Related references
Note: Only part of the references are listed.m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome
Yujiao Tang et al.
NUCLEIC ACIDS RESEARCH (2021)
RNA-binding proteins in human genetic disease
Fatima Gebauer et al.
NATURE REVIEWS GENETICS (2021)
RNA-Centric Methods: Toward the Interactome of Specific RNA Transcripts
Cathrin Grawe et al.
TRENDS IN BIOTECHNOLOGY (2021)
The SARS-CoV-2 RNA-protein interactome in infected human cells
Nora Schmidt et al.
NATURE MICROBIOLOGY (2021)
The kinetic landscape of an RNA-binding protein in cells
Deepak Sharma et al.
NATURE (2021)
A framework for understanding the functions of biomolecular condensates across scales
Andrew S. Lyon et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)
Current approaches for RNA-labelling to identify RNA-binding proteins
Darren Gemmill et al.
BIOCHEMISTRY AND CELL BIOLOGY (2020)
CLIP and RNA interactome studies to unravel genome-wide RNA-protein interactions in vivo in Arabidopsis thaliana
Tino Koester et al.
METHODS (2020)
Improved library preparation with the new iCLIP2 protocol
Andreas Buchbender et al.
METHODS (2020)
dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity
Carlos Marti-Gomez et al.
BIOINFORMATICS (2020)
Deep neural networks for interpreting RNA-binding protein target preferences
Mahsa Ghanbari et al.
GENOME RESEARCH (2020)
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Martin Lewinski et al.
BMC BIOINFORMATICS (2020)
Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA
Robert D. Patton et al.
RNA (2020)
Mechanisms and Regulation of RNA Condensation in RNP Granule Formation
Devin Tauber et al.
TRENDS IN BIOCHEMICAL SCIENCES (2020)
AirID, a novel proximity biotinylation enzyme, for analysis of protein-protein interactions
Kohki Kido et al.
ELIFE (2020)
How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms
Meredith Corley et al.
MOLECULAR CELL (2020)
RIC-seq for global in situ profiling of RNA-RNA spatial interactions
Zhaokui Cai et al.
NATURE (2020)
Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method
Marcel Bach-Pages et al.
BIOMOLECULES (2020)
FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences
Raeann Goering et al.
ELIFE (2020)
How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets
Charlotte Capitanchik et al.
FRONTIERS IN GENETICS (2020)
SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses
Abhik K. Banerjee et al.
CELL (2020)
A large-scale binding and functional map of human RNA-binding proteins
Eric L. Van Nostrand et al.
NATURE (2020)
CRISPR-assisted detection of RNA-protein interactions in living cells
Wenkai Yi et al.
NATURE METHODS (2020)
The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae
Nuria Casas-Vila et al.
NATURE COMMUNICATIONS (2020)
A protein assembly mediates Xist localization and gene silencing
Amy Pandya-Jones et al.
NATURE (2020)
RNA-protein interaction mapping via MS2-or Cas13-based APEX targeting
Shuo Han et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces
Meredith Corley et al.
MOLECULAR CELL (2020)
Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells
Maria Dermit et al.
DEVELOPMENTAL CELL (2020)
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
Eric L. Van Nostrand et al.
GENOME BIOLOGY (2020)
POSTAR2: deciphering the post-transcriptional regulatory logics
Yumin Zhu et al.
NUCLEIC ACIDS RESEARCH (2019)
Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA-Binding Proteins: A Hypothesis
Jan Attig et al.
BIOESSAYS (2019)
The Small Non-coding Vault RNA1-1 Acts as a Riboregulator of Autophagy
Rastislav Horos et al.
CELL (2019)
Methods to study RNA-protein interactions
Muthukumar Ramanathan et al.
NATURE METHODS (2019)
SpyCLIP: an easy-to-use and high-throughput compatible CLIP platform for the characterization of protein-RNA interactions with high accuracy
Ya Zhao et al.
NUCLEIC ACIDS RESEARCH (2019)
Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition
Miha Modic et al.
MOLECULAR CELL (2019)
Beyond CLIP: advances and opportunities to measure RBP-RNA and RNA-RNA interactions
Chenyu Lin et al.
NUCLEIC ACIDS RESEARCH (2019)
Enhanced Crosslinking Immunoprecipitation (eCLIP) Method for Efficient Identification of Protein-bound RNA in Mouse Testis
Qiushi Xu et al.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2019)
Atlas of Subcellular RNA Localization Revealed by APEX-Seq
Furqan M. Fazal et al.
CELL (2019)
Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3
Saifeng Wang et al.
GENES & DEVELOPMENT (2019)
Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites
Huijuan Feng et al.
MOLECULAR CELL (2019)
β-Actin mRNA interactome mapping by proximity biotinylation
Joyita Mukherjee et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Neuronal ribonucleoprotein granules: Dynamic sensors of localized signals
Nadia Formicola et al.
TRAFFIC (2019)
Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules
Alejandro Padron et al.
MOLECULAR CELL (2019)
A systems view of spliceosomal assembly and branchpoints with iCLIP
Michael Briese et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution
Jernej Ule et al.
MOLECULAR CELL (2019)
Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling
Pengchong Wang et al.
NATURE CHEMICAL BIOLOGY (2019)
Identification of proteins and miRNAs that specifically bind an mRNA in vivo
Kathrin Theil et al.
NATURE COMMUNICATIONS (2019)
Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function
Yuhki Saito et al.
NEURON (2019)
Deciphering human ribonucleoprotein regulatory networks
Neelanjan Mukherjee et al.
NUCLEIC ACIDS RESEARCH (2019)
Directed Evolution of Split APEX2 Peroxidase
Yisu Han et al.
ACS CHEMICAL BIOLOGY (2019)
dLimited antibody specificity compromises epitranscriptomic analyses
Mark Helm et al.
NATURE COMMUNICATIONS (2019)
FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
Kirsty Sawicka et al.
ELIFE (2019)
Mechanistic implications of enhanced editing by a HyperTRIBE RNA-binding protein
Weijin Xu et al.
RNA (2018)
Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA-Protein Complexes
Ying Li et al.
BIOCHEMISTRY (2018)
In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
F. X. Reymond Sutandy et al.
GENOME RESEARCH (2018)
Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) Identifies Kaposi's Sarcoma-Associated Herpesvirus MicroRNA Targets in Endothelial Cells
Lauren A. Gay et al.
JOURNAL OF VIROLOGY (2018)
Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation
Tomohiro Yamazaki et al.
MOLECULAR CELL (2018)
Advances in CLIP Technologies for Studies of Protein-RNA Interactions
Flora C. Y. Lee et al.
MOLECULAR CELL (2018)
Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing
Jan Attig et al.
CELL (2018)
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability
Mathias Munschauer et al.
NATURE (2018)
Efficient proximity labeling in living cells and organisms with TurboID
Tess C. Branon et al.
NATURE BIOTECHNOLOGY (2018)
The Future of Cross-Linking and Immunoprecipitation (CLIP)
Jernej Ule et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2018)
microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions
Maria D. Paraskevopoulou et al.
NATURE COMMUNICATIONS (2018)
Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Lorea Blazquez et al.
MOLECULAR CELL (2018)
Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments
Daniel Benhalevy et al.
NATURE METHODS (2018)
CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals
Sihyung Park et al.
NUCLEIC ACIDS RESEARCH (2018)
Investigations on the interface of nucleic acid aptamers and binding targets
Shundong Cai et al.
ANALYST (2018)
Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
Andreas J. Gruber et al.
GENOME BIOLOGY (2018)
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
Philipp Drewe-Boss et al.
GENOME BIOLOGY (2018)
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
Ankeeta Shah et al.
BIOINFORMATICS (2017)
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
Tom Smith et al.
GENOME RESEARCH (2017)
A versatile tandem RNA isolation procedure to capture in vivo formed mRNA-protein complexes
Ana M. Matia-Gonzalez et al.
METHODS (2017)
DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs
Masashi Yamaji et al.
NATURE (2017)
cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation
Hun-Way Hwang et al.
NEURON (2017)
CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome
Zijun Zhang et al.
NUCLEIC ACIDS RESEARCH (2017)
Specific RNP capture with antisense LNA/DNA mixmers
Birgit Rogell et al.
RNA (2017)
RNA-Binding Proteins Revisited - The Emerging Arabidopsis mRNA Interactome
Tino Koester et al.
TRENDS IN PLANT SCIENCE (2017)
High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43
Gregor Rot et al.
CELL REPORTS (2017)
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
Pornchai Kaewsapsak et al.
ELIFE (2017)
PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data
Sabrina Krakau et al.
GENOME BIOLOGY (2017)
Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7
Katja Meyer et al.
GENOME BIOLOGY (2017)
Assaying RNA Localization in Situ with Spatially Restricted Nucleobase Oxidation
Ying Li et al.
ACS CHEMICAL BIOLOGY (2017)
Dynamic RNA Modifications in Gene Expression Regulation
Ian A. Roundtree et al.
CELL (2017)
A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate
Shawn W. Foley et al.
DEVELOPMENTAL CELL (2017)
BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data
Monica Golumbeanu et al.
BIOINFORMATICS (2016)
catRAPID signature: identification of ribonucleoproteins and RNA-binding regions
Carmen Maria Livi et al.
BIOINFORMATICS (2016)
Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation
Jeff G. Blackinton et al.
NUCLEIC ACIDS RESEARCH (2016)
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins
Martin Strazar et al.
BIOINFORMATICS (2016)
TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins
Aoife C. McMahon et al.
CELL (2016)
Decoding the RNA structurome
Zhipeng Lu et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
Erik Holmqvist et al.
EMBO JOURNAL (2016)
The interaction of PRC2 with RNA or chromatin is mutually antagonistic
Manuel Beltran et al.
GENOME RESEARCH (2016)
An improved smaller biotin ligase for BioID proximity labeling
Dae In Kim et al.
MOLECULAR BIOLOGY OF THE CELL (2016)
Sequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasm
Anastassios Vourekas et al.
NATURE (2016)
irCLIP platform for efficient characterization of protein-RNA interactions
Brian J. Zarnegar et al.
NATURE METHODS (2016)
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Eric L. Van Nostrand et al.
NATURE METHODS (2016)
Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2
Victoria Hung et al.
NATURE PROTOCOLS (2016)
Lessons from non-canonical splicing
Christopher R. Sibley et al.
NATURE REVIEWS GENETICS (2016)
A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications
Marco Pietrosanto et al.
NUCLEIC ACIDS RESEARCH (2016)
In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings
Marlene Reichel et al.
PLANT CELL (2016)
UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts
Zhicheng Zhang et al.
PLANT METHODS (2016)
The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila
Qingqing Wang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
High-throughput analyses of hnRNP H1 dissects its multi-functional aspect
Philip J. Uren et al.
RNA BIOLOGY (2016)
An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR
Emily K. Meredith et al.
RNA (2016)
Generation of Recombinant Polioviruses Harboring RNA Affinity Tags in the 5′ and 3′ Noncoding Regions of Genomic RNAs
Dylan Flather et al.
VIRUSES-BASEL (2016)
ATtRACT-a database of RNA-binding proteins and associated motifs
Girolamo Giudice et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)
The RNA-binding protein repertoire of Arabidopsis thaliana
Claudius Marondedze et al.
SCIENTIFIC REPORTS (2016)
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Federico Comoglio et al.
BMC BIOINFORMATICS (2015)
Systematic Discovery of Xist RNA Binding Proteins
Ci Chu et al.
CELL (2015)
Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation
Yong Zhang et al.
CELL RESEARCH (2015)
The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing
Anastassios Vourekas et al.
GENES & DEVELOPMENT (2015)
Quantifying the strength of miRNA-target interactions
Jeremie Breda et al.
METHODS (2015)
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3
Colleen A. McHugh et al.
NATURE (2015)
hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1
Yoichiro Sugimoto et al.
NATURE (2015)
Recursive splicing in long vertebrate genes
Christopher R. Sibley et al.
NATURE (2015)
N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions
Nian Liu et al.
NATURE (2015)
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi et al.
NATURE BIOTECHNOLOGY (2015)
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
Bastian Linder et al.
NATURE METHODS (2015)
Specificity and nonspecificity in RNA-protein interactions
Eckhard Jankowsky et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)
MS2 coat proteins bound to yeast mRNAs block 5 ' to 3 ' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system
Jennifer F. Garcia et al.
RNA (2015)
The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs
Benedikt M. Beckmann et al.
NATURE COMMUNICATIONS (2015)
Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1
Luis Apolonia et al.
PLOS PATHOGENS (2015)
Leveraging cross-link modification events in CLIP-seq for motif discovery
Emad Bahrami-Samani et al.
NUCLEIC ACIDS RESEARCH (2015)
DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation
Kai Blin et al.
NUCLEIC ACIDS RESEARCH (2015)
Dissecting noncoding and pathogen RNA-protein interactomes
Ryan A. Flynn et al.
RNA (2015)
Global Changes in the RNA Binding Specificity of HIV-1 Gag Regulate Virion Genesis
Sebla B. Kutluay et al.
CELL (2014)
RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins
Nicole Lambert et al.
MOLECULAR CELL (2014)
Unambiguous Identification of miRNA: Target Site Interactions by Different Types of Ligation Reactions
Stefanie Grosswendt et al.
MOLECULAR CELL (2014)
Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli
Jai J. Tree et al.
MOLECULAR CELL (2014)
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
Katharina Kramer et al.
NATURE METHODS (2014)
Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis
Michael J. Moore et al.
NATURE PROTOCOLS (2014)
A census of human RNA-binding proteins
Stefanie Gerstberger et al.
NATURE REVIEWS GENETICS (2014)
Rbfox3 controls the biogenesis of a subset of microRNAs
Kee K. Kim et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)
iCLIP: Protein-RNA interactions at nucleotide resolution
Ina Huppertz et al.
METHODS (2014)
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
Jun-Hao Li et al.
NUCLEIC ACIDS RESEARCH (2014)
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
Aurelie Kapusta et al.
TRENDS IN GENETICS (2014)
Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs
Matthew B. Friedersdorf et al.
GENOME BIOLOGY (2014)
GraphProt: modeling binding preferences of RNA-binding proteins
Daniel Maticzka et al.
GENOME BIOLOGY (2014)
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data
Tsukasa Fukunaga et al.
GENOME BIOLOGY (2014)
Scientific migration of junior scientists to China
Ling-Ling Chen
GENOME BIOLOGY (2014)
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
Alper Kucukural et al.
BIOINFORMATICS (2013)
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Helga Thorvaldsdottir et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding
Aleksandra Helwak et al.
CELL (2013)
Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements
Kathi Zarnack et al.
CELL (2013)
Tissue-specific control of brain-enriched miR-7 biogenesis
Nila Roy Choudhury et al.
GENES & DEVELOPMENT (2013)
A compendium of RNA-binding motifs for decoding gene regulation
Debashish Ray et al.
NATURE (2013)
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets
Mohsen Khorshid et al.
NATURE METHODS (2013)
The CRAPome: a contaminant repository for affinity purification-mass spectrometry data
Dattatreya Mellacheruvu et al.
NATURE METHODS (2013)
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges
Michael T. Lovci et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)
RNA-protein analysis using a conditional CRISPR nuclease
Ho Young Lee et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression
Anneke Bruemmer et al.
RNA (2013)
NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs
Shobbir Hussain et al.
CELL REPORTS (2013)
A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana
Christoph Schmal et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Site identification in high-throughput RNA-protein interaction data
Philip J. Uren et al.
BIOINFORMATICS (2012)
Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins
Alfredo Castello et al.
CELL (2012)
Transcriptome-wide Analysis of Exosome Targets
Claudia Schneider et al.
MOLECULAR CELL (2012)
Protein-RNA interactions: new genomic technologies and perspectives
Julian Koenig et al.
NATURE REVIEWS GENETICS (2012)
Mill and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis
Anastassios Vourekas et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)
MS2-TRAP (MS2-tagged RNA affinity purification): Tagging RNA to identify associated miRNAs
Je-Hyun Yoon et al.
METHODS (2012)
Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
Boris Rogelj et al.
SCIENTIFIC REPORTS (2012)
Identification of RNA-protein interaction networks using PAR-CLIP
Manuel Ascano et al.
WILEY INTERDISCIPLINARY REVIEWS-RNA (2012)
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Yoichiro Sugimoto et al.
GENOME BIOLOGY (2012)
FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism
Jennifer C. Darnell et al.
CELL (2011)
Viral MicroRNA Targetome of KSHV-Infected Primary Effusion Lymphoma Cell Lines
Eva Gottwein et al.
CELL HOST & MICROBE (2011)
A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1
Jane E. Wright et al.
EMBO JOURNAL (2011)
Quantitative Profiling of In Vivo-assembled RNA-Protein Complexes Using a Novel Integrated Proteomic Approach
Becky Pinjou Tsai et al.
MOLECULAR & CELLULAR PROTEOMICS (2011)
In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites
Anna-Carina Jungkamp et al.
MOLECULAR CELL (2011)
Quantitative analysis demonstrates most transcription factors require only simple models of specificity
Yue Zhao et al.
NATURE BIOTECHNOLOGY (2011)
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data
Chaolin Zhang et al.
NATURE BIOTECHNOLOGY (2011)
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins
Shivendra Kishore et al.
NATURE METHODS (2011)
Characterizing the RNA targets and position-dependent splicing regulation by TDP-43
James R. Tollervey et al.
NATURE NEUROSCIENCE (2011)
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain
Adam Ameur et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)
The genomic binding sites of a noncoding RNA
Matthew D. Simon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries
Markus Hafner et al.
RNA (2011)
Understanding splicing regulation through RNA splicing maps
Joshua T. Witten et al.
TRENDS IN GENETICS (2011)
Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
Markus Hafner et al.
CELL (2010)
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz et al.
MOLECULAR CELL (2010)
APPLICATIONS OF NEXT-GENERATION SEQUENCING RNA processing and its regulation: global insights into biological networks
Donny D. Licatalosi et al.
NATURE REVIEWS GENETICS (2010)
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans
Dimitrios G. Zisoulis et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
Julian Koenig et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)
Nucleolin binds to a subset of selenoprotein mRNAs and regulates their expression
Angela C. Miniard et al.
NUCLEIC ACIDS RESEARCH (2010)
A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes
Boris Slobodin et al.
RNA (2010)
iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions
Zhen Wang et al.
PLOS BIOLOGY (2010)
How Common Are Extraribosomal Functions of Ribosomal Proteins?
Jonathan R. Warner et al.
MOLECULAR CELL (2009)
Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
Sung Wook Chi et al.
NATURE (2009)
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Debashish Ray et al.
NATURE BIOTECHNOLOGY (2009)
TU-tagging: cell type-specific RNA isolation from intact complex tissues
Michael R. Miller et al.
NATURE METHODS (2009)
MEME SUITE: tools for motif discovery and searching
Timothy L. Bailey et al.
NUCLEIC ACIDS RESEARCH (2009)
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
Sander Granneman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Diversity and Complexity in DNA Recognition by Transcription Factors
Gwenael Badis et al.
SCIENCE (2009)
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Nicholas T. Ingolia et al.
SCIENCE (2009)
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Donny D. Licatalosi et al.
NATURE (2008)
Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing
Markus Hafner et al.
METHODS (2008)
Database resources of the national center for biotechnology information
David L. Wheeler et al.
NUCLEIC ACIDS RESEARCH (2008)
RNA-binding proteins: modular design for efficient function
Bradley M. Lunde et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)
RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation
J. Robert Hogg et al.
RNA (2007)
An RNA map predicting Nova-dependent splicing regulation
Jernej Ule et al.
NATURE (2006)
Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions
Jochen Deckert et al.
MOLECULAR AND CELLULAR BIOLOGY (2006)
In vivo identification of ribonucleoprotein-RNA interactions
J Zielinski et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
A protocol for PAIR : PNA-assisted identification of RNA binding proteins in living cells
Fanyi Zeng et al.
NATURE PROTOCOLS (2006)
Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer
Nikolai Windbichler et al.
NATURE PROTOCOLS (2006)
CLIP: A method for identifying protein-RNA interaction sites in living cells
J Ule et al.
METHODS (2005)
PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny
Rahul Siddharthan et al.
PLOS COMPUTATIONAL BIOLOGY (2005)
Targeted and proximity-dependent promiscuous protein biotinylation by a mutant Escherichia coli biotin protein ligase
JE Cronan
JOURNAL OF NUTRITIONAL BIOCHEMISTRY (2005)
Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties
T Blondal et al.
NUCLEIC ACIDS RESEARCH (2005)
Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses
S Mili et al.
RNA (2004)
CLIP identifies Nova-regulated RNA networks in the brain
J Ule et al.
SCIENCE (2003)
Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method
K Hartmuth et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo
S Niranjanakumari et al.
METHODS (2002)
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
NC Lau et al.
SCIENCE (2001)
Translational repression and specific RNA binding by the coat protein of the Pseudomonas phage PP7
F Lim et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays
SA Tenenbaum et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)
Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase
B van Steensel et al.
NATURE BIOTECHNOLOGY (2000)
Share Paper
