SmithRNAs: Could Mitochondria “Bend” Nuclear Regulation?

Dynamics of nuclear receptor gene expression during Pacific oyster development

(2016) Susanne Vogeler et al.   BMC DEVELOPMENTAL BIOLOGY

A Happy 3′ Ending to the piRNA Maturation Story

(2016) Benjamin Czech et al.   CELL

The RNase PARN-1 Trims piRNA 3′ Ends to Promote Transcriptome Surveillance in C. elegans

(2016) Wen Tang et al.   CELL

Identification and Functional Analysis of the Pre-piRNA 3′ Trimmer in Silkworms

(2016) Natsuko Izumi et al.   CELL

Mitochondrial selfish elements and the evolution of biological novelties

(2016) Liliana Milani et al.   Current Zoology

Comparative analyses of the complete mitochondrial genomes of the two murine pinworms Aspiculuris tetraptera and Syphacia obvelata

(2016) Chun-Ren Wang et al.   GENE

Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor

(2016) Sriram G. Garg et al.   Genome Biology and Evolution

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

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

Evolutionary dynamics of cytoplasmic segregation and fusion: Mitochondrial mixing facilitated the evolution of sex at the origin of eukaryotes

(2016) Arunas L. Radzvilavicius   JOURNAL OF THEORETICAL BIOLOGY

Miro sculpts mitochondrial dynamics in neuronal health and disease

(2016) Michael J. Devine et al.   NEUROBIOLOGY OF DISEASE

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase

(2016) Ryan M. Nottingham et al.   RNA

Comparative and Transcriptome Analyses Uncover Key Aspects of Coding- and Long Noncoding RNAs in Flatworm Mitochondrial Genomes

(2016) Eric Ross et al.   G3-Genes Genomes Genetics

Selection for Mitochondrial Quality Drives Evolution of the Germline

(2016) Arunas L. Radzvilavicius et al.   PLOS BIOLOGY

Mitochondrial selfish elements and the evolution of biological novelties

(2016) Liliana Milani et al.   Current Zoology

Re-thinking miRNA-mRNA interactions: Intertwining issues confound target discovery

(2015) Nicole Cloonan   BIOESSAYS

The evolution of sex: A new hypothesis based on mitochondrial mutational erosion

(2015) Justin C. Havird et al.   BIOESSAYS

Mitochondrial activity in gametes and transmission of viable mtDNA

(2015) Liliana Milani et al.   Biology Direct

Mechanistic insights on the Dicer-independent AGO2-mediated processing of AgoshRNAs

(2015) Ying Poi Liu et al.   RNA Biology

Mitochondrial Proteins Moonlighting in the Nucleus

(2015) Richard M. Monaghan et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Expression of a Novel Mitochondrially-Encoded Gene in Gonadic Precursors May Drive Paternal Inheritance of Mitochondria

(2015) Liliana Milani et al.   PLoS One

An integrated phylogenomic approach toward pinpointing the origin of mitochondria

(2015) Zhang Wang et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group

(2014) Susanne Vogeler et al.   BMC GENOMICS

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

(2014) Liliana Milani et al.   CURRENT GENETICS

Paternally Transmitted Mitochondria Express a New Gene of Potential Viral Origin

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

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

5′ isomiR variation is of functional and evolutionary importance

(2014) Geok Chin Tan et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Sophie Breton et al.   TRENDS IN GENETICS

Low hydrogen peroxide production in mitochondria of the long-livedArctica islandica: underlying mechanisms for slow aging

(2013) Daniel Munro et al.   AGING CELL

The complete mitochondrial genome of Solemya velum (Mollusca: Bivalvia) and its relationships with Conchifera

(2013) Federico Plazzi et al.   BMC GENOMICS

The mitochondrial genome encodes abundant small noncoding RNAs

(2013) Seungil Ro et al.   CELL RESEARCH

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

Identification and Characterization of MicroRNAs in Pearl Oyster Pinctada martensii by Solexa Deep Sequencing

(2013) Yu Jiao et al.   MARINE BIOTECHNOLOGY

Proteomic Analysis of Eggs fromMytilus edulisFemales Differing in Mitochondrial DNA Transmission Mode

(2013) Angel P. Diz et al.   MOLECULAR & CELLULAR PROTEOMICS

The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis

(2013) Dong Ju Son et al.   Nature Communications

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

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

(2012) Eleftherios Zouros   Evolutionary Biology

Sex-Linked Mitochondrial Behavior During Early Embryo Development in Ruditapes philippinarum (Bivalvia Veneridae) a Species with the Doubly Uniparental Inheritance (DUI) of Mitochondria

(2012) LILIANA MILANI et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function

(2011) Jaret P Bilewitch et al.   BMC EVOLUTIONARY BIOLOGY

The Human Mitochondrial Transcriptome

(2011) Tim R. Mercer et al.   CELL

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

Dicer recognizes the 5′ end of RNA for efficient and accurate processing

(2011) Jong-Eun Park et al.   NATURE

Nuclear Outsourcing of RNA Interference Components to Human Mitochondria

(2011) Simonetta Bandiera et al.   PLoS One

Doubly Uniparental Inheritance of Mitochondria As a Model System for Studying Germ Line Formation

(2011) Liliana Milani et al.   PLoS One

DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria

(2011) Lisa S. Shock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA

(2010) Hélène Doucet-Beaupré et al.   BMC EVOLUTIONARY BIOLOGY

New Insights into the Role of RNase L in Innate Immunity

(2010) Arindam Chakrabarti et al.   JOURNAL OF INTERFERON AND CYTOKINE RESEARCH

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

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

Human tRNA-derived small RNAs in the global regulation of RNA silencing

(2010) D. Haussecker et al.   RNA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

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

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

A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)

(2009) Yong Sun Lee et al.   GENES & DEVELOPMENT

Kinesin superfamily motor proteins and intracellular transport

(2009) Nobutaka Hirokawa et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ALL-MALE ASEXUALITY: ORIGIN AND MAINTENANCE OF ANDROGENESIS IN THE ASIAN CLAM CORBICULA

(2008) Shannon M. Hedtke et al.   EVOLUTION

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

Coordination of gene expression between organellar and nuclear genomes

(2008) Jesse D. Woodson et al.   NATURE REVIEWS GENETICS

Origins and evolution of eukaryotic RNA interference

(2008) S SHABALINA et al.   TRENDS IN ECOLOGY & EVOLUTION