Mining long noncoding RNA in livestock

Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome

(2016) Kaori Kashi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The specificity of long noncoding RNA expression

(2016) Brian S. Gloss et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Systematic Identification of Long Noncoding RNAs in Immature and Mature Porcine Testes1

(2016) Maoliang Ran et al.   BIOLOGY OF REPRODUCTION

Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus)

(2016) Hangxing Ren et al.   BMC GENOMICS

Long Noncoding RNAs in Cancer Pathways

(2016) Adam M. Schmitt et al.   CANCER CELL

Emerging role of long noncoding RNAs as regulators of innate immune cell development and inflammatory gene expression

(2016) Roland Elling et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

In silico prediction of long intergenic non-coding RNAs in sheep

(2016) Mohammad Reza Bakhtiarizadeh et al.   GENOME

Long noncoding RNAs in cancer: mechanisms of action and technological advancements

(2016) Nenad Bartonicek et al.   Molecular Cancer

LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress

(2016) Xiaowen Liu et al.   NATURE CELL BIOLOGY

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Long noncoding RNA: Novel links between gene expression and innate immunity

(2016) Susan Carpenter   VIRUS RESEARCH

Long non-coding RNAs in innate and adaptive immunity

(2016) Thomas M. Aune et al.   VIRUS RESEARCH

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

(2016) Yajing Hao et al.   Database-The Journal of Biological Databases and Curation

Progress and prospects of long noncoding RNAs in lipid homeostasis

(2016) Zheng Chen   Molecular Metabolism

iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data

(2016) Kun Sun et al.   BMC GENOMICS

Analyses of Long Non-Coding RNA and mRNA profiling using RNA sequencing during the pre-implantation phases in pig endometrium

(2016) Yueying Wang et al.   Scientific Reports

Global transcriptional profiling of longissimus thoracis muscle tissue in fetal and juvenile domestic goat using RNA sequencing

(2015) Y. H. Wang et al.   ANIMAL GENETICS

Identification and SNP association analysis of a novel gene in chicken

(2015) Xingxing Mei et al.   ANIMAL GENETICS

PU.1antisense lncRNA against its mRNA translation promotes adipogenesis in porcine preadipocytes

(2015) N. Wei et al.   ANIMAL GENETICS

LncRNAs in vertebrates: Advances and challenges

(2015) Allison C. Mallory et al.   BIOCHIMIE

Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

(2015) F. Musacchia et al.   BIOINFORMATICS

LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

(2015) Qinghua Jiang et al.   BMC GENOMICS

Long noncoding RNAs in innate immunity

(2015) Yuan Zhang et al.   Cellular & Molecular Immunology

From Discovery to Function: The Expanding Roles of Long NonCoding RNAs in Physiology and Disease

(2015) Miao Sun et al.   ENDOCRINE REVIEWS

Noncoding RNAs as epigenetic mediators of skeletal muscle regeneration

(2015) Gurjeev Sohi et al.   FEBS Journal

Long Noncoding RNA in Hematopoiesis and Immunity

(2015) Ansuman T. Satpathy et al.   IMMUNITY

Creating reference gene annotation for the mouse C57BL6/J genome assembly

(2015) Jonathan M. Mudge et al.   MAMMALIAN GENOME

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Long noncoding RNAs in cardiac development and ageing

(2015)   Nature Reviews Cardiology

deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data

(2015) Ling-Ling Zheng et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Junk DNA and the long non-coding RNA twist in cancer genetics

(2015) H Ling et al.   ONCOGENE

Exploring Differentially Expressed Genes and Natural Antisense Transcripts in Sheep (Ovis aries) Skin with Different Wool Fiber Diameters by Digital Gene Expression Profiling

(2015) Yaojing Yue et al.   PLoS One

Exploring the function of long non-coding RNA in the development of bovine early embryos

(2015) Julieta Caballero et al.   REPRODUCTION FERTILITY AND DEVELOPMENT

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Long Noncoding RNAs: A New Regulatory Code in Metabolic Control

(2015) Xu-Yun Zhao et al.   TRENDS IN BIOCHEMICAL SCIENCES

Long noncoding RNAs in organogenesis: making the difference

(2015) Phillip Grote et al.   TRENDS IN GENETICS

The conservation and signatures of lincRNAs in Marek’s disease of chicken

(2015) Yanghua He 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

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Non-coding yet non-trivial: a review on the computational genomics of lincRNAs

(2015) Travers Ching et al.   BioData Mining

Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network

(2015) Yun Xiao et al.   Biomed Research International

Noncoding RNAs, Emerging Regulators of Skeletal Muscle Development and Diseases

(2015) Mao Nie et al.   Biomed Research International

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

(2015) Leif Andersson et al.   GENOME BIOLOGY

ALDB: A Domestic-Animal Long Noncoding RNA Database

(2015) Aimin Li et al.   PLoS One

A catalogue of novel bovine long noncoding RNA across 18 tissues

(2015) Lambros T. Koufariotis et al.   PLoS One

Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development

(2015) Weimin Zhao et al.   Scientific Reports

New insights into polar overdominance in callipyge sheep

(2014) C. A. Bidwell et al.   ANIMAL GENETICS

lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs

(2014) Charny Park et al.   BIOINFORMATICS

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

(2014) Coline Billerey et al.   BMC GENOMICS

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

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

(2014) S. Washietl et al.   GENOME RESEARCH

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

RNAcentral: an international database of ncRNA sequences

(2014)   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Independent Polled Mutations Leading to Complex Gene Expression Differences in Cattle

(2014) Natalie Wiedemar et al.   PLoS One

Epigenetic Genes and Emotional Reactivity to Daily Life Events: A Multi-Step Gene-Environment Interaction Study

(2014) Ehsan Pishva et al.   PLoS One

Correction: Characterization of Transcriptional Complexity during Adipose Tissue Development in Bovines of Different Ages and Sexes

(2014)   PLoS One

Databases for lncRNAs: a comparative evaluation of emerging tools

(2014) Sabrina Fritah et al.   RNA

Long non-coding RNAs in the regulation of the immune response

(2014) James A. Heward et al.   TRENDS IN IMMUNOLOGY

Long noncoding RNAs, emerging players in muscle differentiation and disease

(2014) Maria Neguembor et al.   Skeletal Muscle

Regulation of metabolism by long, non-coding RNAs

(2014) Jan-Wilhelm Kornfeld et al.   Frontiers in Genetics

Gene regulation by the act of long non-coding RNA transcription

(2013) Aleksandra E Kornienko et al.   BMC BIOLOGY

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

(2013) Rosemarie Weikard et al.   BMC GENOMICS

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

A long non-coding RNA promotes full activation of adult gene expression in the chicken α-globin domain

(2013) Cristian Arriaga-Canon et al.   Epigenetics

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial retrograde signaling induces epithelial–mesenchymal transition and generates breast cancer stem cells

(2013) M Guha et al.   ONCOGENE

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

(2013) Aurélie Allais-Bonnet et al.   PLoS One

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

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

Truncation of MIMT1 Gene in the PEG3 Domain Leads to Major Changes in Placental Gene Expression and Stillbirth in Cattle1

(2012) Krzysztof Flisikowski et al.   BIOLOGY OF REPRODUCTION

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

The long non-coding RNA, MHM, plays a role in chicken embryonic development, including gonadogenesis

(2012) Kelly N. Roeszler et al.   DEVELOPMENTAL BIOLOGY

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

Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing

(2012) Tingting Li et al.   GENOMICS

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

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks

(2012) Xingli Guo et al.   NUCLEIC ACIDS RESEARCH

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

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

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs

(2012) F. Niazi et al.   RNA

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

(2012) Frank W. Albert et al.   PLoS Genetics

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

(2012) Claudia Kutter et al.   PLoS Genetics

Dark Matter RNA: Existence, Function, and Controversy

(2012) Philipp Kapranov et al.   Frontiers in Genetics

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq

(2011) Wen Huang et al.   BMC GENOMICS

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

(2011) Anna Esteve-Codina et al.   BMC GENOMICS

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

(2011) Igor Ulitsky et al.   CELL

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

The research strategies for probing the function of long noncoding RNAs

(2011) Biao Yan et al.   GENOMICS

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

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

Combining resources to obtain a comprehensive survey of the bovine embryo transcriptome through deep sequencing and microarrays

(2011) Claude Robert et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

ncFANs: a web server for functional annotation of long non-coding RNAs

(2011) Q. Liao et al.   NUCLEIC ACIDS RESEARCH

Corrigendum: Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

The Reality of Pervasive Transcription

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

Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing

(2010) F. Caiment et al.   GENOME RESEARCH

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

A Novel Mutation in the Maternally Imprinted PEG3 Domain Results in a Loss of MIMT1 Expression and Causes Abortions and Stillbirths in Cattle (Bos taurus)

(2010) Krzysztof Flisikowski et al.   PLoS One

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology