The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae)

Next generation sequencing of gonadal transcriptome suggests standard maternal inheritance of mitochondrial DNA in Eurhomalea rufa (Veneridae)

(2017) Marek Lubośny et al.   Marine Genomics

SmithRNAs: Could Mitochondria “Bend” Nuclear Regulation?

(2017) Andrea Pozzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) David Cordero et al.   Scientific Reports

In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide a framework for future studies of their origin and function

(2016) Alyssa Mitchell et al.   BMC GENOMICS

Mitochondrial selfish elements and the evolution of biological novelties

(2016) Liliana Milani et al.   Current Zoology

Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia

(2016) Federico Plazzi et al.   Genome Biology and Evolution

Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages

(2016) Dennis V. Lavrov et al.   Genome Biology and Evolution

Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees

(2016) Zilong He et al.   NUCLEIC ACIDS RESEARCH

Assessing the geographic scale of genetic population management with microsatellites and introns in the clamRuditapes decussatus

(2016) Alberto Arias-Pérez et al.   Ecology and Evolution

Mitochondrial selfish elements and the evolution of biological novelties

(2016) Liliana Milani et al.   Current Zoology

Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA

(2016) Arthur Gusman et al.   PeerJ

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

(2016) Siqi Yuan et al.   PeerJ

Mitochondrial activity in gametes and transmission of viable mtDNA

(2015) Liliana Milani et al.   Biology Direct

MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes

(2015) Mun Hua Tan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evidence for somatic transcription of male-transmitted mitochondrial genome in the DUI species Ruditapes philippinarum (Bivalvia: Veneridae)

(2014) Liliana Milani et al.   CURRENT GENETICS

High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq

(2014) Jonathan L. King et al.   Forensic Science International-Genetics

Paternally Transmitted Mitochondria Express a New Gene of Potential Viral Origin

(2014) Liliana Milani et al.   Genome Biology and Evolution

A Microarray-Based Analysis of Gametogenesis in Two Portuguese Populations of the European Clam Ruditapes decussatus

(2014) Joana Teixeira de Sousa et al.   PLoS One

A resourceful genome: updating the functional repertoire and evolutionary role of animal mitochondrial DNAs

(2014) Sophie Breton et al.   TRENDS IN GENETICS

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

(2013) Ricardo B Leite et al.   BMC GENOMICS

RNA-Seq data: a goldmine for organelle research

(2013) D. R. Smith   Briefings in Functional Genomics

The largest unassigned regions of the male- and female-transmitted mitochondrial DNAs in Musculista senhousia (Bivalvia Mytilidae)

(2013) Davide Guerra et al.   GENE

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

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

A Comparative Analysis of Mitochondrial ORFans: New Clues on Their Origin and Role in Species with Doubly Uniparental Inheritance of Mitochondria

(2013) Liliana Milani et al.   Genome Biology and Evolution

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeographic analysis of introns and mitochondrial DNA in the clam Ruditapes decussatus uncovers the effects of Pleistocene glaciations and endogenous barriers to gene flow

(2013) David Cordero et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The neglected genome

(2012) Graziano Pesole et al.   EMBO REPORTS

Biparental Inheritance Through Uniparental Transmission: The Doubly Uniparental Inheritance (DUI) of Mitochondrial DNA

(2012) Eleftherios Zouros   Evolutionary Biology

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

The Complete Mitochondrial Genomes of Six Heterodont Bivalves (Tellinoidea and Solenoidea): Variable Gene Arrangements and Phylogenetic Implications

(2012) Yang Yuan et al.   PLoS One

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

(2012) Andrew Tritt et al.   PLoS One

Identification and characterization of highly expressed proteins in sperm cells of the marine mussel Mytilus edulis

(2012) Angel P. Diz et al.   PROTEOMICS

Easyfig: a genome comparison visualizer

(2011) M. J. Sullivan et al.   BIOINFORMATICS

Mitochondrial genomes and Doubly Uniparental Inheritance: new insights from Musculista senhousia sex-linked mitochondrial DNAs (Bivalvia Mytilidae)

(2011) Marco Passamonti et al.   BMC GENOMICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

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

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals

(2011) Young Seok Ju et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Marine Bivalve Mitochondrial Genomes

(2011) Hong Yu et al.   PLoS One

Assigning roles to DNA regulatory motifs using comparative genomics

(2010) Fabian A. Buske et al.   BIOINFORMATICS

Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes

(2010) Coren A Milbury et al.   BMC GENOMICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): Identification of the “missing” ATPase 8 gene

(2010) Sophie Breton et al.   Marine Genomics

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

Strict Sex-Specific mtDNA Segregation in the Germ line of the DUI Species Venerupis philippinarum (Bivalvia: Veneridae)

(2010) F. Ghiselli et al.   MOLECULAR BIOLOGY AND EVOLUTION

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Doubly Uniparental Inheritance: Two Mitochondrial Genomes, One Precious Model for Organelle DNA Inheritance and Evolution

(2009) Marco Passamonti et al.   DNA AND CELL BIOLOGY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DOUBLY UNIPARENTAL INHERITANCE (DUI) OF MITOCHONDRIAL DNA INDONAX TRUNCULUS(BIVALVIA: DONACIDAE) AND THE PROBLEM OF ITS SPORADIC DETECTION IN BIVALVIA

(2008) Ioannis Theologidis et al.   EVOLUTION

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

(2008) C Gissi et al.   HEREDITY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH