High-throughput discovery of post-transcriptional cis-regulatory elements

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

(2015) Shiran Naftelberg et al.   Annual Review of Biochemistry

Systematic analysis of theHmga23′ UTR identifies many independent regulatory sequences and a novel interaction between distal sites

(2015) Katla Kristjánsdóttir et al.   RNA

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Principles and Properties of Eukaryotic mRNPs

(2014) Sarah F. Mitchell 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

Massively parallel functional annotation of 3′ untranslated regions

(2014) Wenxue Zhao et al.   NATURE BIOTECHNOLOGY

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Systematic Identification of Regulatory Elements in Conserved 3′ UTRs of Human Transcripts

(2014) Panos Oikonomou et al.   Cell Reports

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

The RNA-binding protein repertoire of embryonic stem cells

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

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

CUG binding protein 1 binds to a specific region within the human albumin 3′ untranslated region

(2012) Siavash Khaziapoul et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2012) Alfredo Castello et al.   CELL

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC

(2012) Marc R Fabian et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells.

(2012) Eva Matoulkova et al.   RNA Biology

RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay

(2012) K. M. Dean et al.   RNA

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

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

A Systematic Analysis of the 3′UTR of HNF4A mRNA Reveals an Interplay of Regulatory Elements Including miRNA Target Sites

(2011) Andrea Wirsing et al.   PLoS One

Upf1 Senses 3′UTR Length to Potentiate mRNA Decay

(2010) J. Robert Hogg et al.   CELL

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

(2010) Markus Hafner et al.   CELL

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

(2009) Melissa J. Moore et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

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

(2008) Donny D. Licatalosi et al.   NATURE

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE