Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing

Skin transcriptome profiles associated with coat color in sheep

(2013) Ruiwen Fan et al.   BMC GENOMICS

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data

(2012) Wen Huang et al.   ANIMAL GENETICS

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

The role of androgen and androgen receptor in skin-related disorders

(2012) Jiann-Jyh Lai et al.   ARCHIVES OF DERMATOLOGICAL RESEARCH

Transcriptional profiling of bovine milk using RNA sequencing

(2012) Saumya Wickramasinghe et al.   BMC GENOMICS

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

(2012) Aran O’Loughlin et al.   BMC GENOMICS

RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance

(2012) Matthew McCabe et al.   BMC GENOMICS

RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts

(2012) Ashley M Driver et al.   BMC GENOMICS

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

Regulation of mammalian cell differentiation by long non-coding RNAs

(2012) Wenqian Hu et al.   EMBO REPORTS

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

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Physiological status alters immunological regulation of bovine follicle differentiation in dairy cattle

(2012) S.W. Walsh et al.   JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers

(2012) Ransom L. Baldwin et al.   PHYSIOLOGICAL GENOMICS

Tissue-specific mRNA expression patterns reveal a coordinated metabolic response associated with genetic selection for milk production in cows

(2012) R. Weikard et al.   PHYSIOLOGICAL GENOMICS

Evidence for an early endometrial response to pregnancy in cattle: both dependent upon and independent of interferon tau

(2012) N. Forde et al.   PHYSIOLOGICAL GENOMICS

Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds

(2012) Wen Huang et al.   PLoS One

Transcriptome Characterization by RNA-seq Unravels the Mechanisms of Butyrate-Induced Epigenomic Regulation in Bovine Cells

(2012) Sitao Wu et al.   PLoS One

Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes

(2012) Zhipeng Qu et al.   PLoS One

Identification and Comparative Analysis of ncRNAs in Human, Mouse and Zebrafish Indicate a Conserved Role in Regulation of Genes Expressed in Brain

(2012) Zhipeng Qu et al.   PLoS One

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

Computational discovery of human coding and non-coding transcripts with conserved splice sites

(2011) Dominic Rose et al.   BIOINFORMATICS

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Spinophilin acts as a tumor suppressor by regulating Rb phosphorylation

(2011) Irene Ferrer et al.   CELL CYCLE

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Human Protein-Coding and Noncoding RNAs between Brain and 10 Mixed Cell Lines by RNA-Seq

(2011) Geng Chen et al.   PLoS One

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

(2010) Angela Cánovas et al.   MAMMALIAN GENOME

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Expression of distinct RNAs from 3′ untranslated regions

(2010) Tim R. Mercer et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Mining Mammalian Transcript Data for Functional Long Non-Coding RNAs

(2010) Amit N. Khachane et al.   PLoS One

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6

(2009) Rosemarie Weikard et al.   BMC GENOMICS

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes

(2009) G. Solda et al.   BRIEFINGS IN BIOINFORMATICS

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH