The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals

(2021) Daniel W. Bellott et al.   GENOME RESEARCH

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

(2021) Jing Liu et al.   GENOME RESEARCH

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

The sex with the reduced sex chromosome dies earlier: a comparison across the tree of life

(2020) Zoe A. Xirocostas et al.   Biology Letters

Sex chromosome evolution: So many exceptions to the rules

(2020) Benjamin L S Furman et al.   Genome Biology and Evolution

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

The Y Chromosome as a Battleground for Intragenomic Conflict

(2020) Doris Bachtrog   TRENDS IN GENETICS

Taming the Turmoil Within: New Insights on the Containment of Transposable Elements

(2020) Erin S. Kelleher et al.   TRENDS IN GENETICS

What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?

(2020) Pavel Jedlicka et al.   Frontiers in Plant Science

The Y chromosome may contribute to sex-specific ageing in Drosophila

(2020) Emily J. Brown et al.   Nature Ecology & Evolution

A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids

(2020) Richard Allen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Discovery and population genomics of structural variation in a songbird genus

(2020) Matthias H. Weissensteiner et al.   Nature Communications

Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

(2020) Jae Young Choi et al.   PLoS Genetics

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

(2020) James D Galbraith et al.   Genome Biology and Evolution

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

(2020) Valentina Peona et al.   Molecular Ecology Resources

Revisiting avian ‘missing’ genes from de novo assembled transcripts

(2019) Zhong-Tao Yin et al.   BMC GENOMICS

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Genomic scans reveal multiple mito-nuclear incompatibilities in population crosses of the copepod Tigriopus californicus

(2019) Thiago G. Lima et al.   EVOLUTION

Convergent regulatory evolution and loss of flight in paleognathous birds

(2019) Timothy B. Sackton et al.   SCIENCE

The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch

(2019) Jesper Boman et al.   Genes

Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds

(2019) Luohao Xu et al.   Genome Biology and Evolution

Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species

(2019) Benoît Piégu et al.   GENOMICS

Programmed DNA elimination of germline development genes in songbirds

(2019) Cormac M. Kinsella et al.   Nature Communications

The role of transposable elements activity in aging and their possible involvement in laminopathic diseases

(2019) Davide Andrenacci et al.   AGEING RESEARCH REVIEWS

Discovery of the First Germline-Restricted Gene by Subtractive Transcriptomic Analysis in the Zebra Finch, Taeniopygia guttata

(2018) Michelle K. Biederman et al.   CURRENT BIOLOGY

Sex differences in life span: Females homozygous for the X chromosome do not suffer the shorter life span predicted by the unguarded X hypothesis

(2018) Martin Brengdahl et al.   EVOLUTION

Why Do Sex Chromosomes Stop Recombining?

(2018) Suvi Ponnikas et al.   TRENDS IN GENETICS

The Role of Transposable Elements in Speciation

(2018) Antonio Serrato-Capuchina et al.   Genes

How complete are “complete” genome assemblies?-An avian perspective

(2018) Valentina Peona et al.   Molecular Ecology Resources

piRNA-Guided Genome Defense: From Biogenesis to Silencing

(2018) Benjamin Czech et al.   Annual Review of Genetics

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

The Genetic Architecture of Intra-Species Hybrid Mito-Nuclear Epistasis

(2018) Rania Haddad et al.   Frontiers in Genetics

A test for Y-linked additive and epistatic effects on surviving bacterial infections in Drosophila melanogaster

(2017) I. C. Kutch et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

(2017) Alexander Suh et al.   MOLECULAR ECOLOGY

Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators

(2017) Daniel W Bellott et al.   NATURE GENETICS

Coevolution between transposable elements and recombination

(2017) Tyler V. Kent et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution

(2017) Peng Yang et al.   TRENDS IN GENETICS

Y and W Chromosome Assemblies: Approaches and Discoveries

(2017) Marta Tomaszkiewicz et al.   TRENDS IN GENETICS

Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells

(2017) Rachael J. Werner et al.   Biology of Sex Differences

SEXCMD: Development and validation of sex marker sequences for whole-exome/genome and RNA sequencing

(2017) Seongmun Jeong et al.   PLoS One

Evolution of bird genomes-a transposon's-eye view

(2016) Aurélie Kapusta et al.   Annals of the New York Academy of Sciences

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Whole Genome Re-Sequencing of Three Domesticated Chicken Breeds

(2016) Dongyep Oh et al.   ZOOLOGICAL SCIENCE

How to make a sex chromosome

(2016) Alison E. Wright et al.   Nature Communications

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

Within-population Y-linked genetic variation for lifespan in Drosophila melanogaster

(2015) R. M. Griffin et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken

(2015) Severin Uebbing et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens

(2015) Ming-Shan Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genetic sex-determination system predicts adult sex ratios in tetrapods

(2015) Ivett Pipoly et al.   NATURE

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

Evolutionary analysis of the female-specific avian W chromosome

(2015) Linnéa Smeds et al.   Nature Communications

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

A new time tree reveals Earth historys imprint on the evolution of modern birds

(2015) S. Claramunt et al.   Science Advances

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

(2014) Alexander Hayward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Sex Determination: Why So Many Ways of Doing It?

(2014) Doris Bachtrog et al.   PLOS BIOLOGY

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

(2014) Cassandra N. Trier et al.   PLoS Genetics

Evolution of sex differences in lifespan and aging: Causes and constraints

(2013) Alexei A. Maklakov et al.   BIOESSAYS

The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease

(2013) L. K. Case et al.   GENOME RESEARCH

Lack of Dosage Compensation Accompanies the Arrested Stage of Sex Chromosome Evolution in Ostriches

(2013) Sofia Adolfsson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Doris Bachtrog   NATURE REVIEWS GENETICS

Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution

(2013) B. Vicoso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome

(2012) Fadi J Charchar et al.   LANCET

Large-Scale Age-Dependent Skewed Sex Ratio in a Sexually Dimorphic Avian Scavenger

(2012) Sergio A. Lambertucci et al.   PLoS One

Small but mighty: the evolutionary dynamics of W and Y sex chromosomes

(2011) Judith E. Mank   CHROMOSOME RESEARCH

Y Not a Dead End: Epistatic Interactions Between Y- Linked Regulatory Polymorphisms and Genetic Background Affect Global Gene Expression in Drosophila melanogaster

(2010) Pan-Pan Jiang et al.   GENETICS

Sex bias and dosage compensation in the zebra finch versus chicken genomes: General and specialized patterns among birds

(2010) Y. Itoh et al.   GENOME RESEARCH

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

(2010) C. Llorens et al.   NUCLEIC ACIDS RESEARCH

Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict

(2010) B. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Mouse Models for Evaluating Sex Chromosome Effects that Cause Sex Differences in Non-Gonadal Tissues

(2009) Arthur P. Arnold   JOURNAL OF NEUROENDOCRINOLOGY

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

Species-Specific Heterochromatin Prevents Mitotic Chromosome Segregation to Cause Hybrid Lethality in Drosophila

(2009) Patrick M. Ferree et al.   PLOS BIOLOGY

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS