Mitochondrial DNA Deficiency and Supplementation in Sus scrofa Oocytes Influence Transcriptome Profiles in Oocytes and Blastocysts

Mitochondrial supplementation of Sus scrofa metaphase II oocytes alters DNA methylation and gene expression profiles of blastocysts

(2022) Takashi Okada et al.   Epigenetics & Chromatin

Tight gene co-expression in BCB positive cattle oocytes and their surrounding cumulus cells

(2022) Bailey N. Walker et al.   Reproductive Biology and Endocrinology

The role of mtDNA in oocyte quality and embryo development

(2022) Justin C. St John et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Emerging Functions for snoRNAs and snoRNA-Derived Fragments

(2021) Maliha Wajahat et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The reactome pathway knowledgebase 2022

(2021) Marc Gillespie et al.   NUCLEIC ACIDS RESEARCH

An improved pig reference genome sequence to enable pig genetics and genomics research

(2020) Amanda Warr et al.   GigaScience

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

(2019) Jüri Reimand et al.   Nature Protocols

Regulation of apoptosis in health and disease: the balancing act of BCL-2 family proteins

(2019) Rumani Singh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Autologous mitochondrial microinjection; a strategy to improve the oocyte quality and subsequent reproductive outcome during aging

(2019) Halimeh Mobarak et al.   Cell and Bioscience

Mogroside V improves porcine oocyte in vitro maturation and subsequent embryonic development

(2019) Junyu Nie et al.   THERIOGENOLOGY

Assembly and Positioning of the Oocyte Meiotic Spindle

(2018) Binyam Mogessie et al.   Annual Review of Cell and Developmental Biology

OUP accepted manuscript

(2018)   BIOINFORMATICS

Embryogenesis and Adult Life in the Absence of Intrinsic Apoptosis Effectors BAX, BAK, and BOK

(2018) Francine F.S. Ke et al.   CELL

The molecular characterisation of mitochondrial DNA deficient oocytes using a pig model

(2018) Te-Sha Tsai et al.   HUMAN REPRODUCTION

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes

(2018) Chan Gu et al.   CELL RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Small Nucleolar RNAs Tell a Different Tale

(2018) Joanna Kufel et al.   TRENDS IN GENETICS

The epigenetic control of transposable elements and imprinted genes in newborns is affected by the mode of conception: ART versus spontaneous conception without underlying infertility

(2017) C Choux et al.   HUMAN REPRODUCTION

Single-cell transcriptome sequencing reveals that cell division cycle 5-like protein is essential for porcine oocyte maturation

(2017) Xiao-Man Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stage specific requirement of platelet-derived growth factor receptor-α in embryonic development

(2017) Chen Qian et al.   PLoS One

Mechanisms of Aneuploidy in Human Eggs

(2017) Alexandre Webster et al.   TRENDS IN CELL BIOLOGY

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

(2017) Sebastian Canovas et al.   eLife

Causes and consequences of chromosome segregation error in preimplantation embryos

(2017) Cayetana Vázquez-Diez et al.   REPRODUCTION

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Segregation of Naturally Occurring Mitochondrial DNA Variants in a Mini-Pig Model

(2016) G. Cagnone et al.   GENETICS

An updated human snoRNAome

(2016) Hadi Jorjani et al.   NUCLEIC ACIDS RESEARCH

Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease

(2016) Jerome Bouquet et al.   mBio

Restoration of normal embryogenesis by mitochondrial supplementation in pig oocytes exhibiting mitochondrial DNA deficiency

(2016) Gael L. M. Cagnone et al.   Scientific Reports

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

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

Tissue-specific regulation of Igf2r/Airn imprinting during gastrulation

(2015) Chelsea Marcho et al.   Epigenetics & Chromatin

The emerging landscape of small nucleolar RNAs in cell biology

(2015) Fabien Dupuis-Sandoval et al.   Wiley Interdisciplinary Reviews-RNA

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

(2014) Søren Lykke-Andersen et al.   GENES & DEVELOPMENT

Altered gene expression in human placentas after IVF/ICSI

(2014) Ewka C.M. Nelissen et al.   HUMAN REPRODUCTION

A KRAS-directed transcriptional silencing pathway that mediates the CpG island methylator phenotype

(2014) Ryan W Serra et al.   eLife

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

The regulation of mitochondrial DNA copy number in glioblastoma cells

(2013) A Dickinson et al.   CELL DEATH AND DIFFERENTIATION

Differences in Cytoplasmic Maturation Between the BCB+ and Control Porcine Oocytes Do Not Justify Application of the BCB Test for a Standard IVM Protocol

(2013) Piotr PAWLAK et al.   JOURNAL OF REPRODUCTION AND DEVELOPMENT

The utility of Brilliant Cresyl Blue (BCB) staining of mammalian oocytes used for in vitro embryo production (IVP)

(2013) Jolanta Opiela et al.   Reproductive Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

Mitochondrial DNA copy number is regulated in a tissue specific manner by DNA methylation of the nuclear-encoded DNA polymerase gamma A

(2012) Richard D. W. Kelly et al.   NUCLEIC ACIDS RESEARCH

Regulation of oocyte mitochondrial DNA copy number by follicular fluid, EGF, and neuregulin 1 during in vitro maturation affects embryo development in pigs

(2012) J. Mao et al.   THERIOGENOLOGY

Brilliant Cresyl Blue stain selects largest oocytes with highest mitochondrial activity, maturation-promoting factor activity and embryo developmental competence in prepubertal sheep

(2011) Maria Gracia Catalá et al.   REPRODUCTION

The Role of Mitochondrial DNA Copy Number in Mammalian Fertility1

(2010) Timothy Wai et al.   BIOLOGY OF REPRODUCTION

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Inter- and Intra-Individual Variation in Allele-Specific DNA Methylation and Gene Expression in Children Conceived using Assisted Reproductive Technology

(2010) Nahid Turan et al.   PLoS Genetics

Transcript expression of mitochondria related genes is correlated with bovine oocyte selection by BCB test

(2009) Jolanta Opiela et al.   ANIMAL REPRODUCTION SCIENCE

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

DNA methylation and gene expression differences in children conceived in vitro or in vivo

(2009) Sunita Katari et al.   HUMAN MOLECULAR GENETICS

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

(2009) Antonio M. Ramos et al.   PLoS One

mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft

(2008) Darren Magda et al.   BMC GENOMICS

Global Survey of Genomic Imprinting by Transcriptome Sequencing

(2008) Tomas Babak et al.   CURRENT BIOLOGY

Neuregulin 1 in neural development, synaptic plasticity and schizophrenia

(2008) Lin Mei et al.   NATURE REVIEWS NEUROSCIENCE

Molecular and subcellular characterisation of oocytes screened for their developmental competence based on glucose-6-phosphate dehydrogenase activity

(2008) Helmut Torner et al.   REPRODUCTION