Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam

Bivalve molluscs as model systems for studying mitochondrial biology

(2021) Fabrizio Ghiselli et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Molluscan mitochondrial genomes break the rules

(2021) Fabrizio Ghiselli et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mitochondrial CHCHD2: Disease-Associated Mutations, Physiological Functions, and Current Animal Models

(2021) Teresa R. Kee et al.   Frontiers in Aging Neuroscience

Gonadal transcriptomes associated with sex phenotypes provide potential male and female candidate genes of sex determination or early differentiation in Crassostrea gigas, a sequential hermaphrodite mollusc

(2021) Coralie Broquard et al.   BMC GENOMICS

Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution

(2021) Gerald P. Maeda et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The influence of environmental conditions on sex determination in the blue mussel Mytilus edulis

(2021) Andréanne Dalpé et al.   ICES JOURNAL OF MARINE SCIENCE

Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes

(2021) Ran Xu et al.   ZOOLOGICAL RESEARCH

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

Doubly uniparental inheritance of mitochondrial DNA: Might it be simpler than we thought?

(2020) Eleftherios Zouros   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

A proteomic study of resistance to Brown Ring disease in the Manila clam, Ruditapes philippinarum

(2020) M. Smits et al.   FISH & SHELLFISH IMMUNOLOGY

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

Chromosome-Level Clam Genome Helps Elucidate the Molecular Basis of Adaptation to a Buried Lifestyle

(2020) Min Wei et al.   iScience

Sex-specific selection drives the evolution of alternative splicing in birds

(2020) Thea F Rogers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biological responses to extreme weather events are detectable but difficult to formally attribute to anthropogenic climate change

(2020) R. M. B. Harris et al.   Scientific Reports

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

Selection shapes turnover and magnitude of sex-biased expression in Drosophila gonads

(2019) Carrie A. Whittle et al.   BMC EVOLUTIONARY BIOLOGY

Natural Heteroplasmy and Mitochondrial Inheritance in Bivalve Molluscs

(2019) Fabrizio Ghiselli et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Integrating gene regulatory pathways into differential network analysis of gene expression data

(2019) Tyler Grimes et al.   Scientific Reports

Putative Mitochondrial Sex Determination in the Bivalvia: Insights From a Hybrid Transcriptome Assembly in Freshwater Mussels

(2019) Charlotte Capt et al.   Frontiers in Genetics

Systematic evaluation of differential splicing tools for RNA-seq studies

(2019) Arfa Mehmood et al.   BRIEFINGS IN BIOINFORMATICS

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Deciphering the Link between Doubly Uniparental Inheritance of mtDNA and Sex Determination in Bivalves: Clues from Comparative Transcriptomics

(2018) Charlotte Capt et al.   Genome Biology and Evolution

Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes

(2018) Fabrizio Ghiselli et al.   Genome Biology and Evolution

Gonad Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Identifies Potential Genes Regulating the Sex Determination and Differentiation Process

(2018) Chenyang Yue et al.   MARINE BIOTECHNOLOGY

Germ cell-intrinsic requirement for the homeodomain transcription factor PKnox1/Prep1 in adult spermatogenesis

(2018) Yasuhiro Kawai et al.   PLoS One

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

(2018) Juan Manuel Crescente et al.   BMC BIOINFORMATICS

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

Clustal Omega for making accurate alignments of many protein sequences

(2017) Fabian Sievers et al.   PROTEIN SCIENCE

Population genetics of the Manila clam (Ruditapes philippinarum) introduced in North America and Europe

(2017) David Cordero et al.   Scientific Reports

Genome-wide analysis of brain and gonad transcripts reveals changes of key sex reversal-related genes expression and signaling pathways in three stages of Monopterus albus

(2017) Wei Chi et al.   PLoS One

Tissue Specificity and Sex-Specific Regulatory Variation Permit the Evolution of Sex-Biased Gene Expression

(2016) Rebecca Dean et al.   AMERICAN NATURALIST

Sex-Biased Gene Expression

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

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

(2016) Mihaela Pertea et al.   Nature Protocols

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Sexual Dimorphism and the Evolution of Sex-Biased Gene Expression in the Brown Alga Ectocarpus

(2015) Agnieszka Lipinska et al.   MOLECULAR BIOLOGY AND EVOLUTION

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Sexual selection drives evolution and rapid turnover of male gene expression

(2015) Peter W. Harrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Sex-Biased Gene Expression and Sexual Conflict throughout Development: Table 1.

(2014) Fiona C. Ingleby et al.   Cold Spring Harbor Perspectives in Biology

Genomic Analysis of the Pacific Oyster ( Crassostrea gigas ) Reveals Possible Conservation of Vertebrate Sex Determination in a Mollusc

(2014) Na Zhang et al.   G3-Genes Genomes Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Structure, Transcription, and Variability of Metazoan Mitochondrial Genome: Perspectives from an Unusual Mitochondrial Inheritance System

(2013) Fabrizio Ghiselli et al.   Genome Biology and Evolution

The Shared Genome Is a Pervasive Constraint on the Evolution of Sex-Biased Gene Expression

(2013) R. M. Griffin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary causes and consequences of sex-biased gene expression

(2013) John Parsch et al.   NATURE REVIEWS GENETICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Rate of Amino Acid Substitution Is Influenced by the Degree and Conservation of Male-Biased Transcription Over 50 Myr of Drosophila Evolution

(2012) Sonja Grath et al.   Genome Biology and Evolution

De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination

(2011) F. Ghiselli et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards a More Nuanced Understanding of the Relationship between Sex-Biased Gene Expression and Rates of Protein-Coding Sequence Evolution

(2011) R. P. Meisel   MOLECULAR BIOLOGY AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Novel Protein Genes in Animal mtDNA: A New Sex Determination System in Freshwater Mussels (Bivalvia: Unionoida)?

(2010) Sophie Breton et al.   MOLECULAR BIOLOGY AND EVOLUTION

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Male infertility caused by spermiogenic defects: Lessons from gene knockouts

(2009) Wei Yan   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Sex-Specific Splicing in Drosophila: Widespread Occurrence, Tissue Specificity and Evolutionary Conservation

(2008) M. Telonis-Scott et al.   GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY

Pleiotropic Constraint Hampers the Resolution of Sexual Antagonism in Vertebrate Gene Expression

(2007) Judith E. Mank et al.   AMERICAN NATURALIST