The landscape of DNA methylation associated with the 1 transcriptomic network in laying hens and broilers generates insight 2 into embryonic muscle development in chicken 3 4 5

[1]  Xiaoling Zhao,et al.  Expression analysis, single-nucleotide polymorphisms of the Myoz1 gene and their association with carcase and meat quality traits in chickens , 2018 .

[2]  Yan Zhang,et al.  Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease , 2017, Nucleic Acids Res..

[3]  Qin Zhang,et al.  Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C , 2017, Scientific Reports.

[4]  Xiaojun Liu,et al.  Genome-wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens , 2017, Scientific Reports.

[5]  Kui Li,et al.  Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs , 2017, Scientific Reports.

[6]  J. García-Pérez,et al.  The impact of transposable elements on mammalian development , 2016, Development.

[7]  Xiaojun Yang,et al.  DNA Methylation Variation Trends during the Embryonic Development of Chicken , 2016, PloS one.

[8]  Hao Wu,et al.  Differential methylation analysis for BS-seq data under general experimental design , 2016, Bioinform..

[9]  Ya-ping Zhang,et al.  DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues , 2015, Scientific Reports.

[10]  Songnian Hu,et al.  Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq , 2015, BMC Genomics.

[11]  Junyi Wang,et al.  LncTar: a tool for predicting the RNA targets of long noncoding RNAs , 2015, Briefings Bioinform..

[12]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[13]  Zhaohui S. Qin,et al.  Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates , 2015, Nucleic acids research.

[14]  I. Cases,et al.  Deconstruction of DNA Methylation Patterns During Myogenesis Reveals Specific Epigenetic Events in the Establishment of the Skeletal Muscle Lineage , 2015, Stem cells.

[15]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[16]  Ning Li,et al.  Genome-wide Mapping Reveals Conservation of Promoter DNA Methylation Following Chicken Domestication , 2015, Scientific Reports.

[17]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[18]  K. Okamura,et al.  DNA methylation analysis of human myoblasts during in vitro myogenic differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation. , 2015, Human molecular genetics.

[19]  Yong-Zhen Huang,et al.  Genome-wide DNA Methylation Profiles and Their Relationships with mRNA and the microRNA Transcriptome in Bovine Muscle Tissue (Bos taurine) , 2014, Scientific Reports.

[20]  K. Conneely,et al.  A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data , 2014, Nucleic acids research.

[21]  M. Bang,et al.  The Role of Myopalladin in Skeletal Muscle , 2014 .

[22]  Yi Zhao,et al.  Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts , 2013, Nucleic acids research.

[23]  Q. Nie,et al.  Comparison of the Genome-Wide DNA Methylation Profiles between Fast-Growing and Slow-Growing Broilers , 2013, PloS one.

[24]  Davis J. McCarthy,et al.  Count-based differential expression analysis of RNA sequencing data using R and Bioconductor , 2013, Nature Protocols.

[25]  Hao Wu,et al.  A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data , 2012, Biostatistics.

[26]  Peter A. Jones.  Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.

[27]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[28]  S. Clarke,et al.  Disruption of MEF2C signaling and loss of sarcomeric and mitochondrial integrity in cancer-induced skeletal muscle wasting , 2012, Aging.

[29]  D. Cacchiarelli,et al.  A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA , 2011, Cell.

[30]  Jinjie Duan,et al.  Genome-Wide Mapping of DNA Methylation in Chicken , 2011, PloS one.

[31]  Michael F. Lin,et al.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.

[32]  S. Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[33]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[34]  Yong Zhang,et al.  CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine , 2007, Nucleic Acids Res..

[35]  A. Feinberg.  Phenotypic plasticity and the epigenetics of human disease , 2007, Nature.

[36]  C. Allis,et al.  Epigenetics: A Landscape Takes Shape , 2007, Cell.

[37]  Mark Groudine,et al.  Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells , 2004, Nature Structural &Molecular Biology.

[38]  Robert A. Waterland,et al.  Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation , 2003, Molecular and Cellular Biology.

[39]  A. Bird,et al.  Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals , 2003, Nature Genetics.

[40]  J. Stull,et al.  Dedicated Myosin Light Chain Kinases with Diverse Cellular Functions* , 2001, The Journal of Biological Chemistry.

[41]  G. Huszar.  Developmental changes of the primary structure and histidine methylation in rabbit skeletal muscle myosin. , 1972, Nature: New biology.