FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome

Melanoma addiction to the long non-coding RNA SAMMSON

(2016) Eleonora Leucci et al.   NATURE

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

LncRNA-ID: Long non-coding RNA IDentification using balanced random forests

(2015) Rujira Achawanantakun et al.   BIOINFORMATICS

Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma

(2015) Yibin Hao et al.   BMC CANCER

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

NONCODE 2016: an informative and valuable data source of long non-coding RNAs

(2015) Yi Zhao et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells

(2015) Silvia Zucchelli et al.   Frontiers in Cellular Neuroscience

Quorum sensing triggers the stochastic escape of individual cells from Pseudomonas putida biofilms

(2015) Gerardo Cárcamo-Oyarce et al.   Nature Communications

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2015) Leif Andersson et al.   GENOME BIOLOGY

Identification of long non-coding RNAs in insects genomes

(2015) Fabrice Legeai et al.   Current Opinion in Insect Science

GATB: Genome Assembly & Analysis Tool Box

(2014) Erwan Drezen et al.   BIOINFORMATICS

New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily

(2014) Christine B Trame et al.   BMC BIOINFORMATICS

A network-based approach to identify substrate classes of bacterial glycosyltransferases

(2014) Aminael Sánchez-Rodríguez et al.   BMC GENOMICS

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

(2014) Søren Lykke-Andersen et al.   GENES & DEVELOPMENT

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm

(2014) Supatcha Lertampaiporn et al.   NUCLEIC ACIDS RESEARCH

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

(2014) Marc P. Hoeppner et al.   PLoS One

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

(2014) R. Johnson et al.   RNA

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation

(2013) Gangqing Hu et al.   NATURE IMMUNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

(2013) Per Johnsson 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

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

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells

(2012) T. Gutschner et al.   CANCER RESEARCH

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

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

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

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

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

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

BlastR—fast and accurate database searches for non-coding RNAs

(2011) Giovanni Bussotti et al.   NUCLEIC ACIDS RESEARCH

SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer

(2011) M. E. Askarian-Amiri et al.   RNA

LUPA: A European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

(2011) Anne-Sophie Lequarré et al.   VETERINARY JOURNAL

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping

(2011) Amaury Vaysse et al.   PLoS Genetics

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

(2008) Minghui Jiang et al.   BMC BIOINFORMATICS

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE