Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model

Swine in Biomedical Research 2014

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Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A Genetic Porcine Model of Cancer

(2015) Lawrence B. Schook et al.   PLoS One

Unraveling the Swine Genome: Implications for Human Health

(2015) Lawrence B. Schook et al.   Annual Review of Animal Biosciences

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

(2014) Juan Herrero-Medrano et al.   BMC GENOMICS

Marked methylation changes in intestinal genes during the perinatal period of preterm neonates

(2014) Fei Gao et al.   BMC GENOMICS

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues

(2014) Kimberly R. Kukurba et al.   PLoS Genetics

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

Locus-Specific DNA Methylation Reprogramming During Early Porcine Embryogenesis1

(2013) Ming-Tao Zhao et al.   BIOLOGY OF REPRODUCTION

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

Artificial Selection on Brain-Expressed Genes during the Domestication of Dog

(2013) Yan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

(2013) Kenjiro Shirane et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker

(2012) H. Heyn et al.   CARCINOGENESIS

Genome-Wide DNA Methylation Changes between the Superficial and Deep Backfat Tissues of the Pig

(2012) Mingzhou Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ENCODE: The human encyclopaedia

(2012) Brendan Maher   NATURE

Analyses of pig genomes provide insight into porcine demography and evolution

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Mammalian cells acquire epigenetic hallmarks of human cancer during immortalization

(2012) Stella Tommasi et al.   NUCLEIC ACIDS RESEARCH

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

An atlas of DNA methylomes in porcine adipose and muscle tissues

(2012) Mingzhou Li et al.   Nature Communications

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

(2012) Mirte Bosse et al.   PLoS Genetics

Changes of DNA Methylation Level and Spatial Arrangement of Primordial Germ Cells in Embryonic Day 15 to Embryonic Day 28 Pig Embryos1

(2011) Sara Maj Watjen Hyldig et al.   BIOLOGY OF REPRODUCTION

Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers

(2011) Brian S. Gloss et al.   CANCER LETTERS

DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer

(2011) Y. Kobayashi et al.   GENOME RESEARCH

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

(2011) T. Hinoue et al.   GENOME RESEARCH

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

(2011) Yufei Xu et al.   MOLECULAR CELL

Genetic modifications of pigs for medicine and agriculture

(2011) Jeffrey J. Whyte et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

CpG Islands Undermethylation in Human Genomic Regions under Selective Pressure

(2011) Sergio Cocozza et al.   PLoS One

Global DNA Demethylation During Mouse Erythropoiesis in Vivo

(2011) J. R. Shearstone et al.   SCIENCE

The pig: a model for human infectious diseases

(2011) François Meurens et al.   TRENDS IN MICROBIOLOGY

DNA methylation biomarkers for lung cancer

(2011) Tibor A. Rauch et al.   TUMOR BIOLOGY

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

(2011) Michael J. Ziller et al.   PLoS Genetics

Glucose Intolerance and Reduced Proliferation of Pancreatic  -Cells in Transgenic Pigs With Impaired Glucose-Dependent Insulinotropic Polypeptide Function

(2010) S. Renner et al.   DIABETES

Comparative analysis of DNA methylation profiles in peripheral blood leukocytes versus lymphoblastoid cell lines

(2010) Eoin P. Brennan et al.   Epigenetics

Cell culture-induced aberrant methylation of the imprinted IG DMR in human lymphoblastoid cell lines

(2010) Aabida Saferali et al.   Epigenetics

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Placentation in the pig visualized by eGFP fluorescence in eNOS over-expressing cloned transgenic swine

(2010) Jeffrey Whyte et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils

(2010) Yukio Yasukochi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines

(2009) D. Grafodatskaya et al.   GENOMICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Hemizygous minipigs produced by random gene insertion and handmade cloning express the Alzheimer’s disease-causing dominant mutation APPsw

(2009) Peter M. Kragh et al.   TRANSGENIC RESEARCH

Dominant-negative mutant hepatocyte nuclear factor 1α induces diabetes in transgenic-cloned pigs

(2009) Kazuhiro Umeyama et al.   TRANSGENIC RESEARCH

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH