Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly

Satellite DNA-mediated diversification of a sex-ratio meiotic drive gene family in Drosophila

(2021) Christina A. Muirhead et al.   Nature Ecology & Evolution

Rapid evolutionary dynamics of an expanding family of meiotic drive factors and their hpRNA suppressors

(2021) Jeffrey Vedanayagam et al.   Nature Ecology & Evolution

Drosophila P75 safeguards oogenesis by preventing H3K9me2 spreading

(2020) Kun Dou et al.   Journal of Genetics and Genomics

Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in Drosophila pseudoobscura

(2020) Zachary L. Fuller et al.   GENETICS

The processivity factor Pol32 mediates nuclear localization of DNA polymerase delta and prevents chromosomal fragile site formation in Drosophila development

(2019) Jingyun Ji et al.   PLoS Genetics

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Maintenance of fertility in the face of meiotic drive

(2019) Lara Meade et al.   AMERICAN NATURALIST

JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila

(2019) Christian Albig et al.   Nature Communications

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

(2018) Helen C. Poynton et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

The hpRNA/RNAi Pathway Is Essential to Resolve Intragenomic Conflict in the Drosophila Male Germline

(2018) Ching-Jung Lin et al.   DEVELOPMENTAL CELL

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

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

Direct determination of diploid genome sequences

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

Contrasting patterns of X-chromosome divergence underlie multiple sex-ratio polymorphisms in stalk-eyed flies

(2017) K. A. Paczolt et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genetic conflicts: the usual suspects and beyond

(2017) Richard N. McLaughlin et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

wtf genes are prolific dual poison-antidote meiotic drivers

(2017) Nicole L Nuckolls et al.   eLife

A large gene family in fission yeast encodes spore killers that subvert Mendel’s law

(2017) Wen Hu et al.   eLife

Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae)

(2016) Richard H. Baker et al.   Genome Biology and Evolution

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

(2016) Robert Kofler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive

(2016) Quentin Helleu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ecology and Evolutionary Dynamics of Meiotic Drive

(2016) Anna K. Lindholm et al.   TRENDS IN ECOLOGY & EVOLUTION

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

Numerous Transitions of Sex Chromosomes in Diptera

(2015) Beatriz Vicoso et al.   PLOS BIOLOGY

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive

(2014) Amanda M Larracuente   BMC EVOLUTIONARY BIOLOGY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Haldane's Rule Is Linked to Extraordinary Sex Ratios and Sperm Length in Stalk-Eyed Flies

(2014) G. S. Wilkinson et al.   GENETICS

Male eyespan size is associated with meiotic drive in wild stalk-eyed flies (Teleopsis dalmanni)

(2014) A J Cotton et al.   HEREDITY

Sex-ratio meiotic drive and interspecific competition

(2014) R. L. Unckless et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies

(2014) Josephine A. Reinhardt et al.   PLoS Genetics

Genes That Bias Mendelian Segregation

(2014) Pierre Grognet et al.   PLoS Genetics

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Characterization of an Ancient Lepidopteran Lateral Gene Transfer

(2013) David Wheeler et al.   PLoS One

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

(2012) Grzegorz Sienski et al.   CELL

Mutations to the piRNA Pathway Component Aubergine Enhance Meiotic Drive of Segregation Distorter in Drosophila melanogaster

(2012) S. L. Gell et al.   GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Chromatin and the genome integrity network

(2012) Manolis Papamichos-Chronakis et al.   NATURE REVIEWS GENETICS

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Reduced Polymorphism Associated with X Chromosome Meiotic Drive in the Stalk-Eyed Fly Teleopsis dalmanni

(2011) Sarah J. Christianson et al.   PLoS One

Selfish genetic elements, genetic conflict, and evolutionary innovation

(2011) J. H. Werren   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis

(2010) A. Nagao et al.   RNA

Comparative Genomic Hybridization (CGH) Reveals a Neo-X Chromosome and Biased Gene Movement in Stalk-Eyed Flies (Genus Teleopsis)

(2010) Richard H. Baker et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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