starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

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

(2010) Markus Hafner et al.   CELL

Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

(2010) Chanseok Shin et al.   MOLECULAR CELL

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

RNA processing and its regulation: global insights into biological networks

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

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

(2009) Gene W Yeo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ensembl Genomes: Extending Ensembl across the taxonomic space

(2009) P. J. Kersey et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

deepBase: a database for deeply annotating and mining deep sequencing data

(2009) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Rice MicroRNA Effector Complexes and Targets

(2009) L. Wu et al.   PLANT CELL

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

MicroRNA-10a Binds the 5′UTR of Ribosomal Protein mRNAs and Enhances Their Translation

(2008) Ulf Andersson Ørom et al.   MOLECULAR CELL

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

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

(2008) Donny D. Licatalosi et al.   NATURE

MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation

(2008) Yvonne Tay et al.   NATURE

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

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

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

The database of experimentally supported targets: a functional update of TarBase

(2008) G. L. Papadopoulos et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH