Differential protein occupancy profiling of the mRNA transcriptome

Diversity in sequence-dependent control of GRO chemokine mRNA half-life

(2013) Tomasz Herjan et al.   JOURNAL OF LEUKOCYTE BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

How cells get the message: dynamic assembly and function of mRNA–protein complexes

(2013) Michaela Müller-McNicoll et al.   NATURE REVIEWS GENETICS

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR 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

Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins

(2012) Eric T. Wang et al.   CELL

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

Downregulation of HuR as a new mechanism of doxorubicin resistance in breast cancer cells

(2012) Elisa Latorre et al.   Molecular Cancer

LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor Abundance

(2012) Melissa L. Wilbert et al.   MOLECULAR CELL

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

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

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS 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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

(2011) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

doRiNA: a database of RNA interactions in post-transcriptional regulation

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide analysis of protein–RNA interactions using high-throughput sequencing

(2011) Miha Milek et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Identification of RNA-protein interaction networks using PAR-CLIP

(2011) Manuel Ascano et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

The Quaking family of RNA-binding proteins: Coordinators of the cell cycle and differentiation

(2010) Bjoern Biedermann et al.   CELL CYCLE

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RBPDB: a database of RNA-binding specificities

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

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

Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein

(2008) Kirsty Sawicka et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Post-transcriptional gene regulation by HuR promotes a more tumorigenic phenotype

(2008) K Mazan-Mamczarz et al.   ONCOGENE

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY