Tuning the engine

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

(2012) Alfredo Castello et al.   CELL

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon 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

DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways

(2012) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update)

(2012) A. Bisognin et al.   NUCLEIC ACIDS RESEARCH

Regulation of cellular iron metabolism

(2011) Jian Wang et al.   BIOCHEMICAL JOURNAL

AURA: Atlas of UTR Regulatory Activity

(2011) E. Dassi et al.   BIOINFORMATICS

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

mirConnX: condition-specific mRNA-microRNA network integrator

(2011) G. T. Huang et al.   NUCLEIC ACIDS RESEARCH

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Non-coding RNAs: Meet thy masters

(2010) Fabrício F. Costa   BIOESSAYS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

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

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

miRGator v2.0 : an integrated system for functional investigation of microRNAs

(2010) S. Cho et al.   NUCLEIC ACIDS RESEARCH

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

AREsite: a database for the comprehensive investigation of AU-rich elements

(2010) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

RBPDB: a database of RNA-binding specificities

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

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu 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

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

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

SIREs: searching for iron-responsive elements

(2010) M. Campillos et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

(2009) Giorgio Grillo et al.   NUCLEIC ACIDS RESEARCH

IRESite—a tool for the examination of viral and cellular internal ribosome entry sites

(2009) Martin Mokrejš et al.   NUCLEIC ACIDS RESEARCH

To localize or not to localize: mRNA fate is in 3′UTR ends

(2009) Catia Andreassi et al.   TRENDS IN CELL BIOLOGY

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

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

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

(2008) Sergi Castellano et al.   NUCLEIC ACIDS RESEARCH

NRED: a database of long noncoding RNA expression

(2008) Marcel E. Dinger et al.   NUCLEIC ACIDS RESEARCH

Transterm: a database to aid the analysis of regulatory sequences in mRNAs

(2008) G. H. Jacobs et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

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