Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese- and mini-type pigs

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

(2015) Kyle M. Schachtschneider et al.   BMC GENOMICS

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

Wnt antagonist, secreted frizzled-related protein 1, is involved in prenatal skeletal muscle development and is a target of miRNA-1/206 in pigs

(2015) Yalan Yang et al.   BMC MOLECULAR BIOLOGY

Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing

(2015) Minkyeung Choi et al.   DNA RESEARCH

Malat1 regulates serum response factor through miR-133 as a competing endogenous RNA in myogenesis

(2015) Xiaorui Han et al.   FASEB JOURNAL

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

(2015) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

Simple scheme for encoding and decoding a qubit in unknown state for various topological codes

(2015) Justyna Łodyga et al.   Scientific Reports

DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues

(2015) Zhong-Yin Zhou et al.   Scientific Reports

Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs

(2015) Lu Jing et al.   Scientific Reports

DNA methylation dynamics in muscle development and disease

(2015) Elvira Carrió   Frontiers in Aging Neuroscience

FHL1 activates myostatin signalling in skeletal muscle and promotes atrophy

(2015) Jen Y. Lee et al.   FEBS Open Bio

MicroRNA-21 Regulates PI3K/Akt/mTOR Signaling by Targeting TGFβI during Skeletal Muscle Development in Pigs

(2015) Lijing Bai et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Genome-wide analysis of DNA methylation patterns in horse

(2014) Ja-Rang Lee et al.   BMC GENOMICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

A genome-wide association study of seed protein and oil content in soybean

(2014) Eun-Young Hwang et al.   BMC GENOMICS

Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer

(2014) Xiaojing Yang et al.   CANCER CELL

MicroRNAs Emerge as Modulators of NAD+-Dependent Energy Metabolism in Skeletal Muscle

(2014) Kristoffer Svensson et al.   DIABETES

The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration

(2014) B. K. Dey et al.   GENES & DEVELOPMENT

Genome-Wide Identification of Long Intergenic Noncoding RNA Genes and Their Potential Association with Domestication in Pigs

(2014) Zhong-Yin Zhou et al.   Genome Biology and Evolution

Grb10 Deletion Enhances Muscle Cell Proliferation, Differentiation and GLUT4 Plasma Membrane Translocation

(2014) Nancy Mokbel et al.   JOURNAL OF CELLULAR PHYSIOLOGY

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

Long noncoding RNAs, emerging players in muscle differentiation and disease

(2014) Maria Neguembor et al.   Skeletal Muscle

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

FoxO transcription factors: their roles in the maintenance of skeletal muscle homeostasis

(2013) Anthony M. J. Sanchez et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Cell cycle regulation by long non-coding RNAs

(2013) Masatoshi Kitagawa et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

(2013) Phillip Grote et al.   DEVELOPMENTAL CELL

Early de novo DNA methylation and prolonged demethylation in the muscle lineage

(2013) Koji Tsumagari et al.   Epigenetics

Comparative genomics as a tool to understand evolution and disease

(2013) J. Alfoldi et al.   GENOME RESEARCH

The influence of fiber size distribution of type IIB on carcass traits and meat quality in pigs

(2013) Gap-Don Kim et al.   MEAT SCIENCE

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Distinctive Genes Determine Different Intramuscular Fat and Muscle Fiber Ratios of the longissimus dorsi Muscles in Jinhua and Landrace Pigs

(2013) Ting Wu et al.   PLoS One

Long noncoding RNAs regulate adipogenesis

(2013) Lei Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNA-26 Family Is Required for Human Adipogenesis and Drives Characteristics of Brown Adipocytes

(2013) Michael Karbiener et al.   STEM CELLS

Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes

(2012) Ignasi Morán et al.   Cell Metabolism

Grb10 regulates the development of fiber number in skeletal muscle

(2012) Lowenna J. Holt et al.   FASEB JOURNAL

miR-26a is required for skeletal muscle differentiation and regeneration in mice

(2012) B. K. Dey et al.   GENES & DEVELOPMENT

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

The insulin-like growth factor 1 receptor (IGF1R) contributes to reduced size in dogs

(2012) Barbara C. Hoopes et al.   MAMMALIAN GENOME

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

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

(2012) Satish Sati et al.   NUCLEIC ACIDS RESEARCH

Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

(2012) Zhi-Liang Hu et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation Patterns in Cord Blood DNA and Body Size in Childhood

(2012) Caroline L. Relton et al.   PLoS One

Discovery of MicroRNAs Associated with Myogenesis by Deep Sequencing of Serial Developmental Skeletal Muscles in Pigs

(2012) Xinhua Hou et al.   PLoS One

An atlas of DNA methylomes in porcine adipose and muscle tissues

(2012) Mingzhou Li et al.   Nature Communications

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

(2012) Jordana T. Bell et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

Epigenetic DNA methylation in the promoters of the Igf1 receptor and insulin receptor genes in db/db mice

(2011) Andrej Nikoshkov et al.   Epigenetics

A DNA methylation fingerprint of 1628 human samples

(2011) A. F. Fernandez et al.   GENOME RESEARCH

Study of the differential transcription in liver of growth hormone receptor (GHR), insulin-like growth factors (IGF1, IGF2) and insulin-like growth factor receptor (IGF1R) genes at different postnatal developmental ages in pig breeds

(2011) Mariusz Pierzchała et al.   MOLECULAR BIOLOGY REPORTS

Comparative Analyses by Sequencing of Transcriptomes during Skeletal Muscle Development between Pig Breeds Differing in Muscle Growth Rate and Fatness

(2011) Xiao Zhao et al.   PLoS One

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

(2010) Tim van Zutphen et al.   BMC GENOMICS

IGF-I induced genes in stromal fibroblasts predict the clinical outcome of breast and lung cancer patients

(2010) Michal Rajski et al.   BMC Medicine

Insulin-like growth factors (IGFs), IGF receptors, and IGF-binding proteins: Roles in skeletal muscle growth and differentiation

(2010) Cunming Duan et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

MicroRNAs in skeletal muscle: their role and regulation in development, disease and function

(2010) Isabelle Güller et al.   JOURNAL OF PHYSIOLOGY-LONDON

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

(2010) Hui Xiang et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Histone modifications and skeletal muscle metabolic gene expression

(2009) Sean L McGee et al.   CLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY

Fast/Glycolytic Muscle Fiber Growth Reduces Fat Mass and Improves Metabolic Parameters in Obese Mice

(2008) Yasuhiro Izumiya et al.   Cell Metabolism

Identification of FHL1 as a regulator of skeletal muscle mass: implications for human myopathy

(2008) Belinda S. Cowling et al.   JOURNAL OF CELL BIOLOGY

Comparing the histochemical characteristics and meat quality traits of different pig breeds

(2008) Y.C. Ryu et al.   MEAT SCIENCE

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

(2008) Robert Illingworth et al.   PLOS BIOLOGY