POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)

(2016) Nathan D. Berkowitz et al.   BMC BIOINFORMATICS

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation

(2016) Saber HafezQorani et al.   NUCLEIC ACIDS RESEARCH

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data

(2016) Yang Wu et al.   NUCLEIC ACIDS RESEARCH

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

(2015) Peter Kerpedjiev et al.   BIOINFORMATICS

CLIPdb: a CLIP-seq database for protein-RNA interactions

(2015) Yu-Cheng T Yang et al.   BMC GENOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

(2015) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

DGIdb 2.0: mining clinically relevant drug–gene interactions

(2015) Alex H. Wagner et al.   NUCLEIC ACIDS RESEARCH

RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins

(2015) Fengbiao Mao et al.   NUCLEIC ACIDS RESEARCH

RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

(2015) Wen-Ju Sun et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

(2015) Lee E. Vandivier et al.   PLANT CELL

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

(2015) et al.   SCIENCE

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

The Pivotal Regulatory Landscape of RNA Modifications

(2014) Sheng Li et al.   Annual Review of Genomics and Human Genetics

Regulation of Pluripotency by RNA Binding Proteins

(2014) Julia Ye et al.   Cell Stem Cell

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis

(2014) Michael J Moore et al.   Nature Protocols

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Competition between target sites of regulators shapes post-transcriptional gene regulation

(2014) Marvin Jens et al.   NATURE REVIEWS GENETICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes 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

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger 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

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

Computational approaches to interpreting genomic sequence variation

(2014) Graham RS Ritchie et al.   Genome Medicine

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

(2014) Ian M Silverman et al.   GENOME BIOLOGY

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

(2013) F. Agostini et al.   BIOINFORMATICS

Multi-disciplinary methods to define RNA–protein interactions and regulatory networks

(2013) Manuel Ascano et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

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

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara 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

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

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

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) Anmol M. Kiran et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

(2011) B. J. Parker et al.   GENOME RESEARCH

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

(2011) Neelanjan Mukherjee et al.   MOLECULAR CELL

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

TGF-β induces the expression of the adaptor Ndfip1 to silence IL-4 production during iTreg cell differentiation

(2011) Allison M Beal et al.   NATURE IMMUNOLOGY

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

BioMart: driving a paradigm change in biological data management

(2011) A. Kasprzyk   Database-The Journal of Biological Databases and Curation

SpeCond: a method to detect condition-specific gene expression

(2011) Florence MG Cavalli et al.   GENOME BIOLOGY

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

(2011) David L Corcoran et al.   GENOME BIOLOGY

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

Effect of Genetic Variations in Syntaxin-Binding Protein-5 and Syntaxin-2 on von Willebrand Factor Concentration and Cardiovascular Risk

(2010) Janine E. van Loon et al.   Circulation-Cardiovascular Genetics

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

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

(2010) Hilal Kazan et al.   PLoS Computational Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Mammalian pre-mRNA 3′ End Processing Factor CF Im68 Functions in mRNA Export

(2009) Marc-David Ruepp et al.   MOLECULAR BIOLOGY OF THE CELL

TiGER: a database for tissue-specific gene expression and regulation

(2008) Xiong Liu et al.   BMC BIOINFORMATICS

Diverse molecular functions of Hu proteins

(2008) M. N. Hinman et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

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

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA