Revealing protein–lncRNA interaction

A global view of network of lncRNAs and their binding proteins

(2015) Desi Shang et al.   Molecular BioSystems

Technologies to probe functions and mechanisms of long noncoding RNAs

(2015) Ci Chu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information

(2015) V. Suresh et al.   NUCLEIC ACIDS RESEARCH

Technologies to probe functions and mechanisms of long noncoding RNAs

(2015) Ci Chu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Computationally predicting protein-RNA interactions using only positive and unlabeled examples

(2015) Zhanzhan Cheng et al.   Journal of Bioinformatics and Computational Biology

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

(2015) Joseph Mazar et al.   Oncotarget

Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures

(2014) Carmen M Livi et al.   BMC BIOINFORMATICS

High-throughput characterization of protein-RNA interactions

(2014) K. B. Cook et al.   Briefings in Functional Genomics

Ribonomic approaches to study the RNA-binding proteome

(2014) Camilla Faoro et al.   FEBS LETTERS

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins

(2014) Nicole Lambert et al.   MOLECULAR CELL

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

(2014) Jason D Buenrostro et al.   NATURE BIOTECHNOLOGY

A novel approach to represent and compare RNA secondary structures

(2014) Eugenio Mattei et al.   NUCLEIC ACIDS RESEARCH

Leveraging cross-link modification events in CLIP-seq for motif discovery

(2014) Emad Bahrami-Samani et al.   NUCLEIC ACIDS RESEARCH

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

(2014) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

An update on LNCipedia: a database for annotated human lncRNA sequences

(2014) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

RBPmap: a web server for mapping binding sites of RNA-binding proteins

(2014) Inbal Paz et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data

(2014) Tao Wang et al.   PLoS One

Long noncoding RNA HOTAIR involvement in cancer

(2014) Yansheng Wu et al.   TUMOR BIOLOGY

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

(2014) Je-Hyun Yoon et al.   Nature Communications

Dissecting the expression landscape of RNA-binding proteins in human cancers

(2014) Bobak Kechavarzi et al.   GENOME BIOLOGY

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

(2014) Beibei Chen et al.   GENOME BIOLOGY

Methods for comprehensive experimental identification of RNA-protein interactions

(2014) Colleen A McHugh et al.   GENOME BIOLOGY

linc-UBC1 physically associates with polycomb repressive complex 2 (PRC2) and acts as a negative prognostic factor for lymph node metastasis and survival in bladder cancer

(2013) Wang He et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Collective judgment predicts disease-associated single nucleotide variants

(2013) Emidio Capriotti et al.   BMC GENOMICS

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

(2013) Qiongshi Lu et al.   BMC GENOMICS

A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs

(2013) Alex Charles Tuck et al.   CELL

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Identification of a long non-coding RNA-associated RNP complex regulating metastasis at the translational step

(2013) Kiranmai Gumireddy et al.   EMBO JOURNAL

Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators

(2013) M. Scheibe et al.   GENOME RESEARCH

Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1)

(2013) Monika Hämmerle et al.   HEPATOLOGY

The Non-Coding RNA Llme23 Drives the Malignant Property of Human Melanoma Cells

(2013) Chuan-Fang Wu et al.   Journal of Genetics and Genomics

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon 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

NPInter v2.0: an updated database of ncRNA interactions

(2013) Jiao Yuan et al.   NUCLEIC ACIDS RESEARCH

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins

(2013) Hilal Kazan et al.   NUCLEIC ACIDS RESEARCH

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

(2013) Yue Li et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

RAPID-SELEX for RNA Aptamers

(2013) Kylan Szeto et al.   PLoS One

Function of lncRNAs and approaches to lncRNA-protein interactions

(2013) JuanJuan Zhu et al.   Science China-Life Sciences

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

Analysis of long non-coding RNA expression profiles in gastric cancer

(2013) Wei-Jun Cao   WORLD JOURNAL OF GASTROENTEROLOGY

Finding the target sites of RNA-binding proteins

(2013) Xiao Li et al.   Wiley Interdisciplinary Reviews-RNA

Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers

(2012) J. Hoinka et al.   BIOINFORMATICS

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

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

(2012) T. Derrien et al.   GENOME RESEARCH

Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes

(2012) Chenguang Gong et al.   METHODS

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

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

(2012) Claudia Carrieri et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

DGCR8 HITS-CLIP reveals novel functions for the Microprocessor

(2012) Sara Macias et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity

(2012) Olga Bannikova et al.   NUCLEIC ACIDS RESEARCH

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

(2012) Cem Sievers 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

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

RNA–protein interactions in vivo: global gets specific

(2012) Minna-Liisa Änkö et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

(2011) Sonja Althammer et al.   BIOINFORMATICS

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

Long Intergenic Noncoding RNAs: New Links in Cancer Progression

(2011) M.-C. Tsai et al.   CANCER RESEARCH

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

(2011) Marcella Cesana et al.   CELL

The functional role of long non-coding RNA in human carcinomas

(2011) Ewan A Gibb et al.   Molecular Cancer

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

(2011) Ci Chu et al.   MOLECULAR CELL

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

(2011) James R Tollervey et al.   NATURE NEUROSCIENCE

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA

(2011) Joseph D. Shih et al.   NUCLEIC ACIDS RESEARCH

In silico characterization and prediction of global protein–mRNA interactions in yeast

(2011) Vera Pancaldi et al.   NUCLEIC ACIDS RESEARCH

Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast

(2011) G. Kudla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

Large non-coding RNAs: missing links in cancer?

(2010) M. Huarte et al.   HUMAN MOLECULAR GENETICS

Genomic SELEX: A discovery tool for genomic aptamers

(2010) Bob Zimmermann et al.   METHODS

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

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Molecular Interplay of the Noncoding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a

(2010) Kyoko L. Yap et al.   MOLECULAR CELL

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts

(2010) C. Lorenz et al.   NUCLEIC ACIDS RESEARCH

RBPDB: a database of RNA-binding specificities

(2010) K. B. Cook et al.   NUCLEIC ACIDS RESEARCH

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

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

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

(2010) Hilal Kazan et al.   PLoS Computational Biology

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

(2009) Barrett C Foat et al.   Molecular Systems Biology

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

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

(2009) S. Granneman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

Non-coding RNAs regulating the transcriptional machinery

(2008) Charlotte Barrandon et al.   BIOLOGY OF THE CELL

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

NRED: a database of long noncoding RNA expression

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

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

(2008) M. Rabani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology