Computational approaches towards understanding human long non-coding RNA biology

Genetic variation in the non-coding genome: Involvement of micro-RNAs and long non-coding RNAs in disease

(2014) Barbara Hrdlickova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome

(2014) Wen-Ling Chan et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Inferring novel lncRNA–disease associations based on a random walk model of a lncRNA functional similarity network

(2014) Jie Sun et al.   Molecular BioSystems

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Identification and characterization of RNA guanine-quadruplex binding proteins

(2014) Annekathrin von Hacht et al.   NUCLEIC ACIDS RESEARCH

lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse

(2014) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

A Network Based Method for Analysis of lncRNA-Disease Associations and Prediction of lncRNAs Implicated in Diseases

(2014) Xiaofei Yang et al.   PLoS One

Microarray Profiling and Co-Expression Network Analysis of Circulating lncRNAs and mRNAs Associated with Major Depressive Disorder

(2014) Zhifen Liu et al.   PLoS One

lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

(2014) Shaoli Das et al.   PLoS One

Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs

(2014) Giang Huong Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) R. Johnson et al.   RNA

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

(2014) A. Pauli et al.   SCIENCE

The four dimensions of noncoding RNA conservation

(2014) Sven Diederichs   TRENDS IN GENETICS

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

(2013) Per Johnsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis

(2013) Ke Liu et al.   BIOINFORMATICS

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

(2013) F. Agostini et al.   BIOINFORMATICS

Computational prediction of associations between long non-coding RNAs and proteins

(2013) Qiongshi Lu et al.   BMC GENOMICS

A genetic polymorphism in lincRNA-uc003opf.1 is associated with susceptibility to esophageal squamous cell carcinoma in Chinese populations

(2013) Hongchun Wu et al.   CARCINOGENESIS

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

The large non-coding RNA ANRIL, which is associated with atherosclerosis, periodontitis and several forms of cancer, regulates ADIPOR1, VAMP3 and C11ORF10

(2013) Gregor Bochenek et al.   HUMAN MOLECULAR GENETICS

Distinct Patterns of Genetic Variations in Potential Functional Elements in Long Noncoding RNAs

(2013) Deeksha Bhartiya et al.   HUMAN MUTATION

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

(2013) Radhakrishnan Sabarinathan et al.   HUMAN MUTATION

Detecting and Comparing Non-Coding RNAs in the High-Throughput Era

(2013) Giovanni Bussotti et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptome-wide identification of RNA binding sites by CLIP-seq

(2013) Valentine Murigneux et al.   METHODS

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions

(2013) Saakshi Jalali et al.   PLoS One

Sequence and Expression Characteristics of Long Noncoding RNAs in Honey Bee Caste Development – Potential Novel Regulators for Transgressive Ovary Size

(2013) Fernanda C. Humann et al.   PLoS One

RNA-protein analysis using a conditional CRISPR nuclease

(2013) H. Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs

(2013) Deeksha Bhartiya et al.   Database-The Journal of Biological Databases and Curation

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

(2013) Vinod Kumar et al.   PLoS Genetics

Cell-Type Specific Features of Circular RNA Expression

(2013) Julia Salzman et al.   PLoS Genetics

VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer

(2013) Georges St Laurent et al.   GENOME BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome

(2012) Ashwini Jeggari et al.   BIOINFORMATICS

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs

(2012) Saakshi Jalali et al.   Biology Direct

Transcriptome analysis using next-generation sequencing

(2012) Kai-Oliver Mutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Conceptual approaches for lncRNA drug discovery and future strategies

(2012) Deeksha Bhartiya et al.   Expert Opinion on Drug Discovery

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data

(2012) F. A. Buske et al.   GENOME 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

Long Noncoding RNAs: Insights from Biological Features and Functions to Diseases

(2012) Xiaolei Li et al.   MEDICINAL RESEARCH REVIEWS

MS2-TRAP (MS2-tagged RNA affinity purification): Tagging RNA to identify associated miRNAs

(2012) Je-Hyun Yoon et al.   METHODS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease

(2012) Irfan A. Qureshi et al.   NATURE REVIEWS NEUROSCIENCE

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

(2012) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Noncoder: a web interface for exon array-based detection of long non-coding RNAs

(2012) Pascal Gellert et al.   NUCLEIC ACIDS RESEARCH

DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs

(2012) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

Computational Prediction of Polycomb-Associated Long Non-Coding RNAs

(2012) Galina V. Glazko et al.   PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

(2012) W. R. Jeck et al.   RNA

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs

(2012) F. Niazi et al.   RNA

Cooperativity in RNA-Protein Interactions: Global Analysis of RNA Binding Specificity

(2012) Zachary T. Campbell et al.   Cell Reports

Chromatin Isolation by RNA Purification (ChIRP)

(2012) Ci Chu et al.   Jove-Journal of Visualized Experiments

Evolutionary conservation and functional roles of ncRNA

(2012) Zhipeng Qu et al.   Frontiers in Genetics

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

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

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

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk

(2011) Guangfu Jin et al.   CARCINOGENESIS

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity

(2011) T. Wongsurawat et al.   NUCLEIC ACIDS RESEARCH

ncFANs: a web server for functional annotation of long non-coding RNAs

(2011) Q. Liao et al.   NUCLEIC ACIDS RESEARCH

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer

(2011) C Braconi et al.   ONCOGENE

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) S. Washietl et al.   RNA

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

(2011) Jan Gorodkin et al.   PLoS Computational Biology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

(2010) Tim R Mercer et al.   BMC NEUROSCIENCE

Emerging Roles for Natural MicroRNA Sponges

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

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz 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

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein 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

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

The UCSC cancer genomics browser: update 2011

(2010) J. Zachary Sanborn et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling

(2010) X. Peng et al.   mBio

GeneCards Version 3: the human gene integrator

(2010) M. Safran et al.   Database-The Journal of Biological Databases and Curation

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

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

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

Predicting and understanding the stability of G-quadruplexes

(2009) Oliver Stegle et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

(2009) Roberto T Arrial et al.   BMC 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

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

(2009) Ana C Marques et al.   GENOME BIOLOGY

The GAS5 (growth arrest-specific transcript 5) gene fuses to BCL6 as a result of t(1;3)(q25;q27) in a patient with B-cell lymphoma

(2008) Yuichi Nakamura et al.   CANCER GENETICS AND CYTOGENETICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Kcnq1ot1/Lit1 Noncoding RNA Mediates Transcriptional Silencing by Targeting to the Perinucleolar Region

(2008) F. Mohammad et al.   MOLECULAR AND CELLULAR BIOLOGY

Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase

(2008) Mohammad Ali Faghihi et al.   NATURE MEDICINE

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

NRED: a database of long noncoding RNA expression

(2008) Marcel E. Dinger et al.   NUCLEIC ACIDS RESEARCH

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology