Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat

[1]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

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

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

[4]  中山 幸輝.  A long noncoding RNA protects the heart from pathological hypertrophy , 2015 .

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

[6]  Hannah Dueck,et al.  Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation , 2015, Genome Biology.

[7]  Lei Wang,et al.  ALDB: A Domestic-Animal Long Noncoding RNA Database , 2015, PloS one.

[8]  S. Dhanasekaran,et al.  The landscape of long noncoding RNAs in the human transcriptome , 2015, Nature Genetics.

[9]  Mo Li,et al.  Roles for noncoding RNAs in cell-fate determination and regeneration , 2015, Nature Structural &Molecular Biology.

[10]  B. Joe,et al.  Genome-Wide Identification of Long Noncoding RNAs in Rat Models of Cardiovascular and Renal Disease , 2015, Hypertension.

[11]  E. Petretto,et al.  Genetic Analysis of the Cardiac Methylome at Single Nucleotide Resolution in a Model of Human Cardiovascular Disease , 2014, PLoS genetics.

[12]  Lewis Y. Geer,et al.  Database resources of the National Center for Biotechnology Information , 2014, Nucleic Acids Res..

[13]  Yong Liu,et al.  Abstract 570: Characteristics of Long Non-coding RNAs in the Brown Norway Rat and Alterations in the Dahl Salt-Sensitive Rat , 2014 .

[14]  Ya-ping Zhang,et al.  Genome-Wide Identification of Long Intergenic Noncoding RNA Genes and Their Potential Association with Domestication in Pigs , 2014, Genome biology and evolution.

[15]  C. Mason,et al.  A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages , 2014, Nature Communications.

[16]  Frank Grützner,et al.  The evolution of lncRNA repertoires and expression patterns in tetrapods , 2014, Nature.

[17]  C. Ponting,et al.  Sequencing depth and coverage: key considerations in genomic analyses , 2014, Nature Reviews Genetics.

[18]  Daniel R. Zerbino,et al.  Ensembl 2014 , 2013, Nucleic Acids Res..

[19]  Melissa J. Landrum,et al.  RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..

[20]  R. Shiekhattar,et al.  Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers , 2013, Cell.

[21]  A. Gnirke,et al.  Charting a dynamic DNA methylation landscape of the human genome , 2013, Nature.

[22]  Michael D. Wilson,et al.  Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals , 2013, Cell.

[23]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[24]  D. Gauguier,et al.  Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat , 2013, Cell.

[25]  Dustin E. Schones,et al.  Novel Long Noncoding RNAs Are Regulated by Angiotensin II in Vascular Smooth Muscle Cells , 2013, Circulation research.

[26]  F. Montorsi,et al.  Intratunical injection of human adipose tissue-derived stem cells prevents fibrosis and is associated with improved erectile function in a rat model of Peyronie's disease. , 2013, European urology.

[27]  Jeannie T. Lee.  Epigenetic Regulation by Long Noncoding RNAs , 2012, Science.

[28]  Zhihua Zhang,et al.  Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study , 2012, BMC Bioinformatics.

[29]  C. Calaminus,et al.  A Novel BACHD Transgenic Rat Exhibits Characteristic Neuropathological Features of Huntington Disease , 2012, The Journal of Neuroscience.

[30]  Kevin Y. Yip,et al.  Understanding transcriptional regulation by integrative analysis of transcription factor binding data , 2012, Genome research.

[31]  S. Sengupta,et al.  Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci , 2012, Nucleic acids research.

[32]  Chris P. Ponting,et al.  Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression , 2012, PLoS genetics.

[33]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[34]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[35]  J. Rinn,et al.  Modular regulatory principles of large non-coding RNAs , 2012, Nature.

[36]  Hui Xiao,et al.  NONCODE v3.0: integrative annotation of long noncoding RNAs , 2011, Nucleic Acids Res..

[37]  M. Esteller.  Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.

[38]  M. Gerstein,et al.  Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells , 2011, Nucleic acids research.

[39]  J. Rinn,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[40]  E. Kojro,et al.  Neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) slows down Alzheimer's disease-like pathology in amyloid precursor protein-transgenic mice , 2011, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[41]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[42]  Patrick O. McGowan,et al.  Broad Epigenetic Signature of Maternal Care in the Brain of Adult Rats , 2011, PloS one.

[43]  L. Leventhal,et al.  Inhibition of osteoclasts prevents cartilage loss and pain in a rat model of degenerative joint disease. , 2010, Osteoarthritis and cartilage.

[44]  Leonard Lipovich,et al.  Genome-wide computational identification and manual annotation of human long noncoding RNA genes. , 2010, RNA.

[45]  T. Ishrat,et al.  Resveratrol attenuates 6-hydroxydopamine-induced oxidative damage and dopamine depletion in rat model of Parkinson's disease , 2010, Brain Research.

[46]  Howard Y. Chang,et al.  Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis , 2010, Nature.

[47]  Julie A. Law,et al.  Establishing, maintaining and modifying DNA methylation patterns in plants and animals , 2010, Nature Reviews Genetics.

[48]  P. Laird.  Principles and challenges of genome-wide DNA methylation analysis , 2010, Nature Reviews Genetics.

[49]  Qing Zhou,et al.  ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells , 2009, Proceedings of the National Academy of Sciences.

[50]  Patricia P. Chan,et al.  GtRNAdb: a database of transfer RNA genes detected in genomic sequence , 2008, Nucleic Acids Res..

[51]  David W Mount,et al.  Using the Basic Local Alignment Search Tool (BLAST). , 2007, CSH protocols.

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

[53]  A. Mortazavi,et al.  Genome-Wide Mapping of in Vivo Protein-DNA Interactions , 2007, Science.

[54]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[55]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[56]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[57]  S. File,et al.  Validation of open : closed arm entries in an elevated plus-maze as a measure of anxiety in the rat , 1985, Journal of Neuroscience Methods.

[58]  W. Freed,et al.  Transplanted adrenal chromaffin cells in rat brain reduce lesion-induced rotational behaviour , 1981, Nature.

[59]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.