Protein–RNA interactions: new genomic technologies and perspectives

Fast and accurate short read alignment with Burrows-Wheeler transform

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

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TopHat: discovering splice junctions with RNA-Seq

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MEME SUITE: tools for motif discovery and searching

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Mammalian microRNAs predominantly act to decrease target mRNA levels

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

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

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

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Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

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

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RNA regulons: coordination of post-transcriptional events

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

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CLIP Identifies Nova-Regulated RNA Networks in the Brain

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Counting absolute numbers of molecules using unique molecular identifiers

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From Birth to Death: The Complex Lives of Eukaryotic mRNAs

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A window into third-generation sequencing

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Nascent transcript sequencing visualizes transcription at nucleotide resolution

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

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

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Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability

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CLIP: A method for identifying protein–RNA interaction sites in living cells

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Defining mechanisms that regulate RNA polymerase II transcription in vivo

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

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The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a

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

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An RNA map predicting Nova-dependent splicing regulation

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

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

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Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays

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

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Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses

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Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

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PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

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RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

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Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast

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Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

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PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny

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Understanding splicing regulation through RNA splicing maps

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Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

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iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

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CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

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The fungal RNA‐binding protein Rrm4 mediates long‐distance transport of ubi1 and rho3 mRNAs

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A two-tracked approach to analyze RNA–protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles

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Finding the right RNA: Identification of cellular mRNA substrates for RNA-binding proteins

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Characterization of the mRNA ligands bound by the RNA binding protein hnRNP A2 utilizing a novel in vivo technique

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Erratum: Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

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Mechanisms and Regulation of Alternative Pre-mRNA Splicing

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Regulation by 3′-Untranslated Regions

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Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

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Quantitative neuroanatomy for connectomics in Drosophila

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The neurogenetics of alternative splicing

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Kinesin-1–syntaphilin coupling mediates activity-dependent regulation of axonal mitochondrial transport

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Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

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Soluble forms of tau are toxic in Alzheimer's disease

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RNA Protein Interaction in Neurons

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Alternative splicing: decoding an expansive regulatory layer

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Motor neuron mitochondrial dysfunction in spinal muscular atrophy

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A PGAM5–KEAP1–Nrf2 complex is required for stress-induced mitochondrial retrograde trafficking

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Age-Related Phasic Patterns of Mitochondrial Maintenance in Adult<i>Caenorhabditis elegans</i>Neurons

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MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells

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The Tissue-Specific RNA Binding Protein T-STAR Controls Regional Splicing Patterns of Neurexin Pre-mRNAs in the Brain

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Cooperation and competition by RNA-binding proteins in cancer

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RNA-Binding Proteins Hold Key Roles in Function, Dysfunction, and Disease

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RNA-binding protein-mediated post-transcriptional controls of gene expression: Integration of molecular mechanisms at the 3′ end of mRNAs?

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The complex world of post-transcriptional mechanisms: is their deregulation a common link for diseases? Focus on ELAV-like RNA-binding proteins

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RNA binding proteins in MLL-rearranged leukemia

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