY

Genome size estimation with quantitative real-time PCR in two Tephritidae species: Ceratitis capitata and Bactrocera oleae

(2011) K. T. Tsoumani et al.   JOURNAL OF APPLIED ENTOMOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes

(2011) Torsten Wenke et al.   PLANT CELL

Interchromosomal Duplications on the Bactrocera oleae Y Chromosome Imply a Distinct Evolutionary Origin of the Sex Chromosomes Compared to Drosophila

(2011) Paolo Gabrieli et al.   PLoS One

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Isolation, annotation and applications of expressed sequence tags from the olive fly, Bactrocera oleae

(2010) K. T. Tsoumani et al.   MOLECULAR GENETICS AND GENOMICS

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

Single-molecule denaturation mapping of DNA in nanofluidic channels

(2010) W. Reisner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Give us the tools and we will do the job: symbiotic bacteria affect olive fly fitness in a diet-dependent fashion

(2010) M. Ben-Yosef et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

(2010) Nynke L. van Berkum et al.   Jove-Journal of Visualized Experiments

Olive Fruit Fly: Managing an Ancient Pest in Modern Times

(2009) Kent M. Daane et al.   Annual Review of Entomology

Acetobacter tropicalis Is a Major Symbiont of the Olive Fruit Fly (Bactrocera oleae)

(2009) I. Kounatidis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Isolation and characterization of microsatellite markers from the olive fly, Bactrocera oleae, and their cross-species amplification in the Tephritidae family

(2009) Antonios A Augustinos et al.   BMC GENOMICS

Structure-based discovery and description of plant and animal Helitrons

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Low conservation of gene content in the Drosophila Y chromosome

(2008) Leonardo B. Koerich et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE