4.7 Article

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biotechnology & Applied Microbiology

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

Yoosook Lee et al.

BMC GENOMICS (2019)

Review Biochemistry & Molecular Biology

Insect genomes: progress and challenges

F. Li et al.

INSECT MOLECULAR BIOLOGY (2019)

Review Physiology

RNA Interference in Insects: Protecting Beneficials and Controlling Pests

Elise Vogel et al.

FRONTIERS IN PHYSIOLOGY (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemical Research Methods

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

Ian C. McDowell et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Review Biology

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

Chris S. Clarkson et al.

CURRENT OPINION IN INSECT SCIENCE (2018)

Review Genetics & Heredity

Computational tools to unmask transposable elements

Patricia Goerner-Potvin et al.

NATURE REVIEWS GENETICS (2018)

Article Multidisciplinary Sciences

Improved reference genome of Aedes aegypti informs arbovirus vector control

Benjamin J. Matthews et al.

NATURE (2018)

Article Biochemistry & Molecular Biology

Direct determination of diploid genome sequences

Neil I. Weisenfeld et al.

GENOME RESEARCH (2017)

Editorial Material Biochemistry & Molecular Biology

New advances in sequence assembly

Adam M. Phillippy

GENOME RESEARCH (2017)

Article Biochemistry & Molecular Biology

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

Sergey Koren et al.

GENOME RESEARCH (2017)

Article Multidisciplinary Sciences

Massive horizontal transfer of transposable elements in insects

Jean Peccoud et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Review Genetics & Heredity

Y and W Chromosome Assemblies: Approaches and Discoveries

Marta Tomaszkiewicz et al.

TRENDS IN GENETICS (2017)

Article Biochemical Research Methods

GenomeScope: fast reference-free genome profiling from short reads

Gregory W. Vurture et al.

BIOINFORMATICS (2017)

Review Ecology

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

Andrew D. Gloss et al.

ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 47 (2016)

Article Biochemistry & Molecular Biology

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

Nicholas H. Putnam et al.

GENOME RESEARCH (2016)

Article Biotechnology & Applied Microbiology

Haplotypes drop by drop

Jacob O. Kitzman

NATURE BIOTECHNOLOGY (2016)

Article Biotechnology & Applied Microbiology

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

Grace X. Y. Zheng et al.

NATURE BIOTECHNOLOGY (2016)

Article Biochemistry & Molecular Biology

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

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biotechnology & Applied Microbiology

A survey of best practices for RNA-seq data analysis

Ana Conesa et al.

GENOME BIOLOGY (2016)

Article Biochemical Research Methods

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

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

Genomics of adaptation to host-plants in herbivorous insects

Jean-Christophe Simon et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2015)

Editorial Material Biochemical Research Methods

Successful test launch for nanopore sequencing

Nicholas J. Loman et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

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

Nicholas J. Loman et al.

NATURE METHODS (2015)

Article Multidisciplinary Sciences

Birth of a new gene on the Y chromosome of Drosophila melanogaster

Antonio Bernardo Carvalho et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biology

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

Stephen Richards et al.

CURRENT OPINION IN INSECT SCIENCE (2015)

Article Biology

Impact of transposable elements on insect genomes and biology

Florian Maumus et al.

CURRENT OPINION IN INSECT SCIENCE (2015)

Article Biochemistry & Molecular Biology

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

Monica Poelchau et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

jvenn: an interactive Venn diagram viewer

Philippe Bardou et al.

BMC BIOINFORMATICS (2014)

Article Genetics & Heredity

The molecular biology of the olive fly comes of age

Efthimia Sagri et al.

BMC GENETICS (2014)

Article Biotechnology & Applied Microbiology

Olive fly transcriptomics analysis implicates energy metabolism genes in spinosad resistance

Efthimia Sagri et al.

BMC GENOMICS (2014)

Article Entomology

Genetic changes during laboratory domestication of an olive fly SIT strain

N. E. Zygouridis et al.

JOURNAL OF APPLIED ENTOMOLOGY (2014)

Article Multidisciplinary Sciences

PASTEC: An Automatic Transposable Element Classification Tool

Claire Hoede et al.

PLOS ONE (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

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

Andrew Brantley Hall et al.

BMC GENOMICS (2013)

Article Biochemistry & Molecular Biology

Efficient identification of Y chromosome sequences in the human and Drosophila genomes

Antonio Bernardo Carvalho et al.

GENOME RESEARCH (2013)

Review Genetics & Heredity

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

Doris Bachtrog

NATURE REVIEWS GENETICS (2013)

Article Multidisciplinary Sciences

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

Jennifer F. Hughes et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

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

Boc Alix et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

Primer3-new capabilities and interfaces

Andreas Untergasser et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

Ray Meta: scalable de novo metagenome assembly and profiling

Sebastien Boisvert et al.

GENOME BIOLOGY (2012)

Article Biochemical Research Methods

Scaffolding pre-assembled contigs using SSPACE

Marten Boetzer et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

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

Guillaume Marcais et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

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

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

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

K. T. Tsoumani et al.

MOLECULAR GENETICS AND GENOMICS (2011)

Article Biotechnology & Applied Microbiology

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

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Multidisciplinary Sciences

Considering Transposable Element Diversification in De Novo Annotation Approaches

Timothee Flutre et al.

PLOS ONE (2011)

Review Entomology

Olive Fruit Fly: Managing an Ancient Pest in Modern Times

Kent M. Daane et al.

ANNUAL REVIEW OF ENTOMOLOGY (2010)

Article Biochemistry & Molecular Biology

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

Yujun Han et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Single-molecule denaturation mapping of DNA in nanofluidic channels

Walter Reisner et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biology

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

Michael Ben-Yosef et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)

Article Multidisciplinary Sciences

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

Nynke L. van Berkum et al.

Jove-Journal of Visualized Experiments (2010)

Article Biotechnology & Applied Microbiology

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

Ilias Kounatidis et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Multidisciplinary Sciences

Structure-based discovery and description of plant and animal Helitrons

Lixing Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

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

Erez Lieberman-Aiden et al.

SCIENCE (2009)

Article Biochemical Research Methods

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

David Ellinghaus et al.

BMC BIOINFORMATICS (2008)

Article Multidisciplinary Sciences

Low conservation of gene content in the Drosophila Y chromosome

Leonardo B. Koerich et al.

NATURE (2008)

Article Multidisciplinary Sciences

Accurate whole human genome sequencing using reversible terminator chemistry

David R. Bentley et al.

NATURE (2008)

Review Genetics & Heredity

A unified classification system for eukaryotic transposable elements

Thomas Wicker et al.

NATURE REVIEWS GENETICS (2007)

Article Multidisciplinary Sciences

Evolution of genes and genomes on the Drosophila phylogeny

Andrew G. Clark et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

g:Profiler -: a web-based toolset for functional profiling of gene lists from large-scale experiments

Jueri Reimand et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biotechnology & Applied Microbiology

De novo identification of LTR retrotransposons in eukaryotic genomes

Mina Rho et al.

BMC GENOMICS (2007)

Article Biochemical Research Methods

De novo identification of repeat families in large genomes

AL Price et al.

BIOINFORMATICS (2005)

Article Biotechnology & Applied Microbiology

Versatile and open software for comparing large genomes

S Kurtz et al.

GENOME BIOLOGY (2004)

Article Biochemistry & Molecular Biology

The mitochondrial genome of the olive fly Bactrocera oleae: two haplotypes from distant geographical locations

F Nardi et al.

INSECT MOLECULAR BIOLOGY (2003)

Article Multidisciplinary Sciences

The genome sequence of the malaria mosquito Anopheles gambiae

RA Holt et al.

SCIENCE (2002)

Article Genetics & Heredity

Sex determination in flies, fruitflies and butterflies

G Saccone et al.

GENETICA (2002)

Article Multidisciplinary Sciences

Identification of five new genes on the Y chromosome of Drosophila melanogaster

AB Carvalho et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biochemistry & Molecular Biology

Insect metamorphosis: Out with the old, in with the new

M Buszczak et al.

CURRENT BIOLOGY (2000)

Review Multidisciplinary Sciences

The genome sequence of Drosophila melanogaster

MD Adams et al.

SCIENCE (2000)