Multi-omics annotation of human long non-coding RNAs

Estimating the power of sequence covariation for detecting conserved RNA structure

(2020) Elena Rivas et al.   BIOINFORMATICS

Keth-seq for transcriptome-wide RNA structure mapping

(2020) Xiaocheng Weng et al.   Nature Chemical Biology

Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types

(2020) Huajing Teng et al.   NUCLEIC ACIDS RESEARCH

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

(2020) Doo Nam Kim et al.   Nature Communications

LEADeR role of miR-205 host gene as long noncoding RNA in prostate basal cell differentiation

(2019) Valentina Profumo et al.   Nature Communications

Developmental dynamics of lncRNAs across mammalian organs and species

(2019) Ioannis Sarropoulos et al.   NATURE

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

An expanded landscape of human long noncoding RNA

(2019) Shuai Jiang et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNA LCAT1 functions as a ceRNA to regulate RAC1 function by sponging miR-4715-5p in lung cancer

(2019) Juze Yang et al.   Molecular Cancer

DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts

(2019) Dimitra Karagkouni et al.   NUCLEIC ACIDS RESEARCH

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

(2018) Zehua Wang et al.   CANCER CELL

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

Towards a complete map of the human long non-coding RNA transcriptome

(2018) Barbara Uszczynska-Ratajczak et al.   NATURE REVIEWS GENETICS

Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls

(2018) Huifen Cao et al.   TRENDS IN GENETICS

LnChrom: a resource of experimentally validated lncRNA–chromatin interactions in human and mouse

(2018) Fulong Yu et al.   Database-The Journal of Biological Databases and Curation

Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency

(2018) Colleen S. Stein et al.   Cell Reports

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

(2018) Jason C Bell et al.   eLife

LINC01133 as ceRNA inhibits gastric cancer progression by sponging miR-106a-3p to regulate APC expression and the Wnt/β-catenin pathway

(2018) Xian-Zi Yang et al.   Molecular Cancer

Functional classification of long non-coding RNAs by k-mer content

(2018) Jessime M. Kirk et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Detection of lncRNA-mRNA interaction modules by integrating eQTL with weighted gene co-expression network analysis

(2018) Xing-Bo Mo et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

LncBook: a curated knowledgebase of human long non-coding RNAs

(2018) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

EWAS Atlas: a curated knowledgebase of epigenome-wide association studies

(2018) Mengwei Li et al.   NUCLEIC ACIDS RESEARCH

LNCipedia 5: towards a reference set of human long non-coding RNAs

(2018) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

RNAcentral: a hub of information for non-coding RNA sequences

(2018) et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Variant of SNP rs1317082 at CCSlnc362 (RP11-362K14.5) creates a binding site for miR-4658 and diminishes the susceptibility to CRC

(2018) Chaoqin Shen et al.   Cell Death & Disease

High-confidence coding and noncoding transcriptome maps

(2017) Bo-Hyun You et al.   GENOME RESEARCH

lncRInter: A database of experimentally validated long non-coding RNA interaction

(2017) Chun-Jie Liu et al.   Journal of Genetics and Genomics

A novel mechanism of lncRNA and miRNA interaction: CCAT2 regulates miR-145 expression by suppressing its maturation process in colon cancer cells

(2017) Yingjie Yu et al.   Molecular Cancer

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth

(2017) Jin-Zhou Huang et al.   MOLECULAR CELL

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

(2017) Chung-Chau Hon et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

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

(2017) Julien Lagarde et al.   NATURE GENETICS

exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes

(2017) Shengli Li et al.   NUCLEIC ACIDS RESEARCH

Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease

(2017) Hui Zhi et al.   NUCLEIC ACIDS RESEARCH

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling

(2017) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data

(2017) Jia-Jia Xuan et al.   NUCLEIC ACIDS RESEARCH

NONCODEV5: a comprehensive annotation database for long non-coding RNAs

(2017) ShuangSang Fang et al.   NUCLEIC ACIDS RESEARCH

lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs

(2017) Ya-Ru Miao et al.   NUCLEIC ACIDS RESEARCH

m6AVar: a database of functional variants involved in m6A modification

(2017) Yueyuan Zheng et al.   NUCLEIC ACIDS RESEARCH

LncATLAS database for subcellular localization of long noncoding RNAs

(2017) David Mas-Ponte et al.   RNA

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

Dawn of the in vivo RNA structurome and interactome

(2016) Chun Kit Kwok   BIOCHEMICAL SOCIETY TRANSACTIONS

The emerging epitranscriptomics of long noncoding RNAs

(2016) Andrew Shafik et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Long noncoding RNA, the methylation of genomic elements and their emerging crosstalk in hepatocellular carcinoma

(2016) Sheng-xian Yuan et al.   CANCER LETTERS

A-to-I RNA editing promotes developmental stage–specific gene and lncRNA expression

(2016) Boaz Goldstein et al.   GENOME RESEARCH

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

(2016) Marta Melé et al.   GENOME RESEARCH

Whole exome sequencing identifies lncRNAGAS8-AS1andLPAR4as novel papillary thyroid carcinoma driver alternations

(2016) Wenting Pan et al.   HUMAN MOLECULAR GENETICS

Resources for the Comprehensive Discovery of Functional RNA Elements

(2016) Balaji Sundararaman et al.   MOLECULAR CELL

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

(2016) Zhihong Xue et al.   MOLECULAR CELL

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil et al.   NATURE

Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer

(2016) Haiyang Guo et al.   NATURE GENETICS

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

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

(2016) Igor Ulitsky   NATURE REVIEWS GENETICS

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs

(2016) Shangwei Ning et al.   NUCLEIC ACIDS RESEARCH

LNCediting: a database for functional effects of RNA editing in lncRNAs

(2016) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs

(2016) Chunjie Jiang et al.   Oncotarget

A genomic screen for long noncoding RNA genes epigenetically silenced by aberrant DNA methylation in colorectal cancer

(2016) Kohei Kumegawa et al.   Scientific Reports

A Cytoplasmic NF-κB Interacting Long Noncoding RNA Blocks IκB Phosphorylation and Suppresses Breast Cancer Metastasis

(2015) Bodu Liu et al.   CANCER CELL

TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer

(2015) Jun Li et al.   CANCER RESEARCH

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

Determinants of the Usage of Splice-Associatedcis-Motifs Predict the Distribution of Human Pathogenic SNPs

(2015) XianMing Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

The Roadmap Epigenomics Project opens new drug development avenues

(2015) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

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

(2015) et al.   SCIENCE

RNA–RNA interactions in gene regulation: the coding and noncoding players

(2015) Sonia Guil et al.   TRENDS IN BIOCHEMICAL SCIENCES

Long noncoding RNAs in human disease: emerging mechanisms and therapeutic strategies

(2015) Sébastien Lalevée et al.   Epigenomics

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

(2015) Viren Amin et al.   Nature Communications

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

(2015) Tanmoy Mondal et al.   Nature Communications

Profiling RNA editing in human tissues: towards the inosinome Atlas

(2015) Ernesto Picardi et al.   Scientific Reports

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome

(2014) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

miRDB: an online resource for microRNA target prediction and functional annotations

(2014) Nathan Wong et al.   NUCLEIC ACIDS RESEARCH

The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation

(2014) P. Wang et al.   SCIENCE

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

(2013) L. Bazak et al.   GENOME RESEARCH

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

The long non-coding RNAFendrrlinks epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis

(2013) Phillip Grote et al.   RNA Biology

Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination

(2013) Je-Hyun Yoon et al.   Nature Communications

Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

(2013) Vinod Kumar et al.   PLoS Genetics

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

(2012) T. Derrien et al.   GENOME RESEARCH

Control of somatic tissue differentiation by the long non-coding RNA TINCR

(2012) Markus Kretz et al.   NATURE

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

(2012) Francesca Tuorto et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

Darned in 2013: inclusion of model organisms and linking with Wikipedia

(2012) Anmol M. Kiran 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

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

(2011) Ci Chu et al.   MOLECULAR CELL

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Long noncoding RNAs and human disease

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

Role of H3K27 methylation in the regulation of lncRNA expression

(2010) Susan C Wu et al.   CELL RESEARCH

Emerging Roles for Natural MicroRNA Sponges

(2010) Margaret S. Ebert et al.   CURRENT BIOLOGY

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin 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

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE