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

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

(2012) Rasna R Walia et al.   BMC BIOINFORMATICS

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

(2012) Alfredo Castello et al.   CELL

Functional Interplay between RNA-Binding Protein HuR and microRNAs

(2012) Subramanya Srikantan et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

(2012) Hani Goodarzi et al.   NATURE

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

(2012) Minna-Liisa Änkö et al.   GENOME BIOLOGY

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

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

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

(2011) B. J. Parker et al.   GENOME RESEARCH

Genomic Analyses of the RNA-binding Protein Hu Antigen R (HuR) Identify a Complex Network of Target Genes and Novel Characteristics of Its Binding Sites

(2011) Philip J. Uren et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrating post-transcriptional regulation into the embryonic stem cell gene regulatory network

(2011) Paul A. Cassar et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Interplay between Posttranscriptional and Posttranslational Interactions of RNA-Binding Proteins

(2011) Nitish Mittal et al.   JOURNAL OF MOLECULAR BIOLOGY

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Intranasal delivery to the brain

(2011) Robert I Henkin   NATURE BIOTECHNOLOGY

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

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

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

(2011) Shivendra Kishore et al.   NATURE METHODS

Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction

(2011) Huiying Zhao et al.   RNA Biology

Gene regulation by RNA binding proteins and microRNAs in angiogenesis

(2011) Sung-Hee Chang et al.   TRENDS IN MOLECULAR MEDICINE

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Identification of RNA-protein interaction networks using PAR-CLIP

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

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

SVM based prediction of RNA-binding proteins using binding residues and evolutionary information

(2010) Manish Kumar et al.   JOURNAL OF MOLECULAR RECOGNITION

A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility

(2010) Martijn Kedde et al.   NATURE CELL BIOLOGY

Grand Challenge Commentary: RNA epigenetics?

(2010) Chuan He   Nature Chemical Biology

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

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

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

(2010) Daniel P. Riordan et al.   NUCLEIC ACIDS RESEARCH

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

(2010) H. Zhao et al.   NUCLEIC ACIDS RESEARCH

Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae

(2010) Nikoleta G. Tsvetanova et al.   PLoS One

A Screen for RNA-Binding Proteins in Yeast Indicates Dual Functions for Many Enzymes

(2010) Tanja Scherrer et al.   PLoS One

A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue; identification of potential players in tumor formation

(2010) Pedro A. F. Galante et al.   RNA Biology

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

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

Genome-wide analysis of mRNA decay patterns during early Drosophila development

(2010) Stefan Thomsen et al.   GENOME BIOLOGY

Protein function annotation from sequence: prediction of residues interacting with RNA

(2009) R. V. Spriggs et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling

(2009) Shaohui Hu et al.   CELL

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Predicting DNA- and RNA-binding proteins from sequences with kernel methods

(2009) Xiaojian Shao et al.   JOURNAL OF THEORETICAL BIOLOGY

SR Proteins in Vertical Integration of Gene Expression from Transcription to RNA Processing to Translation

(2009) Xiang-Yang Zhong et al.   MOLECULAR CELL

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

(2009) Barrett C Foat et al.   Molecular Systems Biology

Coordinated posttranscriptional mRNA population dynamics during T-cell activation

(2009) Neelanjan Mukherjee et al.   Molecular Systems Biology

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

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2

(2009) Agnieszka Rybak et al.   NATURE CELL BIOLOGY

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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

Unbiased RNA-protein interaction screen by quantitative proteomics

(2009) F. Butter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

The RNA infrastructure: dark matter of the eukaryotic cell?

(2009) Lesley J. Collins et al.   TRENDS IN GENETICS

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

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Eukaryotic gene regulation in three dimensions and its impact on genome evolution

(2008) M Madan Babu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

RNA-binding proteins and post-transcriptional gene regulation

(2008) Tina Glisovic et al.   FEBS LETTERS

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

A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment

(2008) Agnieszka Rybak et al.   NATURE CELL BIOLOGY

Detecting microRNA binding and siRNA off-target effects from expression data

(2008) Stijn van Dongen et al.   NATURE METHODS

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System

(2008) Alessia Galgano et al.   PLoS One

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

(2008) M. Rabani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY