Developmental dynamics of lncRNAs across mammalian organs and species

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance

(2018) Assaf C. Bester et al.   CELL

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

Insulinpromoter in human pancreatic β cells contacts diabetes susceptibility loci and regulates genes affecting insulin metabolism

(2018) Xing Jian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon et al.   NATURE

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

(2017) Julien Lagarde et al.   NATURE GENETICS

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

(2017) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

(2016) Marta Melé et al.   GENOME RESEARCH

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

(2016) Ivan Yevshin et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast Nonparametric Clustering of Structured Time-Series

(2015) James Hensman et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

The Pfam protein families database: towards a more sustainable future

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

Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain

(2015) Loyal A. Goff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNAs in organogenesis: making the difference

(2015) Phillip Grote et al.   TRENDS IN GENETICS

The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2 Expression

(2015) Wei Jiang et al.   Cell Reports

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

(2015) Hadas Hezroni et al.   Cell Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) S. Washietl et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

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

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

Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters

(2013) James Hensman et al.   BMC BIOINFORMATICS

Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo

(2013) Alexander D. Ramos et al.   Cell Stem Cell

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Magali Soumillon et al.   Cell Reports

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

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

(2012) T. Derrien et al.   GENOME RESEARCH

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

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

(2012) Cole Trapnell et al.   Nature Protocols

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

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

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

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

(2011) Sandra Ruf et al.   NATURE GENETICS

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Regulation of Emx2 Expression by Antisense Transcripts in Murine Cortico-Cerebral Precursors

(2010) Giulia Spigoni et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson 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

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY