Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles

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

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

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

(2015) Federico Comoglio et al.   BMC BIOINFORMATICS

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

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

The human RBPome: From genes and proteins to human disease

(2015) Yaseswini Neelamraju et al.   Journal of Proteomics

DDX6 Orchestrates Mammalian Progenitor Function through the mRNA Degradation and Translation Pathways

(2015) Ying Wang et al.   MOLECULAR CELL

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation

(2015) Johannes Popow et al.   RNA

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

(2014) Nicole Lambert et al.   MOLECULAR CELL

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

ChIP-Enrich: gene set enrichment testing for ChIP-seq data

(2014) Ryan P. Welch et al.   NUCLEIC ACIDS RESEARCH

dCLIP: a computational approach for comparative CLIP-seq analyses

(2014) Tao Wang et al.   GENOME BIOLOGY

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

(2014) Beibei Chen et al.   GENOME BIOLOGY

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RIP-chip enrichment analysis

(2012) Florian Erhard et al.   BIOINFORMATICS

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks

(2012) S. C. Janga   Briefings in Functional Genomics

t(11;14)(q23;q32) involvingIGHandDDX6in nodal marginal zone lymphoma

(2012) Susanne Stary et al.   GENES CHROMOSOMES & CANCER

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

(2012) Marija Milacic et al.   Cancers

Emerging roles of RNA and RNA-binding protein network in cancer cells

(2011) Mee-Young Kim et al.   BMB Reports

RNA structure and the mechanisms of alternative splicing

(2011) C Joel McManus et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

(2011) David L Corcoran et al.   GENOME BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

DDX6 (Rck/p54) Is Required for Efficient Hepatitis C Virus Replication but Not for Internal Ribosome Entry Site-Directed Translation

(2010) R. K. Jangra et al.   JOURNAL OF VIROLOGY

Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: Focus on hnRNP E1's multifunctional regulatory roles

(2010) A. Chaudhury et al.   RNA

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

(2010) Robert B. Darnell   Wiley Interdisciplinary Reviews-RNA

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks

(2009) N. Mittal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

FASTKD2 Nonsense Mutation in an Infantile Mitochondrial Encephalomyopathy Associated with Cytochrome C Oxidase Deficiency

(2008) Daniele Ghezzi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH