Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster

Genome-Wide Identification, Characterization and Evolutionary Analysis of Long Intergenic Noncoding RNAs in Cucumber

(2015) Zhiqiang Hao 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

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Intergenic lncRNAs and the evolution of gene expression

(2014) Ana C Marques et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development

(2014) Jie Lv et al.   MOLECULAR GENETICS AND GENOMICS

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

(2014) Lin Li et al.   GENOME BIOLOGY

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

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

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Genome and Transcriptome Analyses Provide Insight into the Euryhaline Adaptation Mechanism of Crassostrea gigas

(2013) Jie Meng et al.   PLoS One

Unipro UGENE: a unified bioinformatics toolkit

(2012) Konstantin Okonechnikov et al.   BIOINFORMATICS

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

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

Identification of differentially expressed proteins involved in the early larval development of the Pacific oyster Crassostrea gigas

(2012) Pin Huan et al.   Journal of Proteomics

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

Transcriptomic Responses to Salinity Stress in the Pacific Oyster Crassostrea gigas

(2012) Xuelin Zhao et al.   PLoS One

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing

(2010) Melody S Clark et al.   BMC GENOMICS

Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: focus on biomineralization

(2010) Caroline Joubert et al.   BMC GENOMICS

Sex Determination: Genetic Models for Oysters

(2010) P. W. Hedrick et al.   JOURNAL OF HEREDITY

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

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS