The evolution of lncRNA repertoires and expression patterns in tetrapods

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

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

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

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

(2012) T. Derrien et al.   GENOME RESEARCH

Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation

(2012) Jennifer Grant et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r

(2012) Andrew Keniry et al.   NATURE CELL BIOLOGY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

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

(2012) Claudia Kutter et al.   PLoS Genetics

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

(2011) Igor Ulitsky et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells

(2011) Emily Walker 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

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The transcriptional foundation of pluripotency

(2009) I. Chambers et al.   DEVELOPMENT

Coherent but overlapping expression of microRNAs and their targets during vertebrate development

(2009) A. Shkumatava et al.   GENES & DEVELOPMENT

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

(2009) Mitchell Guttman et al.   NATURE

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

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

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

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

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics