Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts

Derepression of Y-linked multicopy protamine-like genes interferes with sperm nuclear compaction in D. melanogaster

(2023) Jun I. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of genome structure in the Drosophila simulans species complex

(2021) Mahul Chakraborty et al.   GENOME RESEARCH

Distinct spermiogenic phenotypes underlie sperm elimination in the Segregation Distorter meiotic drive system

(2021) Marion Herbette et al.   PLoS Genetics

Hybrid Sterility, Genetic Conflict and Complex Speciation: Lessons From the Drosophila simulans Clade Species

(2021) Daven C. Presgraves et al.   Frontiers in Genetics

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

The Y Chromosome as a Battleground for Intragenomic Conflict

(2020) Doris Bachtrog   TRENDS IN GENETICS

A Protamine Knockdown Mimics the Function of Sd in Drosophila melanogaster

(2020) Luke F. Gingell et al.   G3-Genes Genomes Genetics

Telomeric TART elements target the piRNA machinery in Drosophila

(2020) Christopher E. Ellison et al.   PLOS BIOLOGY

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

(2019) Danang Crysnanto et al.   BMC EVOLUTIONARY BIOLOGY

Recurrent gene co-amplification on Drosophila X and Y chromosomes

(2019) Christopher Ellison et al.   PLoS Genetics

Nuclear RNA export factor variant initiates piRNA‐guided co‐transcriptional silencing

(2019) Kensaku Murano et al.   EMBO JOURNAL

A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation

(2019) Kang Zhao et al.   NATURE CELL BIOLOGY

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation

(2019) Julia Batki et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA

(2018) Michael A. Schon et al.   GENOME RESEARCH

Selfish genetic elements

(2018) J. Arvid Ågren et al.   PLoS Genetics

New genes often acquire male-specific functions but rarely become essential inDrosophila

(2017) Shu Kondo et al.   GENES & DEVELOPMENT

Repeated Duplication of Argonaute2 Is Associated with Strong Selection and Testis Specialization in Drosophila

(2016) S. H. Lewis et al.   GENETICS

Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and Aubergine

(2016) Samuel H. Lewis et al.   Genome Biology and Evolution

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

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

The HMG-box-containing proteins tHMG-1 and tHMG-2 interact during the histone-to-protamine transition in Drosophila spermatogenesis

(2015) Stefanie M.K. Gärtner et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Adaptive Regulation of Testis Gene Expression and Control of Male Fertility by the Drosophila Hairpin RNA Pathway

(2015) Jiayu Wen et al.   MOLECULAR CELL

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A Testis-Specific Chaperone and the Chromatin Remodeler ISWI Mediate Repackaging of the Paternal Genome

(2015) Cécile M. Doyen et al.   Cell Reports

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

(2014) Fabio Mohn et al.   CELL

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters

(2014) Jaaved Mohammed et al.   RNA

Adaptive evolution of testis-specific, recently evolved, clustered miRNAs inDrosophila

(2014) Jaaved Mohammed et al.   RNA

IsoSCM: improved and alternative 3′ UTR annotation using multiple change-point inference

(2014) Sol Shenker et al.   RNA

Ballchen is required for self-renewal of germline stem cells in Drosophila melanogaster

(2014) B. Herzig et al.   Biology Open

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

(2013) Y. Liao et al.   BIOINFORMATICS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Neofunctionalization of young duplicate genes in Drosophila

(2013) R. Assis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subunits of the Histone Chaperone CAF1 Also Mediate Assembly of Protamine-Based Chromatin

(2013) Cécile M. Doyen et al.   Cell Reports

The genetics of sex chromosomes: evolution and implications for hybrid incompatibility

(2012) Norman A. Johnson et al.   Annals of the New York Academy of Sciences

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

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

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The Drosophila HP1 Homolog Rhino Is Required for Transposon Silencing and piRNA Production by Dual-Strand Clusters

(2009) Carla Klattenhoff et al.   CELL

Genetic conflict and sex chromosome evolution

(2009) Colin D. Meiklejohn et al.   TRENDS IN ECOLOGY & EVOLUTION

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

X chromosome drive

(2008) John Jaenike   CURRENT BIOLOGY

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

(2008) Katsutomo Okamura et al.   NATURE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

A Single Gene Causes Both Male Sterility and Segregation Distortion in Drosophila Hybrids

(2008) N. Phadnis et al.   SCIENCE