Clustering of Sex-Biased Genes and Transposable Elements in the Genome of the Medaka Fish Oryzias latipes

Transcriptomic analyses reveal novel genes with sexually dimorphic expression in Takifugu rubripes brain during gonadal sex differentiation

(2020) Xufang Shen et al.   Genes & Genomics

Measuring and interpreting transposable element expression

(2020) Sophie Lanciano et al.   NATURE REVIEWS GENETICS

SQuIRE reveals locus-specific regulation of interspersed repeat expression

(2019) Wan R Yang et al.   NUCLEIC ACIDS RESEARCH

Comparative Transcriptome Analysis Reveals Differentially Expressed Genes and Signaling Pathways Between Male and Female Red-Tail Catfish (Mystus wyckioides)

(2019) Jun-Jie Wu et al.   MARINE BIOTECHNOLOGY

Increase of cortisol levels after temperature stress activates dmrt1a causing female‐to‐male sex reversal and reduced germ cell number in medaka

(2019) Mateus Contar Adolfi et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specific genes prior to the sex-determination stage in medaka

(2019) Amaury Herpin et al.   PLOS BIOLOGY

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

TADs as the Caller Calls Them

(2019) Elzo de Wit   JOURNAL OF MOLECULAR BIOLOGY

Sex and the TEs: transposable elements in sexual development and function in animals

(2019) Corentin Dechaud et al.   Mobile DNA

Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis

(2018) Wenjing Tao et al.   BMC GENOMICS

Using RNA-seq to determine patterns of sex-bias in gene expression in the brain of the sex-role reversed Gulf Pipefish ( Syngnathus scovelli )

(2018) Andria P. Beal et al.   Marine Genomics

Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression

(2018) Qinyu Sun et al.   TRENDS IN GENETICS

The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish

(2018) A. Tsakogiannis et al.   Scientific Reports

Retrotransposon targeting to RNA polymerase III-transcribed genes

(2018) Stephanie Cheung et al.   Mobile DNA

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants

(2017) Gökhan Karakülah et al.   GENOMICS

Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints

(2017) Corinne N. Simonti et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integration site selection by retroviruses and transposable elements in eukaryotes

(2017) Tania Sultana et al.   NATURE REVIEWS GENETICS

Sex-Biased Gene Expression

(2016) Sonja Grath et al.   Annual Review of Genetics

Transcriptome Display During Testicular Differentiation of Channel Catfish (Ictalurus punctatus) as Revealed by RNA-Seq Analysis

(2016) Q. Zeng et al.   BIOLOGY OF REPRODUCTION

Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models

(2016) Susanne Kneitz et al.   BMC GENOMICS

Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)

(2016) Ido Bar et al.   BMC GENOMICS

Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes

(2016) Liandong Yang et al.   Genome Biology and Evolution

Androgen induces gonadal soma-derived factor, Gsdf, in XX gonads correlated to sex-reversal but not Dmrt1 directly, in the teleost fish, northern medaka (Oryzias sakaizumii)

(2016) Yoshifumi Horie et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

(2016) Peter J. Thompson et al.   MOLECULAR CELL

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

(2016) Mihaela Pertea et al.   Nature Protocols

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

Convergent evolution of tRNA gene targeting preferences in compact genomes

(2016) Thomas Spaller et al.   Mobile DNA

Gene expression analysis at the onset of sex differentiation in turbot (Scophthalmus maximus)

(2015) Diego Robledo et al.   BMC GENOMICS

Making Sense of Transcription Networks

(2015) Trevor R. Sorrells et al.   CELL

Plasticity of gene-regulatory networks controlling sex determination: of masters, slaves, usual suspects, newcomers, and usurpators

(2015) A. Herpin et al.   EMBO REPORTS

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Ballgown bridges the gap between transcriptome assembly and expression analysis

(2015) Alyssa C Frazee et al.   NATURE BIOTECHNOLOGY

Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

(2015) Christopher E Ellison et al.   eLife

A long terminal repeat retrotransposon of Schizosaccharomyces japonicus integrates upstream of RNA pol III transcribed genes

(2015) Yabin Guo et al.   Mobile DNA

Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish

(2015) Hui Liu et al.   Biology of Sex Differences

Comparative Transcriptomics in East African Cichlids Reveals Sex- and Species-Specific Expression and New Candidates for Sex Differentiation in Fishes

(2014) Astrid Böhne et al.   Genome Biology and Evolution

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

(2014) W. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena

(2014) Yusuke Takehana et al.   Nature Communications

Sex Determination: Why So Many Ways of Doing It?

(2014) Doris Bachtrog et al.   PLOS BIOLOGY

Evolution of Hox gene clusters in deuterostomes

(2013) Juan Pascual-Anaya et al.   BMC DEVELOPMENTAL BIOLOGY

Novel sex-determining genes in fish and sex chromosome evolution

(2013) Kiyoshi Kikuchi et al.   DEVELOPMENTAL DYNAMICS

Divergent Expression Regulation of Gonad Development Genes in Medaka Shows Incomplete Conservation of the Downstream Regulatory Network of Vertebrate Sex Determination

(2013) Amaury Herpin et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets

(2013) Li Teng et al.   NUCLEIC ACIDS RESEARCH

Dosage Compensation via Transposable Element Mediated Rewiring of a Regulatory Network

(2013) C. E. Ellison et al.   SCIENCE

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

Cis-regulatory properties of medaka synexpression groups

(2012) M. Ramialison et al.   DEVELOPMENT

Sex-Biased Transcriptome Evolution in Drosophila

(2012) Raquel Assis et al.   Genome Biology and Evolution

Disentangling the relationship between sex-biased gene expression and X-linkage

(2012) R. P. Meisel et al.   GENOME RESEARCH

Diversity and Plasticity of Sex Determination and Differentiation in Fishes

(2012) Y. Kobayashi et al.   Sexual Development

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

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

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements

(2010) Amaury Herpin et al.   PLoS Genetics

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS