eCLIP
Assay76
Publications
63
geo_metadata
35
abstract
11
keywords_mesh
Publications
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy.
Neurobiology of disease
(2026)
PMID:41644016
geo_metadata
Single-cell and isoform-specific translational profiling of the mouse brain.
Nature
(2026)
PMID:41708856
geo_metadata
RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis.
The Journal of clinical investigation
(2026)
PMID:41746718
abstract
Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.
bioRxiv : the preprint server for biology
(2026)
PMID:41959526
abstract
geo_metadata
Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces.
Cell systems
(2026)
PMID:42025161
geo_metadata
abstract
keywords_mesh
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis.
bioRxiv : the preprint server for biology
(2025)
PMID:39868246
abstract
geo_metadata
Short 5' UTRs serve as a marker for viral mRNA translation inhibition by the IFIT2-IFIT3 antiviral complex.
bioRxiv : the preprint server for biology
(2025)
PMID:39990370
geo_metadata
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.
RNA (New York, N.Y.)
(2025)
PMID:40399037
geo_metadata
Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor.
RNA (New York, N.Y.)
(2025)
PMID:40441874
geo_metadata
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress.
Nature neuroscience
(2025)
PMID:40456907
geo_metadata
Genome-Wide Interrogation of SARS-CoV-2 RNA-Protein Interactions Uncovers Hidden Regulatory Sites.
bioRxiv : the preprint server for biology
(2025)
PMID:40501555
abstract
Integrative CRISPR Screens and RNA-Omics Discover an Essential Role for PUF60-3' Splice Site Interactions in Cancer Progression.
bioRxiv : the preprint server for biology
(2025)
PMID:40655003
abstract
The IFIT2-IFIT3 antiviral complex targets short 5' untranslated regions on viral mRNAs for translation inhibition.
Nature microbiology
(2025)
PMID:41093992
geo_metadata
Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.
bioRxiv : the preprint server for biology
(2025)
PMID:41278797
abstract
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.
Cancer research
(2025)
PMID:41411621
geo_metadata
abstract
circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.
bioRxiv : the preprint server for biology
(2024)
PMID:37745562
abstract
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function.
RNA (New York, N.Y.)
(2024)
PMID:38164626
keywords_mesh
geo_metadata
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.
Nature biotechnology
(2024)
PMID:38168984
geo_metadata
Transcriptome regulation by PARP13 in basal and antiviral states in human cells.
iScience
(2024)
PMID:38495826
abstract
A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
Nucleic acids research
(2024)
PMID:38554115
geo_metadata
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
Neuron
(2024)
PMID:38697111
geo_metadata
Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.
Cell genomics
(2024)
PMID:38955188
geo_metadata
abstract
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
Nature communications
(2024)
PMID:39152130
geo_metadata
Large-scale map of RNA-binding protein interactomes across the mRNA life cycle.
Molecular cell
(2024)
PMID:39303721
geo_metadata
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.
Molecular cell
(2024)
PMID:39303722
keywords_mesh
geo_metadata
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.
Nature methods
(2023)
PMID:36550273
abstract
geo_metadata
Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.
Nature communications
(2023)
PMID:36759613
geo_metadata
In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target.
Blood cancer discovery
(2023)
PMID:36763002
geo_metadata
Remodeling oncogenic transcriptomes by small molecules targeting NONO.
Nature chemical biology
(2023)
PMID:36864190
geo_metadata
Proteomic discovery of chemical probes that perturb protein complexes in human cells.
Molecular cell
(2023)
PMID:37084731
geo_metadata
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling.
Nucleic acids research
(2023)
PMID:37224531
geo_metadata
abstract
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics
(2023)
PMID:37388912
abstract
geo_metadata
HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.
Molecular cell
(2023)
PMID:37421941
abstract
geo_metadata
Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery.
Nucleic acids research
(2023)
PMID:37739431
abstract
geo_metadata
Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.
Cancer discovery
(2022)
PMID:34620690
geo_metadata
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
bioRxiv : the preprint server for biology
(2022)
PMID:35233578
geo_metadata
Crosstalk between CRISPR-Cas9 and the human transcriptome.
Nature communications
(2022)
PMID:35236841
geo_metadata
abstract
Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.
Cell reports
(2022)
PMID:35263585
geo_metadata
keywords_mesh
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
Research square
(2022)
PMID:35313591
geo_metadata
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.
Nature protocols
(2022)
PMID:35322209
geo_metadata
abstract
MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.
Science translational medicine
(2022)
PMID:35767654
abstract
geo_metadata
The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.
Nature communications
(2022)
PMID:35781533
geo_metadata
Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.
Molecular cell
(2021)
PMID:33852893
geo_metadata
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Nature methods
(2021)
PMID:33963355
geo_metadata
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.
Molecular cell
(2021)
PMID:34216543
abstract
geo_metadata
Non-microRNA binding competitively inhibits LIN28 regulation.
Cell reports
(2021)
PMID:34380031
geo_metadata
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
STAR protocols
(2021)
PMID:34485935
geo_metadata
abstract
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.
Nature communications
(2021)
PMID:34732726
geo_metadata
abstract
A multi-scale map of cell structure fusing protein images and interactions.
Nature
(2021)
PMID:34819669
geo_metadata
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
Genome biology
(2020)
PMID:32252787
keywords_mesh
abstract
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.
Genes & development
(2020)
PMID:32616519
geo_metadata
The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.
RNA (New York, N.Y.)
(2020)
PMID:32669294
geo_metadata
A large-scale binding and functional map of human RNA-binding proteins.
Nature
(2020)
PMID:32728246
geo_metadata
Large-scale tethered function assays identify factors that regulate mRNA stability and translation.
Nature structural & molecular biology
(2020)
PMID:32807991
geo_metadata
Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.
Proceedings of the National Academy of Sciences of the United States of America
(2020)
PMID:32848060
abstract
Context-dependent functional compensation between Ythdf m<sup>6</sup>A reader proteins.
Genes & development
(2020)
PMID:32943573
geo_metadata
Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
Molecular cell
(2020)
PMID:33242392
abstract
geo_metadata
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.
Genome medicine
(2020)
PMID:33287884
abstract
An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.
Nature cancer
(2020)
PMID:34109316
geo_metadata
abstract
RBP-Maps enables robust generation of splicing regulatory maps.
RNA (New York, N.Y.)
(2019)
PMID:30413564
abstract
keywords_mesh
A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
Molecular cell
(2019)
PMID:30527666
geo_metadata
Widespread RNA editing dysregulation in brains from autistic individuals.
Nature neuroscience
(2019)
PMID:30559470
geo_metadata
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.
Nature communications
(2019)
PMID:30902979
abstract
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.
Scientific reports
(2019)
PMID:31363146
geo_metadata
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell
(2019)
PMID:31588046
geo_metadata
Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels.
Molecular cell
(2018)
PMID:29547715
abstract
keywords_mesh
geo_metadata
Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9.
Nucleic acids research
(2018)
PMID:29733375
geo_metadata
Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.
Acta neuropathologica
(2018)
PMID:29881994
geo_metadata
CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.
Methods (San Diego, Calif.)
(2017)
PMID:28003131
geo_metadata
abstract
keywords_mesh
Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).
Methods in molecular biology (Clifton, N.J.)
(2017)
PMID:28766298
keywords_mesh
abstract
Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions.
Methods (San Diego, Calif.)
(2017)
PMID:28790018
geo_metadata
keywords_mesh
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Nature methods
(2016)
PMID:27018577
geo_metadata
abstract
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
Cell reports
(2016)
PMID:27068461
geo_metadata
abstract
Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.
Advances in experimental medicine and biology
(2016)
PMID:27256380
keywords_mesh
SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.
Molecular cell
(2016)
PMID:27720645
geo_metadata
abstract
Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.
Neuron
(2016)
PMID:27773581
geo_metadata