R3561S last accessed: 2022-11-04

dorina
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:07.319245

Other names: database of RNA interactions in post-transcriptional regulation, dorina

Database of RNA interactions in post-transcriptional regulation.

Webpage:

http://dorina.mdc-berlin.de

Licence:

Name: Copyrights
URL: https://www.mdc-berlin.de/de/impressum

Publications:

Publications
More detailed information about this field from each metasource.

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
PMID: 20371350
metasource: Fairsharing.org
version: FAIRsharing.org: doRiNA; doRiNA; DOI: https://doi.org/10.25504/FAIRsharing.z0ea6a; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

A genome-wide map of conserved microRNA targets in C. elegans
PMID: 16458514
metasource: Fairsharing.org
version: FAIRsharing.org: doRiNA; doRiNA; DOI: https://doi.org/10.25504/FAIRsharing.z0ea6a; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation
PMID: 25416797
metasource: Fairsharing.org
version: FAIRsharing.org: doRiNA; doRiNA; DOI: https://doi.org/10.25504/FAIRsharing.z0ea6a; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:07.319245

http://dx.doi.org/10.1093/nar/
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP PubMed citations: 1493.

1493 articles citing: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4. PMID:35927243
Circular RNA circPBX3 promotes cisplatin resistance of ovarian cancer cells via interacting with IGF2BP2 to stabilize ATP7A mRNA expression. PMID:35907138
RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites. PMID:35819951
Upregulated miRNAs on the TP53 and RB1 Binding Seedless Regions in High-Risk HPV-Associated Penile Cancer. PMID:35812732
Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil. PMID:35796990
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information. PMID:35758792
Anatomy of four human Argonaute proteins. PMID:35736234
PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing. PMID:35736218
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. PMID:35729321
Dual function of SF3B2 on chromatin and RNA to regulate transcription in head and neck squamous cell carcinoma. PMID:35715826
Ribonomics Approaches to Identify RBPome in Plants and Other Eukaryotes: Current Progress and Future Prospects. PMID:35682602
The Emerging Role of Long Non-Coding RNAs in Esophageal Cancer: Functions in Tumorigenesis and Clinical Implications. PMID:35645836
Constant light exposure in early life induces m6A-mediated inhibition of IGF gene family in the chicken. PMID:35641104
Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes. PMID:35581222
Improved Methods for Deamination-Based m6A Detection. PMID:35573664
Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate. PMID:35544276
Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs. PMID:35513423
Epitranscriptomics of SARS-CoV-2 Infection. PMID:35465335
Circular RNA and Its Roles in the Occurrence, Development, Diagnosis of Cancer. PMID:35463362
Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling. PMID:35441143
Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. PMID:35413291
Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants. PMID:35409060
A Brief Review of circRNA Biogenesis, Detection, and Function. PMID:35386433
RNA-binding proteins in diabetic microangiopathy. PMID:35385161
Impaired neurogenesis alters brain biomechanics in a neuroprogenitor-based genetic subtype of congenital hydrocephalus. PMID:35379995
PUMILIO proteins promote colorectal cancer growth via suppressing p21. PMID:35338151
Protein synthesis control in cancer: selectivity and therapeutic targeting. PMID:35315941
Integrative approaches for studying the role of noncoding RNAs in influencing drug efficacy and toxicity. PMID:35296201
CircITGB6 promotes ovarian cancer cisplatin resistance by resetting tumor-associated macrophage polarization toward the M2 phenotype. PMID:35277458
Pum2 and TDP-43 refine area-specific cytoarchitecture post-mitotically and modulate translation of Sox5, Bcl11b, and Rorb mRNAs in developing mouse neocortex. PMID:35262486
Engineering miRNA features into siRNAs: Guide-strand bulges are compatible with gene repression. PMID:35251767
MicroRNA editing patterns in Huntington's disease. PMID:35210471
Inferring RNA-binding protein target preferences using adversarial domain adaptation. PMID:35202389
Hsa-miR-183-5p Modulates Cell Adhesion by Repression of ITGB1 Expression in Prostate Cancer. PMID:35202085
Site-Specific Profiling of 4-Thiouridine Across Transfer RNA Genes in Escherichia coli. PMID:35155896
The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. PMID:35137201
Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data. PMID:35135477
N 6-methyladenosine enhances post-transcriptional gene regulation by microRNAs. PMID:35098135
Screening and Comprehensive Analysis of Cancer-Associated tRNA-Derived Fragments. PMID:35095997
Interplay between K-RAS and miRNAs. PMID:35093302
Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. PMID:35087521
A cerebrospinal fluid microRNA analysis: Progressive supranuclear palsy. PMID:35039873
Comment on: The m6A Reader IGF2BP2 Regulates Macrophage Phenotypic Activation and Inflammatory Diseases by Stabilizing TSC1 and PPARγ. PMID:35038236
An adipose lncRAP2-Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs. PMID:35036870
EWSR1-induced circNEIL3 promotes glioma progression and exosome-mediated macrophage immunosuppressive polarization via stabilizing IGF2BP3. PMID:35031058
miR-214-5p Regulating Differentiation of Intramuscular Preadipocytes in Goats via Targeting KLF12. PMID:35003206
Robust T cell activation requires an eIF3-driven burst in T cell receptor translation. PMID:34970966
Regulation of retinal amacrine cell generation by miR-216b and Foxn3. PMID:34919141
Development of an RNA-protein crosslinker to capture protein interactions with diverse RNA structures in cells. PMID:34916333
Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PMID:34914716
The RNA-binding protein IMP2 drives a stromal-Th17 cell circuit in autoimmune neuroinflammation. PMID:34914635
Research progress on the tsRNA classification, function, and application in gynecological malignant tumors. PMID:34907180
Genome-wide identification of microRNA targets reveals positive regulation of the Hippo pathway by miR-122 during liver development. PMID:34907157
Regulating Polyamine Metabolism by miRNAs in Diabetic Cardiomyopathy. PMID:34902085
Contributions of microRNAs to Peripheral Insulin Sensitivity. PMID:34882766
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. PMID:34850920
RNA Binding Proteins as Pioneer Determinants of Infection: Protective, Proviral, or Both? PMID:34834978
Protein-RNA Interactome Analysis Reveals Wide Association of Kaposi's Sarcoma-Associated Herpesvirus ORF57 with Host Noncoding RNAs and Polysomes. PMID:34787459
Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease. PMID:34784346
Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization. PMID:34781902
Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists. PMID:34765096
tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. PMID:34755848
Loss of Hilnc prevents diet-induced hepatic steatosis through binding of IGF2BP2. PMID:34750570
N6-methyladenosine reader IMP2 stabilizes the ZFAS1/OLA1 axis and activates the Warburg effect: implication in colorectal cancer. PMID:34743750
Peakhood: individual site context extraction for CLIP-seq peak regions. PMID:34734974
RNA-binding proteins and their role in kidney disease. PMID:34732838
Identifying Protein Interactomes of Target RNAs Using HyPR-MS. PMID:34694612
Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression. PMID:34694601
MicroRNAs in the Onset of Schizophrenia. PMID:34685659
HERVH-derived lncRNAs negatively regulate chromatin targeting and remodeling mediated by CHD7. PMID:34663690
ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network. PMID:34659409
Photoactivatable ribonucleosides mark base-specific RNA-binding sites. PMID:34654832
The Functional Role of Long Non-Coding RNAs in Melanoma. PMID:34638331
Interrogating the transcriptome with metabolically incorporated ribonucleosides. PMID:34635895
miR-424/503 modulates Wnt/β-catenin signaling in the mammary epithelium by targeting LRP6. PMID:34633138
Mechanosensitive Non-Coding RNAs in Osteogenesis of Mesenchymal Stem Cells. PMID:34628953
Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) to Identify MicroRNA Targets. PMID:34610213
Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2. PMID:34591015
Co-Expression Network Analysis of MicroRNAs and Proteins in Severe Traumatic Brain Injury: A Systematic Review. PMID:34572074
The RNA binding protein QKI5 suppresses ovarian cancer via downregulating transcriptional coactivator TAZ. PMID:34552820
Genome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution. PMID:34534445
MicroRNA regulation of B cell receptor signaling. PMID:34523719
RNA-binding proteins of COSMIC importance in cancer. PMID:34523614
Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. PMID:34522211
Action and function of helicases on RNA G-quadruplexes. PMID:34509630
Uncovering viral RNA-host cell interactions on a proteome-wide scale. PMID:34509361
Learning noncoding RNA biology from viruses. PMID:34491378
Recent technical advances in the study of nucleic acid modifications. PMID:34480848
Machine Learning Approaches on High Throughput NGS Data to Unveil Mechanisms of Function in Biology and Disease. PMID:34479914
Characterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression. PMID:34478875
Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans. PMID:34478557
Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. PMID:34458792
MicroRNA Targeting. PMID:34432276
Experimental MicroRNA Targeting Validation. PMID:34432274
The RNA binding protein Quaking represses splicing of the Fibronectin EDA exon and downregulates the interferon response. PMID:34428287
Illuminating lncRNA Function Through Target Prediction. PMID:34417758
Characterizing miRNA-lncRNA Interplay. PMID:34417757
The regulatory impact of RNA-binding proteins on microRNA targeting. PMID:34417449
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor. PMID:34406415
Dual Fluorescence Reporter Based Analytical Flow Cytometry for miRNA Induced Regulation in Mammalian Cells. PMID:34395794
Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique. PMID:34376564
Translation Initiation Regulated by RNA-Binding Protein in Mammals: The Modulation of Translation Initiation Complex by Trans-Acting Factors. PMID:34359885
PlasmiR: A Manual Collection of Circulating microRNAs of Prognostic and Diagnostic Value. PMID:34359584
miRNome and Functional Network Analysis of PGRMC1 Regulated miRNA Target Genes Identify Pathways and Biological Functions Associated With Triple Negative Breast Cancer. PMID:34350123
Mapping the miRNA-mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes. PMID:34314509
Genome-Wide Analysis of RNA-Protein Interactions in Plasmodium falciparum Using eCLIP-Seq. PMID:34313988
The RNA-Binding Protein NELFE Promotes Gastric Cancer Growth and Metastasis Through E2F2. PMID:34295816
Evaluating the Effect of 3'-UTR Variants in DICER1 and DROSHA on Their Tissue-Specific Expression by miRNA Target Prediction. PMID:34287278
MicroRNAs Regulating Autophagy in Neurodegeneration. PMID:34260028
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. PMID:34252974
Non-coding RNAs: the extensive and interactive regulators of the blood-brain barrier permeability. PMID:34241576
Large-Scale Computational Discovery of Binding Motifs in tRNA Fragments. PMID:34239893
The Role of N6 -Methyladenosine Modified Circular RNA in Pathophysiological Processes. PMID:34239354
Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins. PMID:34221536
The m6A reader IMP2 directs autoimmune inflammation through an IL-17- and TNFα-dependent C/EBP transcription factor axis. PMID:34215679
m6 A modification of lncRNA PCAT6 promotes bone metastasis in prostate cancer through IGF2BP2-mediated IGF1R mRNA stabilization. PMID:34185427
Epitranscriptomic addition of m6A regulates HIV-1 RNA stability and alternative splicing. PMID:34140354
RBinds: A user-friendly server for RNA binding site prediction. PMID:34136090
NORAD-induced Pumilio phase separation is required for genome stability. PMID:34108682
Argonaute binding within human nuclear RNA and its impact on alternative splicing. PMID:34108230
Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing. PMID:34085242
MiR-25-3p regulates the differentiation of intramuscular preadipocytes in goat via targeting KLF4. PMID:34084900
miRNA-Mediated Control of B Cell Responses in Immunity and SLE. PMID:34079558
Decoding LncRNAs. PMID:34072257
Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing. PMID:34070162
Opportunities and Challenges in Global Quantification of RNA-Protein Interaction via UV Cross-Linking. PMID:34055886
ELAVL1 primarily couples mRNA stability with the 3' UTRs of interferon-stimulated genes. PMID:34038724
Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species. PMID:34030625
Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. PMID:34029587
Alternative splicing perturbation landscape identifies RNA binding proteins as potential therapeutic targets in cancer. PMID:33996260
Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks. PMID:33983921
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. PMID:33979654
EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PMID:33956915
Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology. PMID:33942720
RNA Proximity Labeling: A New Detection Tool for RNA-Protein Interactions. PMID:33919831
DDX3 depletion represses translation of mRNAs with complex 5' UTRs. PMID:33905506
The nuclear functions of long noncoding RNAs come into focus. PMID:33898883
The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. PMID:33876744
Computational methods for cancer driver discovery: A survey. PMID:33859763
In silico Analysis of Polymorphisms in microRNAs Deregulated in Alzheimer Disease. PMID:33841080
IGF2BP1, a Conserved Regulator of RNA Turnover in Cancer. PMID:33829040
Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding. PMID:33823551
Compendium of Methods to Uncover RNA-Protein Interactions In Vivo. PMID:33808611
Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS). PMID:33806612
Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells. PMID:33806450
Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer. PMID:33803328
The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status. PMID:33799602
Linking the YTH domain to cancer: the importance of YTH family proteins in epigenetics. PMID:33795663
Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses. PMID:33794184
Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms. PMID:33772581
Crucial roles of different RNA-binding hnRNP proteins in Stem Cells. PMID:33767590
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA-protein interaction prediction. PMID:33740884
RNA m6A reader IMP2/IGF2BP2 promotes pancreatic β-cell proliferation and insulin secretion by enhancing PDX1 expression. PMID:33705986
YTH Domain Proteins: A Family of m6A Readers in Cancer Progression. PMID:33692959
RNA-Centric Approaches to Profile the RNA-Protein Interaction Landscape on Selected RNAs. PMID:33671874
Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update. PMID:33669207
miTAR: a hybrid deep learning-based approach for predicting miRNA targets. PMID:33639834
Evolutionary conservation of the DRACH signatures of potential N6-methyladenosine (m6A) sites among influenza A viruses. PMID:33633224
tRFTars: predicting the targets of tRNA-derived fragments. PMID:33632236
Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures. PMID:33623109
Conservation and turnover of miRNAs and their highly complementary targets in early branching animals. PMID:33622129
Noncoding RNAs in B cell responses. PMID:33586605
Techniques for Characterizing Cytomegalovirus-Encoded miRNAs. PMID:33555594
Regulation of Gene Expression Associated With the N6-Methyladenosine (m6A) Enzyme System and Its Significance in Cancer. PMID:33552994
A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol. PMID:33503264
The search for RNA-binding proteins: a technical and interdisciplinary challenge. PMID:33492363
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. PMID:33461501
Deciphering molecular interactions by proximity labeling. PMID:33432242
Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing. PMID:33425250
tRNA Biology in the Pathogenesis of Diabetes: Role of Genetic and Environmental Factors. PMID:33419045
Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture. PMID:33413092
QKI is a critical pre-mRNA alternative splicing regulator of cardiac myofibrillogenesis and contractile function. PMID:33397958
Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome. PMID:33397688
Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline. PMID:33376190
miRNA Targets: From Prediction Tools to Experimental Validation. PMID:33374478
A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. PMID:33346941
The p53-induced RNA-binding protein ZMAT3 is a splicing regulator that inhibits the splicing of oncogenic CD44 variants in colorectal carcinoma. PMID:33334821
Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure. PMID:33334313
Improving CLIP-seq data analysis by incorporating transcript information. PMID:33334306
MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome. PMID:33300035
Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes. PMID:33268883
Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces. PMID:33242392
Comprehensive analysis of neuronal guidance cue expression regulation during monocyte-to-macrophage differentiation reveals post-transcriptional regulation of semaphorin7A by the RNA-binding protein quaking. PMID:33241976
TET2 chemically modifies tRNAs and regulates tRNA fragment levels. PMID:33230319
An alternative miRISC targets a cancer-associated coding sequence mutation in FOXL2. PMID:33215742
Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture. PMID:33208978
QKI-5 regulates the alternative splicing of cytoskeletal gene ADD3 in lung cancer. PMID:33196842
miR-550a-5p Functions as a Tumor Promoter by Targeting LIMD1 in Lung Adenocarcinoma. PMID:33194664
Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis. PMID:33179042
Methods to Investigate miRNA Function: Focus on Platelet Reactivity. PMID:33124028
microRNA-483 ameliorates hypercholesterolemia by inhibiting PCSK9 production. PMID:33119548
Ligation of 2', 3'-cyclic phosphate RNAs for the identification of microRNA binding sites. PMID:33113149
Advances in the role of m6A RNA modification in cancer metabolic reprogramming. PMID:33062255
tRNA-Derived Small RNAs and Their Potential Roles in Cardiac Hypertrophy. PMID:33041815
tRFtarget: a database for transfer RNA-derived fragment targets. PMID:33035346
Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. PMID:33020268
Differences in small noncoding RNAs profile between bull X and Y sperm. PMID:32999759
The chemistry and applications of RNA 2'-OH acylation. PMID:32984545
Repurposing Fragile X Drugs to Inhibit SARS-CoV-2 Viral Reproduction. PMID:32984339
Identification of Qk as a Glial Precursor Cell Marker that Governs the Fate Specification of Neural Stem Cells to a Glial Cell Lineage. PMID:32976762
Non-Coding RNAs, a Novel Paradigm for the Management of Gastrointestinal Stromal Tumors. PMID:32972022
RNA-Binding Proteins as Regulators of Migration, Invasion and Metastasis in Oral Squamous Cell Carcinoma. PMID:32957697
Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA. PMID:32943634
It's the Little Things (in Viral RNA). PMID:32934087
Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling. PMID:32876046
High-efficiency unassisted transfection of platelets with naked double-stranded miRNAs modulates signal-activated translation and platelet function. PMID:32838617
Zooming in on protein-RNA interactions: a multi-level workflow to identify interaction partners. PMID:32820806
TRIM71 binds to IMP1 and is capable of positive and negative regulation of target RNAs. PMID:32816599
Plasma tRNA Fragments Derived from 5' Ends as Novel Diagnostic Biomarkers for Early-Stage Breast Cancer. PMID:32814252
Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. PMID:32812257
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. PMID:32807991
Antagonistic control of Caenorhabditis elegans germline stem cell proliferation and differentiation by PUF proteins FBF-1 and FBF-2. PMID:32804074
Cell- and Polymerase-Selective Metabolic Labeling of Cellular RNA with 2'-Azidocytidine. PMID:32786764
The oncofetal RNA-binding protein IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression in cancer. PMID:32761127
Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis. PMID:32753408
Population variation in miRNAs and isomiRs and their impact on human immunity to infection. PMID:32731901
Comprehensive Analysis of LincRNAs in Classical and Basal-Like Subtypes of Pancreatic Cancer. PMID:32727085
MicroRNAs and Their Targetomes in Tumor-Immune Communication. PMID:32722019
Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 Modulates Aggressiveness of Ewing Sarcoma by Regulating the CD164-CXCR4 Axis. PMID:32719743
Inhibition of miR-181a promotes midbrain neuronal growth through a Smad1/5-dependent mechanism: implications for Parkinson's disease. PMID:32714583
Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences. PMID:32703884
Artificial miRNAs targeting CAG repeat expansion in ORFs cause rapid deadenylation and translation inhibition of mutant transcripts. PMID:32696070
PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction. PMID:32678300
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions. PMID:32657407
Human GTPBP5 (MTG2) fuels mitoribosome large subunit maturation by facilitating 16S rRNA methylation. PMID:32652011
Modern epigenetics methods in biological research. PMID:32645449
Placental exosomes isolated from urine of patients with gestational diabetes exhibit a differential profile expression of microRNAs across gestation. PMID:32626972
The human box C/D snoRNA U3 is a miRNA source and miR-U3 regulates expression of sortin nexin 27. PMID:32609813
Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story. PMID:32605220
RNA-Binding Proteins Implicated in Mitochondrial Damage and Mitophagy. PMID:32582692
Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor. PMID:32579929
MiR-181a functions as an oncogene by regulating CCND1 in multiple myeloma. PMID:32566002
Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study. PMID:32560708
DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning. PMID:32558887
System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA-protein complexes. PMID:32554781
Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability. PMID:32533923
Epigenetic and epitranscriptomic regulation of viral replication. PMID:32533130
Argonaute binding within 3'-untranslated regions poorly predicts gene repression. PMID:32501500
High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. PMID:32497496
Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice. PMID:32442168
Proximity-CLIP and Expedited Non-Radioactive Library Preparation of Small RNA Footprints for Next-Generation Sequencing. PMID:32438484
High-Throughput Identification of MiR-145 Targets in Human Articular Chondrocytes. PMID:32403239
The mRNA-binding protein IGF2BP1 maintains intestinal barrier function by up-regulating occludin expression. PMID:32385106
Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP. PMID:32380061
Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. PMID:32376827
Prediction of miRNA targets by learning from interaction sequences. PMID:32369518
Identification of the Potential Prognostic Markers from the miRNA-lncRNA-mRNA Interactions for Metastatic Renal Cancer via Next-Generation Sequencing and Bioinformatics. PMID:32316228
Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model. PMID:32316190
RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia. PMID:32298230
Uncovering the cellular capacity for intensive and specific feedback self-control of the argonautes and MicroRNA targeting activity. PMID:32297952
Mechanisms and consequences of subcellular RNA localization across diverse cell types. PMID:32291836
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. PMID:32252787
Prediction of the miRNA interactome - Established methods and upcoming perspectives. PMID:32211130
Position-wise binding preference is important for miRNA target site prediction. PMID:32186709
Functions and properties of nuclear lncRNAs-from systematically mapping the interactomes of lncRNAs. PMID:32183863
The mRNA-Binding Protein IGF2BP1 Restores Fetal Hemoglobin in Cultured Erythroid Cells from Patients with β-Hemoglobin Disorders. PMID:32154328
Capturing RNA-protein interaction via CRUIS. PMID:32140725
Diverse Roles of PUF Proteins in Germline Stem and Progenitor Cell Development in C. elegans. PMID:32117964
Analysis and Identification of Tumorigenic Targets of MicroRNA in Cancer Cells by Photoreactive Chemical Probes. PMID:32102467
Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. PMID:32094787
miRNA-31 Improves Cognition and Abolishes Amyloid-β Pathology by Targeting APP and BACE1 in an Animal Model of Alzheimer's Disease. PMID:32069773
The RNA-binding protein QKI suppresses tumorigenesis of clear cell renal cell carcinoma by regulating the expression of HIF-1α. PMID:32047543
Deep Sequencing MicroRNAs from Extracellular Membrane Vesicles Revealed the Association of the Vesicle Cargo with Cellular Origin. PMID:32046334
Predicting lncRNA-Protein Interactions With miRNAs as Mediators in a Heterogeneous Network Model. PMID:32038709
Human Long Noncoding RNA Interactome: Detection, Characterization and Function. PMID:32033158
The miR-28-5p Targetome Discovery Identified SREBF2 as One of the Mediators of the miR-28-5p Tumor Suppressor Activity in Prostate Cancer Cells. PMID:32028704
Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2. PMID:32016422
IGF2BP3 From Physiology to Cancer: Novel Discoveries, Unsolved Issues, and Future Perspectives. PMID:32010687
Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL). PMID:31999864
Deep neural networks for interpreting RNA-binding protein target preferences. PMID:31992613
Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation. PMID:31959994
Upregulated miR-222 targets BCL2L11 and promotes apoptosis of mesenchymal stem cells in preeclampsia patients in response to severe hypoxia. PMID:31938092
HMGA Proteins in Stemness and Differentiation of Embryonic and Adult Stem Cells. PMID:31935816
Epigenetic Silencing of CDR1as Drives IGF2BP3-Mediated Melanoma Invasion and Metastasis. PMID:31935372
RNAInter in 2020: RNA interactome repository with increased coverage and annotation. PMID:31906603
Integrated analysis of directly captured microRNA targets reveals the impact of microRNAs on mammalian transcriptome. PMID:31900330
The Complex Landscape of PTEN mRNA Regulation. PMID:31871240
GC content shapes mRNA storage and decay in human cells. PMID:31855182
Functional diversity of small nucleolar RNAs. PMID:31828325
Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far. PMID:31817041
High-throughput approaches to profile RNA-protein interactions. PMID:31812895
The biochemical basis of microRNA targeting efficacy. PMID:31806698
mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site. PMID:31802126
FLASH: ultra-fast protocol to identify RNA-protein interactions in cells. PMID:31802123
Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing. PMID:31799606
Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. PMID:31796550
Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins. PMID:31795425
The RNA-binding protein QKI-7 recruits the poly(A) polymerase GLD-2 for 3' adenylation and selective stabilization of microRNA-122. PMID:31792053
Clip for studying protein-RNA interactions that regulate virus replication. PMID:31765715
The Non-Canonical Aspects of MicroRNAs: Many Roads to Gene Regulation. PMID:31752361
A PUF Hub Drives Self-Renewal in Caenorhabditis elegans Germline Stem Cells. PMID:31740451
Contribution of alternative splicing to breast cancer metastasis. PMID:31737791
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. PMID:31732741
Identifying Cancer-Specific circRNA-RBP Binding Sites Based on Deep Learning. PMID:31703384
Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat. PMID:31699777
A Genetically Encoded Diazirine Analogue for RNA-Protein Photo-crosslinking. PMID:31658407
miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. PMID:31647101
The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. PMID:31640799
N6-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis. PMID:31619685
The RNA-binding protein SART3 promotes miR-34a biogenesis and G1 cell cycle arrest in lung cancer cells. PMID:31619517
Pum2 Shapes the Transcriptome in Developing Axons through Retention of Target mRNAs in the Cell Body. PMID:31606248
Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges. PMID:31602614
Understanding the binding specificities of mRNA targets by the mammalian Quaking protein. PMID:31602485
RNA-binding protein PUM2 regulates mesenchymal stem cell fate via repression of JAK2 and RUNX2 mRNAs. PMID:31595981
Osteoclastic microRNAs and their translational potential in skeletal diseases. PMID:31591677
The structural basis for RNA selectivity by the IMP family of RNA-binding proteins. PMID:31570709
Structural Elucidation of Bisulfite Adducts to Pseudouridine That Result in Deletion Signatures during Reverse Transcription of RNA. PMID:31538776
Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing. PMID:31538617
Identification of proteins and miRNAs that specifically bind an mRNA in vivo. PMID:31527589
Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. PMID:31522987
Post-transcriptional regulation of inflammation by RNA-binding proteins via cis-elements of mRNAs. PMID:31511872
Regulation of La/SSB-dependent viral gene expression by pre-tRNA 3' trailer-derived tRNA fragments. PMID:31504775
Protein Binding to mRNA 3' Isoforms. PMID:31503412
An Overview of Circular RNAs and Their Implications in Myotonic Dystrophy. PMID:31500099
The transcribed pseudogene RPSAP52 enhances the oncofetal HMGA2-IGF2BP2-RAS axis through LIN28B-dependent and independent let-7 inhibition. PMID:31484926
Integration of Bioinformatic Predictions and Experimental Data to Identify circRNA-miRNA Associations. PMID:31450634
Expression profile of tRNA‑derived fragments and their potential roles in human varicose veins. PMID:31432124
Approaches for measuring the dynamics of RNA-protein interactions. PMID:31429211
PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees. PMID:31428122
PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks. PMID:31425505
Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing. PMID:31413137
RNA-Binding Protein IGF2BP2/IMP2 is a Critical Maternal Activator in Early Zygotic Genome Activation. PMID:31406667
The pause-initiation limit restricts transcription activation in human cells. PMID:31399571
A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity. PMID:31397673
Urinary miRNA-27b-3p and miRNA-1228-3p correlate with the progression of Kidney Fibrosis in Diabetic Nephropathy. PMID:31388051
Differential Inhibition of Target Gene Expression by Human microRNAs. PMID:31366019
DDX3X and specific initiation factors modulate FMR1 repeat-associated non-AUG-initiated translation. PMID:31347257
Marking RNA: m6A writers, readers, and functions in Arabidopsis. PMID:31336387
Multidomain Convergence of Argonaute during RISC Assembly Correlates with the Formation of Internal Water Clusters. PMID:31324450
The RNA exosome nuclease complex regulates human embryonic stem cell differentiation. PMID:31308215
Non-Coding RNAs and their Integrated Networks. PMID:31301674
Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. PMID:31294800
Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins. PMID:31284728
Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2. PMID:31268608
Mutant FUS and ELAVL4 (HuD) Aberrant Crosstalk in Amyotrophic Lateral Sclerosis. PMID:31242416
Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data. PMID:31238884
RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. PMID:31235518
Caveolin-1 selectively regulates microRNA sorting into microvesicles after noxious stimuli. PMID:31235510
MicroRNA (miRNA)-to-miRNA Regulation of Programmed Cell Death 4 (PDCD4). PMID:31235478
Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. PMID:31227602
Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites. PMID:31226278
Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3. PMID:31221665
Genome-wide Integrative Analysis of Zika-Virus-Infected Neuronal Stem Cells Reveals Roles for MicroRNAs in Cell Cycle and Stemness. PMID:31216479
β-Actin mRNA interactome mapping by proximity biotinylation. PMID:31189591
Significant epitranscriptomes in heterogeneous cancer. PMID:31187550
Extensive Epitranscriptomic Methylation of A and C Residues on Murine Leukemia Virus Transcripts Enhances Viral Gene Expression. PMID:31186331
Challenges in microRNAs' targetome prediction and validation. PMID:31169173
Could an Impairment in Local Translation of mRNAs in Glia be Contributing to Pathogenesis in ALS? PMID:31164803
Discovering sequence and structure landscapes in RNA interaction motifs. PMID:31162604
DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions. PMID:31160600
Combinatorial recognition of clustered RNA elements by the multidomain RNA-binding protein IMP3. PMID:31118463
Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. PMID:31109287
SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. PMID:31104839
miR-450a Acts as a Tumor Suppressor in Ovarian Cancer by Regulating Energy Metabolism. PMID:31101765
Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs. PMID:31098334
Macro Histone Variants: Emerging Rheostats of Gastrointestinal Cancers. PMID:31096699
A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. PMID:31078383
Beyond CLIP: advances and opportunities to measure RBP-RNA and RNA-RNA interactions. PMID:31076772
MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites. PMID:31074373
Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1. PMID:31061170
Teaching an Old Virus New Tricks: A Review on New Approaches to Study Age-Old Questions in Influenza Biology. PMID:31051174
Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology. PMID:31047772
MicroRNA-139 inhibits hepatocellular carcinoma cell growth through down-regulating karyopherin alpha 2. PMID:31046781
Prediction of binding property of RNA-binding proteins using multi-sized filters and multi-modal deep convolutional neural network. PMID:31026297
MicroRNA-155: A Master Regulator of Inflammation. PMID:30998423
Global identification of functional microRNA-mRNA interactions in Drosophila. PMID:30967537
IsomiRs: Expanding the miRNA repression toolbox beyond the seed. PMID:30953728
The expression of circulating miR-504 in plasma is associated with EGFR mutation status in non-small-cell lung carcinoma patients. PMID:30953094
A novel human lncRNA SANT1 cis-regulates the expression of SLC47A2 by altering SFPQ/E2F1/HDAC1 binding to the promoter region in renal cell carcinoma. PMID:30951404
An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK! PMID:30945176
Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing. PMID:30931476
Systematic evaluation of the microRNAome through miR-CATCHv2.0 identifies positive and negative regulators of BRAF-X1 mRNA. PMID:30929607
Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non-model Organisms. PMID:30919506
Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2. PMID:30914482
Long Noncoding RNA and Protein Interactions: From Experimental Results to Computational Models Based on Network Methods. PMID:30875752
Thermodynamic and structural contributions of the 6-thioguanosine residue to helical properties of RNA. PMID:30867505
The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells. PMID:30867249
IMP1 KH1 and KH2 domains create a structural platform with unique RNA recognition and re-modelling properties. PMID:30864660
The splicing factor U2AF1 contributes to cancer progression through a noncanonical role in translation regulation. PMID:30842218
Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis. PMID:30838214
Colocalization of m6A and G-Quadruplex-Forming Sequences in Viral RNA (HIV, Zika, Hepatitis B, and SV40) Suggests Topological Control of Adenosine N 6-Methylation. PMID:30834310
Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes. PMID:30827501
Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. PMID:30824702
Mammalian Pum1 and Pum2 Control Body Size via Translational Regulation of the Cell Cycle Inhibitor Cdkn1b. PMID:30811992
Methods to study RNA-protein interactions. PMID:30804549
MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis. PMID:30742093
SpyCLIP: an easy-to-use and high-throughput compatible CLIP platform for the characterization of protein-RNA interactions with high accuracy. PMID:30715466
Computational modeling of RNA 3D structure based on experimental data. PMID:30670629
Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. PMID:30670076
Functional Interplay between RNA Viruses and Non-Coding RNA in Mammals. PMID:30646609
The RNA-Binding Protein PUM2 Impairs Mitochondrial Dynamics and Mitophagy During Aging. PMID:30642763
miRNA Targeting: Growing beyond the Seed. PMID:30638669
Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies. PMID:30634534
Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex. PMID:30599151
Genome-wide methods for investigating long noncoding RNAs. PMID:30594777
Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. PMID:30591565
beRBP: binding estimation for human RNA-binding proteins. PMID:30590704
Protein kinase C-α is upregulated by IMP1 in melanoma and is linked to poor survival. PMID:30543563
Partner-specific prediction of RNA-binding residues in proteins: A critical assessment. PMID:30536635
Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. PMID:30529548
Deciphering human ribonucleoprotein regulatory networks. PMID:30517751
miRTrace reveals the organismal origins of microRNA sequencing data. PMID:30514392
Establishment of microRNA, transcript and protein regulatory networks in Alport syndrome induced pluripotent stem cells. PMID:30483741
Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments. PMID:30478324
Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress. PMID:30476744
Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines. PMID:30459181
Dynamic m6A methylation facilitates mRNA triaging to stress granules. PMID:30456371
Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development. PMID:30455455
Computational approaches for the analysis of RNA-protein interactions: A primer for biologists. PMID:30455357
Contemporary Ribonomics Methods for Viral microRNA Target Analysis. PMID:30424002
RNA motifs and combinatorial prediction of interactions, stability and localization of noncoding RNAs. PMID:30420773
IMP1 3' UTR shortening enhances metastatic burden in colorectal cancer. PMID:30407516
Dynamic Changes in the Global MicroRNAome and Transcriptome Identify Key Nodes Associated With Ovarian Development in Chickens. PMID:30405698
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data. PMID:30384847
Long Non-coding RNA NEAT1: A Novel Target for Diagnosis and Therapy in Human Tumors. PMID:30374364
IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner. PMID:30371874
Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. PMID:30370679
Emerging Biomarkers in Bladder Cancer Identified by Network Analysis of Transcriptomic Data. PMID:30370253
HCMV miRNA Targets Reveal Important Cellular Pathways for Viral Replication, Latency, and Reactivation. PMID:30360396
Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine. PMID:30353734
Preparation of Sequencing RNA Libraries through Chemical Cross-linking Coupled to Affinity Purification (cCLAP) in Saccharomyces cerevisiae. PMID:30345328
On the Importance of Host MicroRNAs During Viral Infection. PMID:30333857
Target RNAs Strike Back on MicroRNAs. PMID:30333855
Antagonistic and cooperative AGO2-PUM interactions in regulating mRNAs. PMID:30333515
CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals. PMID:30329090
Deep-RBPPred: Predicting RNA binding proteins in the proteome scale based on deep learning. PMID:30323214
Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers. PMID:30322887
Human GTPBP10 is required for mitoribosome maturation. PMID:30321378
Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins. PMID:30316580
A novel class of microRNA-recognition elements that function only within open reading frames. PMID:30297778
Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts. PMID:30256975
Monitored eCLIP: high accuracy mapping of RNA-protein interactions. PMID:30252095
The APT complex is involved in non-coding RNA transcription and is distinct from CPF. PMID:30247719
The HMGA2-IMP2 Pathway Promotes Granulosa Cell Proliferation in Polycystic Ovary Syndrome. PMID:30247605
Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. PMID:30232334
The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types. PMID:30224821
Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast. PMID:30208026
microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions. PMID:30190538
High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs. PMID:30165668
Argonaute-miRNA Complexes Silence Target mRNAs in the Nucleus of Mammalian Stem Cells. PMID:30146314
Exosomal miRNA Signatures for Late-Onset Acute Graft-Versus-Host Disease in Allogenic Hematopoietic Stem Cell Transplantation. PMID:30142940
Structural basis of IMP3 RRM12 recognition of RNA. PMID:30135093
Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling. PMID:30126842
Human proteins that interact with RNA/DNA hybrids. PMID:30108179
Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation. PMID:30087332
MTG1 couples mitoribosome large subunit assembly with intersubunit bridge formation. PMID:30085276
The Future of Cross-Linking and Immunoprecipitation (CLIP). PMID:30068528
The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock. PMID:30059503
3' RNA Uridylation in Epitranscriptomics, Gene Regulation, and Disease. PMID:30057901
The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells. PMID:30053258
Enhancing Epitranscriptome Module Detection from m6A-Seq Data Using Threshold-Based Measurement Weighting Strategy. PMID:30013979
A Distributed Classifier for MicroRNA Target Prediction with Validation Through TCGA Expression Data. PMID:29993641
Post-transcriptional regulation of microRNAs in cancer: From prediction to validation. PMID:29989022
Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. PMID:29985403
Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs. PMID:29985341
RIG-I Detects Kaposi's Sarcoma-Associated Herpesvirus Transcripts in a RNA Polymerase III-Independent Manner. PMID:29970461
Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks. PMID:29970003
Polymerase pausing induced by sequence-specific RNA-binding protein drives heterochromatin assembly. PMID:29967291
Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2. PMID:29950133
Platforms for Investigating LncRNA Functions. PMID:29945466
Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes. PMID:29930024
Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism. PMID:29925637
SSMART: sequence-structure motif identification for RNA-binding proteins. PMID:29893814
Mex-3B induces apoptosis by inhibiting miR-92a access to the Bim-3'UTR. PMID:29849121
Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. PMID:29846699
tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. PMID:29844106
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. PMID:29800452
How T cells go rogue in the absence of Roquins. PMID:29799562
Direct measurement of pervasive weak repression by microRNAs and their role at the network level. PMID:29764374
Integrated miRNA-mRNA analysis reveals regulatory pathways underlying the curly fleece trait in Chinese tan sheep. PMID:29751742
tRNA-Derived Small RNA: A Novel Regulatory Small Non-Coding RNA. PMID:29748504
Loss of Malat1 does not modify age- or diet-induced adipose tissue accretion and insulin resistance in mice. PMID:29746487
High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients. PMID:29738455
Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 Influences Sensitivity to Anti-IGF System Agents Through the Translational Regulation of IGF1R. PMID:29731738
The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis. PMID:29716990
CLIP-related methodologies and their application to retrovirology. PMID:29716635
YTH Domain: A Family of N6-methyladenosine (m6A) Readers. PMID:29715522
GoldCLIP: Gel-omitted Ligation-dependent CLIP. PMID:29709556
The STAT3 Target Mettl8 Regulates Mouse ESC Differentiation via Inhibiting the JNK Pathway. PMID:29706498
Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing. PMID:29685977
Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs. PMID:29670884
HITS-CLIP in various brain areas reveals new targets and new modalities of RNA binding by fragile X mental retardation protein. PMID:29668986
Deconvolution of seed and RNA-binding protein crosstalk in RNAi-based functional genomics. PMID:29662165
IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors. PMID:29660014
A Brief Review of RNA-Protein Interaction Database Resources. PMID:29657278
Computational Approaches to tRNA-Derived Small RNAs. PMID:29657274
Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. PMID:29636419
RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer. PMID:29627433
MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. PMID:29617966
The microRNA-200 family coordinately regulates cell adhesion and proliferation in hair morphogenesis. PMID:29602800
Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation. PMID:29578509
Identification and characterization of host proteins bound to dengue virus 3' UTR reveal an antiviral role for quaking proteins. PMID:29572260
Metazoan MicroRNAs. PMID:29570994
uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins. PMID:29559621
Long Non-coding MIR205HG Depletes Hsa-miR-590-3p Leading to Unrestrained Proliferation in Head and Neck Squamous Cell Carcinoma. PMID:29556360
A high-throughput 3' UTR reporter screening identifies microRNA interactomes of cancer genes. PMID:29522551
Cytoplasmic functions of long noncoding RNAs. PMID:29516680
Diversification of the muscle proteome through alternative splicing. PMID:29510724
FUS Regulates Activity of MicroRNA-Mediated Gene Silencing. PMID:29499134
RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence. PMID:29495575
High-throughput Methods for Dissection of Trypanosome Gene Regulatory Networks. PMID:29491736
Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. PMID:29476152
Recently Evolved Tumor Suppressor Transcript TP73-AS1 Functions as Sponge of Human-Specific miR-941. PMID:29474580
Sumoylation regulates FMRP-mediated dendritic spine elimination and maturation. PMID:29472612
Anti-miR-17 therapy delays tumorigenesis in MYC-driven hepatocellular carcinoma (HCC). PMID:29464015
Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development. PMID:29449644
Addition of m6A to SV40 late mRNAs enhances viral structural gene expression and replication. PMID:29447282
A systematic approach to RNA-associated motif discovery. PMID:29444662
Oncoprotein AEG-1 is an endoplasmic reticulum RNA-binding protein whose interactome is enriched in organelle resident protein-encoding mRNAs. PMID:29438049
Capturing the interactome of newly transcribed RNA. PMID:29431736
The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression. PMID:29429924
Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis. PMID:29387452
SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA. PMID:29386330
Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) Identifies Kaposi's Sarcoma-Associated Herpesvirus MicroRNA Targets in Endothelial Cells. PMID:29386283
Functional Classification and Experimental Dissection of Long Noncoding RNAs. PMID:29373828
TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. PMID:29355846
miFAST: A novel and rapid microRNA target capture method. PMID:29350431
Interactions, localization, and phosphorylation of the m6A generating METTL3-METTL14-WTAP complex. PMID:29348140
Trans-acting translational regulatory RNA binding proteins. PMID:29341429
A brave new world of RNA-binding proteins. PMID:29339797
Identification and Characterization of Sindbis Virus RNA-Host Protein Interactions. PMID:29321325
The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. PMID:29311343
RNA Binding Protein as an Emerging Therapeutic Target for Cancer Prevention and Treatment. PMID:29302577
Context-dependent deposition and regulation of mRNAs in P-bodies. PMID:29297464
PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. PMID:29284540
Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics. PMID:29246928
Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. PMID:29245011
In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering. PMID:29235467
A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation. PMID:29225039
Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. PMID:29165587
Noncoding RNAs in the Regulation of Pluripotency and Reprogramming. PMID:29143182
Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma. PMID:29132323
Mechanistic implications of enhanced editing by a HyperTRIBE RNA-binding protein. PMID:29127211
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. PMID:29126174
Dynamic miRNA-mRNA paradigms: New faces of miRNAs. PMID:29124222
Molecular roles and function of circular RNAs in eukaryotic cells. PMID:29116363
Protein-mRNA interactome capture: cartography of the mRNP landscape. PMID:29098073
Evaluation of miRNA-196a2 and apoptosis-related target genes: ANXA1, DFFA and PDCD4 expression in gastrointestinal cancer patients: A pilot study. PMID:29091952
A mutually exclusive stem-loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila. PMID:29066499
Detecting and characterizing microRNAs of diverse genomic origins via miRvial. PMID:29036674
RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing. PMID:29031843
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction. PMID:29028895
Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP. PMID:29028411
Autogenous cross-regulation of Quaking mRNA processing and translation balances Quaking functions in splicing and translation. PMID:29021242
An RNA-binding protein, Qki5, regulates embryonic neural stem cells through pre-mRNA processing in cell adhesion signaling. PMID:29021239
Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions. PMID:28994809
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data. PMID:28977546
Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein. PMID:28974714
LncRNA UCA1 in anti-cancer drug resistance. PMID:28969100
Expression and Function of hsa-miR-6165 in Human Cell Lines and During the NT2 Cell Neural Differentiation Process. PMID:28956260
Rules for functional microRNA targeting. PMID:28946941
Thiol-linked alkylation of RNA to assess expression dynamics. PMID:28945705
Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. PMID:28945502
CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome. PMID:28934506
Discovering the miR-26a-5p Targetome in Prostate Cancer Cells. PMID:28928862
Epitranscriptomic Enhancement of Influenza A Virus Gene Expression and Replication. PMID:28910636
eRNA binding produces tailored CBP activity profiles to regulate gene expression. PMID:28891741
Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites. PMID:28886744
Advances and challenges in the detection of transcriptome-wide protein-RNA interactions. PMID:28853213
A Novel IMP1 Inhibitor, BTYNB, Targets c-Myc and Inhibits Melanoma and Ovarian Cancer Cell Proliferation. PMID:28846937
Interaction and cross-talk between non-coding RNAs. PMID:28840253
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins. PMID:28839189
A Macro View of MicroRNAs: The Discovery of MicroRNAs and Their Role in Hematopoiesis and Hematologic Disease. PMID:28838543
Global mapping of miRNA-target interactions in cattle (Bos taurus). PMID:28811507
Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach. PMID:28798471
Post-transcriptional regulation of mouse neurogenesis by Pumilio proteins. PMID:28794184
Transcriptome profiling of mouse brains with qkI-deficient oligodendrocytes reveals major alternative splicing defects including self-splicing. PMID:28790308
The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. PMID:28782243
Architecture and dynamics of overlapped RNA regulatory networks. PMID:28768715
Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). PMID:28766298
Probing Long Non-coding RNA-Protein Interactions. PMID:28744458
Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer. PMID:28735896
Sensing of viral and endogenous RNA by ZBP1/DAI induces necroptosis. PMID:28716805
PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. PMID:28702278
The yeast noncoding RNA interaction network. PMID:28701522
The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. PMID:28685749
RNA stores tau reversibly in complex coacervates. PMID:28683104
Yeast RNA-Binding Protein Nab3 Regulates Genes Involved in Nitrogen Metabolism. PMID:28674185
Human ribosomal protein eS1 is engaged in cellular events related to processing and functioning of U11 snRNA. PMID:28666385
Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants. PMID:28662211
IGF2BP1 overexpression causes fetal-like hemoglobin expression patterns in cultured human adult erythroblasts. PMID:28652347
LARP1 functions as a molecular switch for mTORC1-mediated translation of an essential class of mRNAs. PMID:28650797
The LATS1 and LATS2 tumor suppressors: beyond the Hippo pathway. PMID:28644436
mRNA localization in metazoans: A structural perspective. PMID:28640665
Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. PMID:28605404
Power and sample size calculations for high-throughput sequencing-based experiments. PMID:28605403
DDX54 regulates transcriptome dynamics during DNA damage response. PMID:28596291
Autoregulation of RBM10 and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated decay. PMID:28586478
A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data. PMID:28575488
The Fragment HMGA2-sh-3p20 from HMGA2 mRNA 3'UTR Promotes the Growth of Hepatoma Cells by Upregulating HMGA2. PMID:28522832
Digital analysis and epigenetic regulation of the signature of rejection in colorectal cancer. PMID:28507795
IGF2 mRNA binding protein 3 (IMP3) mediated regulation of transcriptome and translatome in glioma cells. PMID:28485999
Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. PMID:28484853
WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms. PMID:28472401
Detecting RNA-RNA interactions in E. coli using a modified CLASH method. PMID:28468647
IGF2 mRNA binding protein 3 (IMP3) promotes glioma cell migration by enhancing the translation of RELA/p65. PMID:28465487
Identification of N6-methyladenosine reader proteins. PMID:28454774
Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. PMID:28442996
The RNA-binding protein MARF1 promotes cortical neurogenesis through its RNase activity domain. PMID:28442784
Issues in current microRNA target identification methods. PMID:28430005
Managing the sequence-specificity of antisense oligonucleotides in drug discovery. PMID:28426096
Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum. PMID:28416533
Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors. PMID:28410363
MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing. PMID:28402935
Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress. PMID:28400552
Identification of targets of tumor suppressor microRNA-34a using a reporter library system. PMID:28356515
sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs. PMID:28334977
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. PMID:28334930
N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. PMID:28334903
AUF1 facilitates microRNA-mediated gene silencing. PMID:28334781
The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation. PMID:28329689
Recurrent rewiring and emergence of RNA regulatory networks. PMID:28320951
Moving messages in the developing brain-emerging roles for mRNA transport and local translation in neural stem cells. PMID:28304078
DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs. PMID:28297718
DUSP11 - An RNA phosphatase that regulates host and viral non-coding RNAs in mammalian cells. PMID:28296624
Discerning functional hierarchies of microRNAs in pulmonary hypertension. PMID:28289720
Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil. PMID:28286499
Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. PMID:28286470
T-ALL and thymocytes: a message of noncoding RNAs. PMID:28270163
ssc-miR-7134-3p regulates fat accumulation in castrated male pigs by targeting MARK4 gene. PMID:28255271
Viral Epitranscriptomics. PMID:28250115
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. PMID:28245811
The RNA-binding protein QKI5 regulates primary miR-124-1 processing via a distal RNA motif during erythropoiesis. PMID:28244490
Differential Sensitivity of Target Genes to Translational Repression by miR-17~92. PMID:28241004
High-throughput screening identifies microRNAs that target Nox2 and improve function after acute myocardial infarction. PMID:28235791
Finding RNA-Protein Interaction Sites Using HMMs. PMID:28224499
Imaging mRNA and protein interactions within neurons. PMID:28223507
Systems Biology-Derived Discoveries of Intrinsic Clocks. PMID:28220104
Detecting RNA modifications in the epitranscriptome: predict and validate. PMID:28216634
Mapping circulating serum miRNAs to their immune-related target mRNAs. PMID:28203094
Cis-acting single nucleotide polymorphisms alter MicroRNA-mediated regulation of human brain-expressed transcripts. PMID:28171541
Identifying survival-associated modules from the dysregulated triplet network in glioblastoma multiforme. PMID:28168356
Gene-microRNA network module analysis for ovarian cancer. PMID:28155675
Mechanism of β-actin mRNA Recognition by ZBP1. PMID:28147274
RNA modifications and structures cooperate to guide RNA-protein interactions. PMID:28144031
Human eIF3: from 'blobology' to biological insight. PMID:28138064
The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts. PMID:28129347
The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis. PMID:28115624
From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data. PMID:28108660
DMirNet: Inferring direct microRNA-mRNA association networks. PMID:28105958
Insights into the design and interpretation of iCLIP experiments. PMID:28093074
RNA Binding to CBP Stimulates Histone Acetylation and Transcription. PMID:28086087
High Throughput Sequencing of Extracellular RNA from Human Plasma. PMID:28060806
Xenopus Piwi proteins interact with a broad proportion of the oocyte transcriptome. PMID:28031481
High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. PMID:28031372
The role of miR-17-92 in the miRegulatory landscape of Ewing sarcoma. PMID:28030800
RESA identifies mRNA-regulatory sequences at high resolution. PMID:28024160
Bioinformatic tools for analysis of CLIP ribonucleoprotein data. PMID:28008714
CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. PMID:28003131
RNA interactome capture in yeast. PMID:27993706
TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells. PMID:27982722
Integrating Epigenomics into the Understanding of Biomedical Insight. PMID:27980397
Tools for Sequence-Based miRNA Target Prediction: What to Choose? PMID:27941681
IMPs: an RNA-binding protein family that provides a link between stem cell maintenance in normal development and cancer. PMID:27940961
Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins. PMID:27930710
Enriching s4 U-RNA Using Methane Thiosulfonate (MTS) Chemistry. PMID:27925666
Insights into the post-transcriptional regulation of the mitochondrial electron transport chain. PMID:27911731
FXR1a-associated microRNP: A driver of specialized non-canonical translation in quiescent conditions. PMID:27911187
miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data. PMID:27903911
Patterns of ribosomal protein expression specify normal and malignant human cells. PMID:27884178
Mutations Inactivating Herpes Simplex Virus 1 MicroRNA miR-H2 Do Not Detectably Increase ICP0 Gene Expression in Infected Cultured Cells or Mouse Trigeminal Ganglia. PMID:27847363
Qki deficiency maintains stemness of glioma stem cells in suboptimal environment by downregulating endolysosomal degradation. PMID:27841882
DO-RIP-seq to quantify RNA binding sites transcriptome-wide. PMID:27840290
Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe. PMID:27825301
The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PMID:27812418
DUSP11 activity on triphosphorylated transcripts promotes Argonaute association with noncanonical viral microRNAs and regulates steady-state levels of cellular noncoding RNAs. PMID:27798849
Post-transcriptional control of executioner caspases by RNA-binding proteins. PMID:27798844
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. PMID:27797762
A network-biology perspective of microRNA function and dysfunction in cancer. PMID:27795564
CoSpliceNet: a framework for co-splicing network inference from transcriptomics data. PMID:27793091
RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2. PMID:27791065
N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection. PMID:27773535
High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. PMID:27768875
RNA-binding protein QKI-5 inhibits the proliferation of clear cell renal cell carcinoma via post-transcriptional stabilization of RASA1 mRNA. PMID:27767378
Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins. PMID:27765618
Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq. PMID:27742911
Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS). PMID:27729296
Protein Interaction Profile Sequencing (PIP-seq). PMID:27723083
Pairing beyond the Seed Supports MicroRNA Targeting Specificity. PMID:27720646
PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons. PMID:27681424
microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure. PMID:27677491
The RNA-binding protein vigilin regulates VLDL secretion through modulation of Apob mRNA translation. PMID:27665711
STarMir Tools for Prediction of microRNA Binding Sites. PMID:27665594
Template-Based Modeling of Protein-RNA Interactions. PMID:27662342
Bridging the gap between in vitro and in vivo RNA folding. PMID:27658939
Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b. PMID:27630665
Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases. PMID:27625393
Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells. PMID:27597760
Interplay of mitochondrial metabolism and microRNAs. PMID:27563705
The RNA Binding Specificity of Human APOBEC3 Proteins Resembles That of HIV-1 Nucleocapsid. PMID:27541140
microRNA regulatory circuits in a mouse model of inherited retinal degeneration. PMID:27527066
Immune Regulator MCPIP1 Modulates TET Expression during Early Neocortical Development. PMID:27523618
Transposable elements and miRNA: Regulation of genomic stability and plasticity. PMID:27511122
CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs. PMID:27510448
IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction. PMID:27506469
Advances in the characterization of RNA-binding proteins. PMID:27503141
MicroRNA-mRNA regulatory networking fine-tunes the porcine muscle fiber type, muscular mitochondrial respiratory and metabolic enzyme activities. PMID:27485725
Investigating long noncoding RNAs using animal models. PMID:27479747
Ago-RIP-Seq identifies Polycomb repressive complex I member CBX7 as a major target of miR-375 in prostate cancer progression. PMID:27449098
Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data. PMID:27438777
Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP. PMID:27418678
MicroRNA gene expression signatures in long-surviving malignant pleural mesothelioma patients. PMID:27408810
A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells. PMID:27406171
An Integrated Analysis of MicroRNA and mRNA Expression Profiles to Identify RNA Expression Signatures in Lambskin Hair Follicles in Hu Sheep. PMID:27404636
SNHG16 is regulated by the Wnt pathway in colorectal cancer and affects genes involved in lipid metabolism. PMID:27396952
Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. PMID:27390358
IMP2 axonal localization, RNA interactome, and function in the development of axon trajectories. PMID:27385015
Identification of consensus binding sites clarifies FMRP binding determinants. PMID:27378784
The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL. PMID:27377249
N(6)-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression. PMID:27371828
Mapping RNA-RNA interactome and RNA structure in vivo by MARIO. PMID:27338251
The organization and regulation of mRNA-protein complexes. PMID:27324829
Long noncoding RNAs in prostate cancer: mechanisms and applications. PMID:27308347
The Landscape of microRNA Targeting in Prostate Cancer Defined by AGO-PAR-CLIP. PMID:27292025
Human Argonaute 2 Is Tethered to Ribosomal RNA through MicroRNA Interactions. PMID:27288410
Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation. PMID:27267401
Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). PMID:27263052
Easier, Better, Faster, Stronger: Improved Methods for RNA-Protein Interaction Studies. PMID:27259196
Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. PMID:27256380
A Comprehensive Review on the Genetic Regulation of Cisplatin-induced Nephrotoxicity. PMID:27252593
Redesigning CLIP for efficiency, accuracy and speed. PMID:27243472
RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences. PMID:27241757
IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. PMID:27210763
TarPmiR: a new approach for microRNA target site prediction. PMID:27207945
The interaction of PRC2 with RNA or chromatin is mutually antagonistic. PMID:27197219
Inferring RBP-Mediated Regulation in Lung Squamous Cell Carcinoma. PMID:27186987
Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution. PMID:27178967
Slug-upregulated miR-221 promotes breast cancer progression through suppressing E-cadherin expression. PMID:27174021
RNA assemblages orchestrate complex cellular processes. PMID:27172226
The PUF binding landscape in metazoan germ cells. PMID:27165521
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. PMID:27161996
CLIP-seq to Identify KSHV ORF57-Binding RNA in Host B Cells. PMID:27153386
STarMirDB: A database of microRNA binding sites. PMID:27144897
Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum. PMID:27128440
MicroRNA Target Recognition: Insights from Transcriptome-Wide Non-Canonical Interactions. PMID:27117456
Posttranscriptional m(6)A Editing of HIV-1 mRNAs Enhances Viral Gene Expression. PMID:27117054
New frontiers in translational control of the cancer genome. PMID:27112207
irCLIP platform for efficient characterization of protein-RNA interactions. PMID:27111506
miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis. PMID:27105848
QKI5-mediated alternative splicing of the histone variant macroH2A1 regulates gastric carcinogenesis. PMID:27092877
Pathogens Use and Abuse MicroRNAs to Deceive the Immune System. PMID:27070595
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. PMID:27068461
Identification and characterization of an hnRNP E1 translational silencing motif. PMID:27067543
CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction. PMID:27059647
Quaking Regulates Neurofascin 155 Expression for Myelin and Axoglial Junction Maintenance. PMID:27053216
Experimental procedures to identify and validate specific mRNA targets of miRNAs. PMID:27047316
Determination of a Comprehensive Alternative Splicing Regulatory Network and Combinatorial Regulation by Key Factors during the Epithelial-to-Mesenchymal Transition. PMID:27044866
A tale of two sequences: microRNA-target chimeric reads. PMID:27044644
TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins. PMID:27040499
Endogenous microRNA sponges: evidence and controversy. PMID:27040487
Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression. PMID:27029405
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). PMID:27018577
miTALOS v2: Analyzing Tissue Specific microRNA Function. PMID:26998997
Resources for the Comprehensive Discovery of Functional RNA Elements. PMID:26990993
The RNA binding protein IMP3 facilitates tumor immune escape by downregulating the stress-induced ligands ULPB2 and MICB. PMID:26982091
Genome-Wide Profiling of RNA-Protein Interactions Using CLIP-Seq. PMID:26965263
A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration. PMID:26962949
Tiny giants of gene regulation: experimental strategies for microRNA functional studies. PMID:26950183
High-throughput discovery of post-transcriptional cis-regulatory elements. PMID:26941072
Cis-acting elements in its 3' UTR mediate post-transcriptional regulation of KRAS. PMID:26930719
miRepress: modelling gene expression regulation by microRNA with non-conventional binding sites. PMID:26923536
The Emerging Function and Mechanism of ceRNAs in Cancer. PMID:26922301
Posttranscriptional regulation of FOXO expression: microRNAs and beyond. PMID:26920226
The oncogenic triangle of HMGA2, LIN28B and IGF2BP1 antagonizes tumor-suppressive actions of the let-7 family. PMID:26917013
The RNA-binding protein quaking maintains endothelial barrier function and affects VE-cadherin and β-catenin protein expression. PMID:26905650
Transcriptome-scale RNase-footprinting of RNA-protein complexes. PMID:26900662
Upstream ORFs are prevalent translational repressors in vertebrates. PMID:26896445
Widespread RNA binding by chromatin-associated proteins. PMID:26883116
Competing endogenous RNA networks in human cancer: hypothesis, validation, and perspectives. PMID:26872371
Argonaute and Argonaute-Bound Small RNAs in Stem Cells. PMID:26861290
A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1. PMID:26860615
Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. PMID:26859437
A high-throughput pipeline for the production of synthetic antibodies for analysis of ribonucleoprotein complexes. PMID:26847261
Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation. PMID:26837572
Biological Processes Discovered by High-Throughput Sequencing. PMID:26828742
A structural view of microRNA-target recognition. PMID:26825463
Recent transcriptome-wide mapping of UPF1 binding sites reveals evidence for its recruitment to mRNA before translation. PMID:26824025
Re-analysis of genome wide data on mammalian microRNA-mediated suppression of gene expression. PMID:26824020
MicroRNAs Expressed during Viral Infection: Biomarker Potential and Therapeutic Considerations. PMID:26819546
Purification of Messenger Ribonucleoprotein Particles via a Tagged Nascent Polypeptide. PMID:26808308
Molecular mechanisms of long noncoding RNAs on gastric cancer. PMID:26788991
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. PMID:26787667
AURA 2: Empowering discovery of post-transcriptional networks. PMID:26779400
CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. PMID:26773058
Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies. PMID:26743510
Stem Cell Ribonomics: RNA-Binding Proteins and Gene Networks in Stem Cell Differentiation. PMID:26734617
Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins. PMID:26724866
Cross-Linking Immunoprecipitation and qPCR (CLIP-qPCR) Analysis to Map Interactions Between Long Noncoding RNAs and RNA-Binding Proteins. PMID:26721479
miRLAB: An R Based Dry Lab for Exploring miRNA-mRNA Regulatory Relationships. PMID:26716983
Analysis of HIV-1 Gag-RNA Interactions in Cells and Virions by CLIP-seq. PMID:26714708
RNA Binding Proteins in the miRNA Pathway. PMID:26712751
TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network. PMID:26701625
MicroRNAs involved in the browning process of adipocytes. PMID:26695012
Abasic pivot substitution harnesses target specificity of RNA interference. PMID:26679372
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs. PMID:26669964
Target selection by natural and redesigned PUF proteins. PMID:26668354
A cardiac myocyte-restricted Lin28/let-7 regulatory axis promotes hypoxia-mediated apoptosis by inducing the AKT signaling suppressor PIK3IP1. PMID:26655604
MicroRNA Mechanisms of Action: What have We Learned from Mice? PMID:26635864
RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins. PMID:26635394
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. PMID:26612864
MicroRNA target prediction using thermodynamic and sequence curves. PMID:26608597
microRNAs as neuroregulators, biomarkers and therapeutic agents in neurodegenerative diseases. PMID:26608596
A Pleiotropic RNA-Binding Protein Controls Distinct Cell Cycle Checkpoints to Drive Resistance of p53-Defective Tumors to Chemotherapy. PMID:26602816
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. PMID:26602692
miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity. PMID:26602609
RNA mis-splicing in disease. PMID:26593421
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. PMID:26590260
Pinpointing RNA-Protein Cross-Links with Site-Specific Stable Isotope-Labeled Oligonucleotides. PMID:26583201
Bioinformatic tools for microRNA dissection. PMID:26578605
SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. PMID:26578591
CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite. PMID:26577377
Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing. PMID:26575292
The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2. PMID:26574518
A 3' untranslated region variant in FMR1 eliminates neuronal activity-dependent translation of FMRP by disrupting binding of the RNA-binding protein HuR. PMID:26554012
Assessing Computational Steps for CLIP-Seq Data Analysis. PMID:26539468
Protein-RNA networks revealed through covalent RNA marks. PMID:26524240
Long non-coding RNA ZFAS1 interacts with CDK1 and is involved in p53-dependent cell cycle control and apoptosis in colorectal cancer. PMID:26506418
Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis. PMID:26501192
Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein. PMID:26500759
Altered Gene Expression Associated with microRNA Binding Site Polymorphisms. PMID:26496489
Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms. PMID:26495937
The miRNA Interactome in Metabolic Homeostasis. PMID:26492831
MtiBase: a database for decoding microRNA target sites located within CDS and 5'UTR regions from CLIP-Seq and expression profile datasets. PMID:26490638
A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. PMID:26473382
A deep learning framework for modeling structural features of RNA-binding protein targets. PMID:26467480
PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. PMID:26463383
NPGPx modulates CPEB2-controlled HIF-1α RNA translation in response to oxidative stress. PMID:26446990
A Single Let-7 MicroRNA Bypasses LIN28-Mediated Repression. PMID:26440890
MicroRNAs in placental health and disease. PMID:26428496
EBV Noncoding RNAs. PMID:26428375
The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages. PMID:26415947
tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins. PMID:26401098
Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factor. PMID:26395143
Isolation of Endogenously Assembled RNA-Protein Complexes Using Affinity Purification Based on Streptavidin Aptamer S1. PMID:26389898
Impacts of Alternative Splicing Events on the Differentiation of Adipocytes. PMID:26389882
SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. PMID:26383775
Splicing Regulation of Pro-Inflammatory Cytokines and Chemokines: At the Interface of the Neuroendocrine and Immune Systems. PMID:26371053
Diverse regulation of 3' splice site usage. PMID:26370726
RNA regulatory networks diversified through curvature of the PUF protein scaffold. PMID:26364903
Biochemical isolation of Argonaute protein complexes by Ago-APP. PMID:26351695
Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. PMID:26340425
Immunohistochemical, genetic and epigenetic profiles of hereditary and triple negative breast cancers. Relevance in personalized medicine. PMID:26328265
The RNA Binding Protein Igf2bp1 Is Required for Zebrafish RGC Axon Outgrowth In Vivo. PMID:26325373
SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function. PMID:26308709
Identification of miR-215 mediated targets/pathways via translational immunoprecipitation expression analysis (TrIP-chip). PMID:26287603
Specificity and nonspecificity in RNA-protein interactions. PMID:26285679
Predicting effective microRNA target sites in mammalian mRNAs. PMID:26267216
Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network. PMID:26265008
Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP. PMID:26260686
Post-transcriptional regulation of BRCA1 through its coding sequence by the miR-15/107 group of miRNAs. PMID:26257769
AUF1 promotes let-7b loading on Argonaute 2. PMID:26253535
Rare coding variants and X-linked loci associated with age at menarche. PMID:26239645
On the availability of microRNA-induced silencing complexes, saturation of microRNA-binding sites and stoichiometry. PMID:26227970
HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages. PMID:26226348
Identification of the miRNA targetome in hippocampal neurons using RIP-seq. PMID:26219083
MicroRNA as Type I Interferon-Regulated Transcripts and Modulators of the Innate Immune Response. PMID:26217335
MicroRNAs: New Biomarkers for Diagnosis, Prognosis, Therapy Prediction and Therapeutic Tools for Breast Cancer. PMID:26199650
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway. PMID:26170170
Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells. PMID:26162078
Count ratio model reveals bias affecting NGS fold changes. PMID:26160885
Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1. PMID:26152301
Quantifying Protein-mRNA Interactions in Single Live Cells. PMID:26140598
Hepatitis B virus and microRNAs: Complex interactions affecting hepatitis B virus replication and hepatitis B virus-associated diseases. PMID:26139985
Divergent target recognition by coexpressed 5'-isomiRs of miR-142-3p and selective viral mimicry. PMID:26137849
MYCN-driven regulatory mechanisms controlling LIN28B in neuroblastoma. PMID:26123663
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. PMID:26121403
RNA Regulation by Poly(ADP-Ribose) Polymerases. PMID:26091344
Transcriptome dynamics of the microRNA inhibition response. PMID:26089393
MiRBooking simulates the stoichiometric mode of action of microRNAs. PMID:26089388
EBV BART MicroRNAs Target Multiple Pro-apoptotic Cellular Genes to Promote Epithelial Cell Survival. PMID:26070070
Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation. PMID:26054396
Genetic variants in microRNA genes: impact on microRNA expression, function, and disease. PMID:26052338
N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. PMID:26046440
Emerging applications of read profiles towards the functional annotation of the genome. PMID:26042150
Principles of miRNA-mRNA interactions: beyond sequence complementarity. PMID:26037721
LARP4B is an AU-rich sequence associated factor that promotes mRNA accumulation and translation. PMID:26001795
Systematic analysis of the Hmga2 3' UTR identifies many independent regulatory sequences and a novel interaction between distal sites. PMID:25999317
Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR. PMID:25999316
MiR-191 Regulates Primary Human Fibroblast Proliferation and Directly Targets Multiple Oncogenes. PMID:25992613
Prospects for Therapeutic Targeting of MicroRNAs in Human Immunological Diseases. PMID:25980029
An overview of microRNAs. PMID:25979468
Web-Beagle: a web server for the alignment of RNA secondary structures. PMID:25977293
Design and bioinformatics analysis of genome-wide CLIP experiments. PMID:25958398
PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences. PMID:25948580
Lin28 promotes the proliferative capacity of neural progenitor cells in brain development. PMID:25922525
Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis. PMID:25918241
Gemin5 Binds to the Survival Motor Neuron mRNA to Regulate SMN Expression. PMID:25911097
Identification of DNA cleavage- and recombination-specific hnRNP cofactors for activation-induced cytidine deaminase. PMID:25902538
The involvement of insulin-like growth factor 2 binding protein 3 (IMP3) in pancreatic cancer cell migration, invasion, and adhesion. PMID:25886367
Thinking big with small molecules. PMID:25869661
Two Isoforms of the RNA Binding Protein, Coding Region Determinant-binding Protein (CRD-BP/IGF2BP1), Are Expressed in Breast Epithelium and Support Clonogenic Growth of Breast Tumor Cells. PMID:25861986
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
eIF3 targets cell-proliferation messenger RNAs for translational activation or repression. PMID:25849773
Deep sequencing of cardiac microRNA-mRNA interactomes in clinical and experimental cardiomyopathy. PMID:25836573
The RNA recognition motif of NIFK is required for rRNA maturation during cell cycle progression. PMID:25826659
RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation. PMID:25825742
Decoding mechanisms by which silent codon changes influence protein biogenesis and function. PMID:25817479
SubmiRine: assessing variants in microRNA targets using clinical genomic data sets. PMID:25813044
Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells. PMID:25813040
Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. PMID:25800746
miR-200 promotes the mesenchymal to epithelial transition by suppressing multiple members of the Zeb2 and Snail1 transcriptional repressor complexes. PMID:25798844
Mechanisms and Regulation of Alternative Pre-mRNA Splicing. PMID:25784052
Hepatitis C virus RNA functionally sequesters miR-122. PMID:25768906
RNA-binding proteins in neurodegeneration: Seq and you shall receive. PMID:25765321
microRNA-449a functions as a tumor suppressor in neuroblastoma through inducing cell differentiation and cell cycle arrest. PMID:25760387
Plasticity-related microRNA and their potential contribution to the maintenance of long-term potentiation. PMID:25755632
The cell cycle regulator CCDC6 is a key target of RNA-binding protein EWS. PMID:25751255
MicroRNA-10b inhibition reduces E2F1-mediated transcription and miR-15/16 activity in glioblastoma. PMID:25738367
Genome sequence-independent identification of RNA editing sites. PMID:25730491
Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients. PMID:25723320
N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. PMID:25719671
The RNA-binding protein HuR is essential for the B cell antibody response. PMID:25706746
Re-thinking miRNA-mRNA interactions: intertwining issues confound target discovery. PMID:25683051
Identification of metastasis-suppressive microRNAs in primary melanoma. PMID:25677173
Computational Prediction of miRNA Genes from Small RNA Sequencing Data. PMID:25674563
miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing. PMID:25653011
CLIPdb: a CLIP-seq database for protein-RNA interactions. PMID:25652745
Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. PMID:25642422
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data. PMID:25638391
Probing RNA-protein networks: biochemistry meets genomics. PMID:25636997
Alternative splicing: An important mechanism in stem cell biology. PMID:25621101
The assembly of miRNA-mRNA-protein regulatory networks using high-throughput expression data. PMID:25619993
Junk DNA and the long non-coding RNA twist in cancer genetics. PMID:25619839
MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. PMID:25614300
MicroRNAs regulate tight junction proteins and modulate epithelial/endothelial barrier functions. PMID:25610754
Competing endogenous RNA interplay in cancer: mechanism, methodology, and perspectives. PMID:25604144
Noncoding RNA: linking microRNAs to their targets. PMID:25602729
From microRNA target validation to therapy: lessons learned from studies on BDNF. PMID:25601223
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. PMID:25572935
microRNAs function in CD8+T cell biology. PMID:25560605
RNA-binding proteins in pluripotency, differentiation, and reprogramming. PMID:25554730
Silencing of long noncoding RNA MALAT1 by miR-101 and miR-217 inhibits proliferation, migration, and invasion of esophageal squamous cell carcinoma cells. PMID:25538231
ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages. PMID:25533351
miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. PMID:25531890
mRNA and miRNA regulatory networks reflective of multi-walled carbon nanotube-induced lung inflammatory and fibrotic pathologies in mice. PMID:25527334
MicroRNA modules prefer to bind weak and unconventional target sites. PMID:25527098
Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. PMID:25515586
An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments. PMID:25505164
A common set of distinct features that characterize noncoding RNAs across multiple species. PMID:25505163
Leveraging cross-link modification events in CLIP-seq for motif discovery. PMID:25505146
Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. PMID:25502909
Global microRNA expression profiling uncovers molecular markers for classification and prognosis in aggressive B-cell lymphoma. PMID:25498913
High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. PMID:25497548
High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. PMID:25491922
Copy number gain of hsa-miR-569 at 3q26.2 leads to loss of TP53INP1 and aggressiveness of epithelial cancers. PMID:25490449
Competition between target sites of regulators shapes post-transcriptional gene regulation. PMID:25488579
Genomic analysis of RNA localization. PMID:25483039
Of social molecules: The interactive assembly of ASH1 mRNA-transport complexes in yeast. PMID:25482892
MOV10 and FMRP regulate AGO2 association with microRNA recognition elements. PMID:25464849
Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. PMID:25449132
Coordinating expression of RNA binding proteins with their mRNA targets. PMID:25417751
Global changes in the RNA binding specificity of HIV-1 gag regulate virion genesis. PMID:25416948
DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. PMID:25416803
DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. PMID:25416797
Dissecting noncoding and pathogen RNA-protein interactomes. PMID:25411354
G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. PMID:25404306
Molecular insights into the coding region determinant-binding protein-RNA interaction through site-directed mutagenesis in the heterogeneous nuclear ribonucleoprotein-K-homology domains. PMID:25389298
Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models. PMID:25389269
Hunting the needle in the haystack: a guide to obtain biologically meaningful microRNA targets. PMID:25383673
VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. PMID:25380780
Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. PMID:25378249
PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. PMID:25366541
Fingerprints of a message: integrating positional information on the transcriptome. PMID:25364746
mirMark: a site-level and UTR-level classifier for miRNA target prediction. PMID:25344330
Computational Methods for CLIP-seq Data Processing. PMID:25336930
Delineating RBM20 regulation of alternative splicing in dilated cardiomyopathy. PMID:25336447
miR-19, a component of the oncogenic miR-17∼92 cluster, targets the DNA-end resection factor CtIP. PMID:25308476
The many faces of long noncoding RNAs. PMID:25303371
Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. PMID:25301781
CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing. PMID:25301780
Genome-wide mapping of yeast RNA polymerase II termination. PMID:25299594
Exploring the miRNA regulatory network using evolutionary correlations. PMID:25299225
MicroRNA-5p and -3p co-expression and cross-targeting in colon cancer cells. PMID:25287248
Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. PMID:25270025
Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures. PMID:25267525
The microRNA 424/503 cluster reduces CDC25A expression during cell cycle arrest imposed by transforming growth factor β in mammary epithelial cells. PMID:25266660
Control of cell migration through mRNA localization and local translation. PMID:25264217
Role of microRNAs in arbovirus/vector interactions. PMID:25251636
Novel RNA markers in prostate cancer: functional considerations and clinical translation. PMID:25250334
Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. PMID:25242552
A biochemical approach to identify direct microRNA targets. PMID:25240884
Rbfox3 controls the biogenesis of a subset of microRNAs. PMID:25240799
The characterization of microRNA-mediated gene regulation as impacted by both target site location and seed match type. PMID:25238537
A global regulatory mechanism for activating an exon network required for neurogenesis. PMID:25219497
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. PMID:25201102
Comprehensive luciferase-based reporter gene assay reveals previously masked up-regulatory effects of miRNAs. PMID:25192285
The complexity of miRNA-mediated repression. PMID:25190144
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. PMID:25173706
Novel functions and targets of miR-944 in human cervical cancer cells. PMID:25156441
An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines. PMID:25156079
Computational Methods for MicroRNA Target Prediction. PMID:25153283
Target repression induced by endogenous microRNAs: large differences, small effects. PMID:25141277
Understanding functional miRNA-target interactions in vivo by site-specific genome engineering. PMID:25135198
Context-dependent control of alternative splicing by RNA-binding proteins. PMID:25112293
MicroRNA-mediated repression of nonsense mRNAs. PMID:25107276
Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. PMID:25103560
MicroRNAs in the Stressed Heart: Sorting the Signal from the Noise. PMID:25100019
MiR-134-dependent regulation of Pumilio-2 is necessary for homeostatic synaptic depression. PMID:25097251
Effects of genetic variations on microRNA: target interactions. PMID:25081214
Identifying microRNA targets in different gene regions. PMID:25077573
3'LIFE: a functional assay to detect miRNA targets in high-throughput. PMID:25074381
Expanded identification and characterization of mammalian circular RNAs. PMID:25070500
Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion. PMID:25069772
Regulation of miRNA processing and miRNA mediated gene repression in cancer. PMID:25069508
Plant microRNA-target interaction identification model based on the integration of prediction tools and support vector machine. PMID:25051153
PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. PMID:25049417
Functional interactions between microRNAs and RNA binding proteins. PMID:25048093
Not miR-ly micromanagers: the functions and regulatory networks of microRNAs in mammalian skin. PMID:25044412
Identification and consequences of miRNA-target interactions--beyond repression of gene expression. PMID:25022902
Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. PMID:24997788
A protein-RNA specificity code enables targeted activation of an endogenous human transcript. PMID:24997599
Progress and challenge of microRNA research in immunity. PMID:24971086
Single Nucleotide Polymorphisms Associated with MicroRNA Regulation. PMID:24970168
RNA stimulates Aurora B kinase activity during mitosis. PMID:24968351
RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing. PMID:24960161
Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. PMID:24951655
The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation. PMID:24942623
HITS-CLIP and PAR-CLIP advance viral miRNA targetome analysis. PMID:24940765
MicroRNAs and their applications in kidney diseases. PMID:24928414
RNA-binding proteins regulate the expression of the immune activating ligand MICB. PMID:24924487
Cellular microRNAs and picornaviral infections. PMID:24921242
QKI impairs self-renewal and tumorigenicity of oral cancer cells via repression of SOX2. PMID:24918581
Transcriptional and posttranscriptional regulation of cytokine gene expression in HIV-1 antigen-specific CD8+ T cells that mediate virus inhibition. PMID:24899193
RNA-binding protein AUF1 promotes myogenesis by regulating MEF2C expression levels. PMID:24891619
Analysis of FMRP mRNA target datasets reveals highly associated mRNAs mediated by G-quadruplex structures formed via clustered WGGA sequences. PMID:24876161
Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. PMID:24875477
The role of microRNAs in hepatitis C virus replication and related liver diseases. PMID:24871972
MicroRNA-dependent genetic networks during neural development. PMID:24865244
Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. PMID:24857550
Motif-based analysis of large nucleotide data sets using MEME-ChIP. PMID:24853928
MicroRNAs down-regulate homologous recombination in the G1 phase of cycling cells to maintain genomic stability. PMID:24843000
MicroRNA Target Identification-Experimental Approaches. PMID:24832658
Transcriptional Gene Silencing (TGS) via the RNAi Machinery in HIV-1 Infections. PMID:24832229
RBPmap: a web server for mapping binding sites of RNA-binding proteins. PMID:24829458
RNA sequencing: from tag-based profiling to resolving complete transcript structure. PMID:24827995
MicroRNA binding sites in C. elegans 3' UTRs. PMID:24827614
Reading RNA methylation codes through methyl-specific binding proteins. PMID:24823649
Non-inhibited miRNAs shape the cellular response to anti-miR. PMID:24810853
Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. PMID:24809628
STarMir: a web server for prediction of microRNA binding sites. PMID:24803672
MicroRNA roles in the NF- κB signaling pathway during viral infections. PMID:24800225
CAHM, a long non-coding RNA gene hypermethylated in colorectal neoplasia. PMID:24799664
Trans-regulation of RNA-binding protein motifs by microRNA. PMID:24795744
Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. PMID:24793693
A cytoplasmic quaking I isoform regulates the hnRNP F/H-dependent alternative splicing pathway in myelinating glia. PMID:24792162
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. PMID:24780077
Cytomegalovirus microRNAs. PMID:24769092
Illustrating the interplay between the extracellular matrix and microRNAs. PMID:24761792
PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps. PMID:24758252
Derivation and characterization of Dicer- and microRNA-deficient human cells. PMID:24757167
Characterization of miRNomes in acute and chronic myeloid leukemia cell lines. PMID:24755403
A novel approach to represent and compare RNA secondary structures. PMID:24753415
Genome-wide mapping of cellular protein-RNA interactions enabled by chemical crosslinking. PMID:24747191
C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation. PMID:24744981
In vivo ligands of MDA5 and RIG-I in measles virus-infected cells. PMID:24743923
Elements and machinery of non-coding RNAs: toward their taxonomy. PMID:24731943
Similarity in targets with REST points to neural and glioblastoma related miRNAs. PMID:24728992
The RNA-binding protein QKI suppresses cancer-associated aberrant splicing. PMID:24722255
A neuron-specific host microRNA targets herpes simplex virus-1 ICP0 expression and promotes latency. PMID:24721573
Macros in microRNA target identification: a comparative analysis of in silico, in vitro, and in vivo approaches to microRNA target identification. PMID:24717361
Adaptable probabilistic mapping of short reads using position specific scoring matrices. PMID:24717095
A model-based approach to identify binding sites in CLIP-Seq data. PMID:24714572
Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs. PMID:24708618
IGF2BP1 controls cell death and drug resistance in rhabdomyosarcomas by regulating translation of cIAP1. PMID:24704827
Characterization of human pseudogene-derived non-coding RNAs for functional potential. PMID:24699680
Coordinated post-transcriptional regulation of the chemokine system: messages from CCL2. PMID:24697203
A novel mechanism for the control of translation of specific mRNAs by tumor suppressor protein Pdcd4: inhibition of translation elongation. PMID:24681950
Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length. PMID:24681684
Widespread context dependency of microRNA-mediated regulation. PMID:24668909
A versatile assay for RNA-binding proteins in living cells. PMID:24664470
Identifying mRNA sequence elements for target recognition by human Argonaute proteins. PMID:24663241
The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. PMID:24636986
Massively parallel functional annotation of 3' untranslated regions. PMID:24633241
Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs. PMID:24629056
Long non-coding RNA HOTAIR is targeted and regulated by miR-141 in human cancer cells. PMID:24616104
Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach. PMID:24609385
PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins. PMID:24581442
Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque. PMID:24577841
Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). PMID:24577361
Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP. PMID:24571656
Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. PMID:24569168
Extensive sequence variation in the 3' untranslated region of the KRAS gene in lung and ovarian cancer cases. PMID:24552817
Long non-coding RNAs: modulators of nuclear structure and function. PMID:24529241
Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. PMID:24526010
Human platelet microRNA-mRNA networks associated with age and gender revealed by integrated plateletomics. PMID:24523238
Rapid identification of regulatory microRNAs by miTRAP (miRNA trapping by RNA in vitro affinity purification). PMID:24510096
MicroRNAs: master regulators of drug resistance, stemness, and metastasis. PMID:24509937
Library construction for next-generation sequencing: overviews and challenges. PMID:24502796
The RBPome: where the brains meet the brawn. PMID:24485298
Composition of seed sequence is a major determinant of microRNA targeting patterns. PMID:24470575
The panorama of miRNA-mediated mechanisms in mammalian cells. PMID:24468964
Methods for comprehensive experimental identification of RNA-protein interactions. PMID:24467948
Seq and CLIP through the miRNA world. PMID:24460822
Role of IGF2BP3 in trophoblast cell invasion and migration. PMID:24457969
Applying thiouracil tagging to mouse transcriptome analysis. PMID:24457332
PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. PMID:24451213
GraphProt: modeling binding preferences of RNA-binding proteins. PMID:24451197
Analysis of the mRNA targetome of microRNAs expressed by Marek's disease virus. PMID:24449754
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. PMID:24447569
Sequencing depth and coverage: key considerations in genomic analyses. PMID:24434847
The multilayered complexity of ceRNA crosstalk and competition. PMID:24429633
Differential protein occupancy profiling of the mRNA transcriptome. PMID:24417896
Single molecule fluorescence approaches shed light on intracellular RNAs. PMID:24417544
Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. PMID:24407421
Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. PMID:24407355
Global target mRNA specification and regulation by the RNA-binding protein ZFP36. PMID:24401661
Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets. PMID:24398324
dCLIP: a computational approach for comparative CLIP-seq analyses. PMID:24398258
RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins. PMID:24393626
RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. PMID:24393486
Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. PMID:24393468
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. PMID:24393166
Transcriptome-wide discovery of microRNA binding sites in human brain. PMID:24389009
Demystifying the nuclear function of Argonaute proteins. PMID:24384674
Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin. PMID:24374312
Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. PMID:24339831
Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination. PMID:24326307
A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. PMID:24316715
New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. PMID:24311560
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. PMID:24304892
Long noncoding RNAs: fresh perspectives into the RNA world. PMID:24290031
Single nucleotide polymorphisms in microRNA binding sites of oncogenes: implications in cancer and pharmacogenomics. PMID:24286505
N6-methyladenosine-dependent regulation of messenger RNA stability. PMID:24284625
Systems biology approach to the dissection of the complexity of regulatory networks in the S. scrofa cardiocirculatory system. PMID:24284405
Evolutionary conservation of primate lymphocryptovirus microRNA targets. PMID:24257599
Interplay of chromatin modifications and non-coding RNAs in the heart. PMID:24247090
How do viruses avoid inhibition by endogenous cellular microRNAs? PMID:24244153
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. PMID:24243805
MicroRNA levels are modulated in Aedes aegypti after exposure to Dengue-2. PMID:24237456
Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. PMID:24220575
Dynamically regulated miRNA-mRNA networks revealed by exercise. PMID:24219008
Finding the target sites of RNA-binding proteins. PMID:24217996
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. PMID:24213538
Parallel measurement of dynamic changes in translation rates in single cells. PMID:24213167
The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. PMID:24212931
Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. PMID:24211736
Loss of miR-10a activates lpo and collaborates with activated Wnt signaling in inducing intestinal neoplasia in female mice. PMID:24204315
A network of heterochronic genes including Imp1 regulates temporal changes in stem cell properties. PMID:24192035
iCLIP: protein-RNA interactions at nucleotide resolution. PMID:24184352
Complexity of the alternative splicing landscape in plants. PMID:24179125
The trypanosome Pumilio domain protein PUF5. PMID:24167571
PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. PMID:24163105
MicroRNA 4423 is a primate-specific regulator of airway epithelial cell differentiation and lung carcinogenesis. PMID:24158479
An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. PMID:24157833
HuR-regulated mRNAs associated with nuclear hnRNP A1-RNP complexes. PMID:24152440
PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells. PMID:24141703
Chronic academic stress increases a group of microRNAs in peripheral blood. PMID:24130753
The dataset for protein-RNA binding affinity. PMID:24127340
An extensive network of TET2-targeting MicroRNAs regulates malignant hematopoiesis. PMID:24120864
High-throughput fluorescence anisotropy screen for inhibitors of the oncogenic mRNA binding protein, IMP-1. PMID:24108120
RIPiT-Seq: a high-throughput approach for footprinting RNA:protein complexes. PMID:24096052
Zebrafish embryonic neurons transport messenger RNA to axons and growth cones in vivo. PMID:24089481
In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions. PMID:24082822
The evolution of evolvability in microRNA target sites in vertebrates. PMID:24077390
3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. PMID:24072873
The imprinted H19 lncRNA antagonizes let-7 microRNAs. PMID:24055342
Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. PMID:24038734
Reciprocal regulation of microRNA-122 and c-Myc in hepatocellular cancer: role of E2F1 and transcription factor dimerization partner 2. PMID:24038073
4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response. PMID:24025460
miR-1247 functions by targeting cartilage transcription factor SOX9. PMID:24014021
Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia. PMID:24009312
Non-coding RNAs turn up the heat: an emerging layer of novel regulators in the mammalian heat shock response. PMID:24002685
Integrative analysis revealed the molecular mechanism underlying RBM10-mediated splicing regulation. PMID:24000153
Developing microRNA screening as a functional genomics tool for disease research. PMID:23986717
Kaposi's sarcoma-associated herpesvirus encodes a mimic of cellular miR-23. PMID:23986579
Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression. PMID:23974436
Principles of miRNA-target regulation in metazoan models. PMID:23965954
A quantitative method to identify microRNAs targeting a messenger RNA using a 3'UTR RNA affinity technique. PMID:23938772
Decrease of miR-202-3p expression, a novel tumor suppressor, in gastric cancer. PMID:23936094
Divergent MicroRNA targetomes of closely related circulating strains of a polyomavirus. PMID:23926342
RFMirTarget: predicting human microRNA target genes with a random forest classifier. PMID:23922946
MicroRNA-17~92 plays a causative role in lymphomagenesis by coordinating multiple oncogenic pathways. PMID:23921550
Comprehensive analysis of microRNA (miRNA) targets in breast cancer cells. PMID:23921383
RNA polymerase II transcription elongation control. PMID:23919563
Emerging roles of competing endogenous RNAs in cancer: insights from the regulation of PTEN. PMID:23918803
MicroRNA-mediated regulation of T helper cell differentiation and plasticity. PMID:23907446
PARma: identification of microRNA target sites in AGO-PAR-CLIP data. PMID:23895117
Large-scale screens of miRNA-mRNA interactions unveiled that the 3'UTR of a gene is targeted by multiple miRNAs. PMID:23874542
MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets. PMID:23863844
Regulatory non-coding RNAs in pluripotent stem cells. PMID:23852015
Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation. PMID:23844135
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. PMID:23816784
Functional genomics approaches to understand cytomegalovirus replication, latency and pathogenesis. PMID:23816389
Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation. PMID:23792593
Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW. PMID:23788626
Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation. PMID:23770886
Uniform, optimal signal processing of mapped deep-sequencing data. PMID:23770639
Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. PMID:23749060
γ-Herpesvirus-encoded miRNAs and their roles in viral biology and pathogenesis. PMID:23743127
Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay. PMID:23737738
Control of metastatic progression by microRNA regulatory networks. PMID:23728460
mRNA on the move: the road to its biological destiny. PMID:23720759
Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. PMID:23717260
Translation initiation factor eIF3h targets specific transcripts to polysomes during embryogenesis. PMID:23716667
Emerging tools for synthetic genome design. PMID:23708771
MicroRNA target site identification by integrating sequence and binding information. PMID:23708386
Identifying and characterizing Hfq-RNA interactions. PMID:23707622
Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing. PMID:23706177
CLIP-based prediction of mammalian microRNA binding sites. PMID:23703212
ComiR: Combinatorial microRNA target prediction tool. PMID:23703208
RNA protein interaction in neurons. PMID:23701460
MicroRNA-185 oscillation controls circadian amplitude of mouse Cryptochrome 1 via translational regulation. PMID:23699394
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. PMID:23696454
The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance. PMID:23696004
DRIMust: a web server for discovering rank imbalanced motifs using suffix trees. PMID:23685432
Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq. PMID:23684513
IGF2BP1 promotes mesenchymal cell properties and migration of tumor-derived cells by enhancing the expression of LEF1 and SNAI2 (SLUG). PMID:23677615
Genome-wide identification of translationally inhibited and degraded miR-155 targets using RNA-interacting protein-IP. PMID:23673373
Biological basis of miRNA action when their targets are located in human protein coding region. PMID:23671676
Drosophila miR-277 controls branched-chain amino acid catabolism and affects lifespan. PMID:23669073
Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface. PMID:23665222
Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. PMID:23630077
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. PMID:23622248
Iron-responsive miR-485-3p regulates cellular iron homeostasis by targeting ferroportin. PMID:23593016
In-depth analysis of the interaction of HIV-1 with cellular microRNA biogenesis and effector mechanisms. PMID:23592263
Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP. PMID:23583680
CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders. PMID:23583633
microRNA-mediated regulation of innate immune response in rheumatic diseases. PMID:23582400
Regulation of miRNA biogenesis and turnover in the immune system. PMID:23550654
Exploring the RNA world in hematopoietic cells through the lens of RNA-binding proteins. PMID:23550653
Regulation of immune responses and tolerance: the microRNA perspective. PMID:23550642
MicroRNA regulation of T-cell differentiation and function. PMID:23550639
MicroRNA function in NK-cell biology. PMID:23550637
Regulation of B-cell development and function by microRNAs. PMID:23550636
RNA regulation of the immune system. PMID:23550634
A regulatory role for microRNA 33* in controlling lipid metabolism gene expression. PMID:23547260
Mutational inactivation of herpes simplex virus 1 microRNAs identifies viral mRNA targets and reveals phenotypic effects in culture. PMID:23536669
Oncogenic NRAS, required for pathogenesis of embryonic rhabdomyosarcoma, relies upon the HMGA2-IGF2BP2 pathway. PMID:23536553
Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation. PMID:23525800
Solution structure of the QUA1 dimerization domain of pXqua, the Xenopus ortholog of Quaking. PMID:23520467
Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans. PMID:23516374
Needles in the genetic haystack of lipid disorders: single nucleotide polymorphisms in the microRNA regulome. PMID:23505316
Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition. PMID:23481595
How cells get the message: dynamic assembly and function of mRNA-protein complexes. PMID:23478349
Bridging epigenomics and complex disease: the basics. PMID:23463237
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. PMID:23455476
Multi-disciplinary methods to define RNA-protein interactions and regulatory networks. PMID:23453689
A functional genomics screen for microRNA regulators of NF-kappaB signaling. PMID:23448136
Circular RNAs are a large class of animal RNAs with regulatory potency. PMID:23446348
Noncoding RNA and Polycomb recruitment. PMID:23431328
Alternative polyadenylation in glioblastoma multiforme and changes in predicted RNA binding protein profiles. PMID:23421905
MicroRNAs distinguish cytogenetic subgroups in pediatric AML and contribute to complex regulatory networks in AML-relevant pathways. PMID:23418555
System-wide identification of RNA-binding proteins by interactome capture. PMID:23411631
Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. PMID:23409723
Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PMID:23405074
Searching the coding region for microRNA targets. PMID:23404894
Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. PMID:23392611
mTOR complex 2 phosphorylates IMP1 cotranslationally to promote IGF2 production and the proliferation of mouse embryonic fibroblasts. PMID:23388827
MicroRNAs in human cancer. PMID:23377965
Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. PMID:23376935
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. PMID:23374342
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. PMID:23368412
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. PMID:23335364
mirTarPri: improved prioritization of microRNA targets through incorporation of functional genomics data. PMID:23326485
Isolation and identification of cell-specific microRNAs targeting a messenger RNA using a biotinylated anti-sense oligonucleotide capture affinity technique. PMID:23325846
The QKI-5 and QKI-6 RNA binding proteins regulate the expression of microRNA 7 in glial cells. PMID:23319046
Mechanisms coordinating ELAV/Hu mRNA regulons. PMID:23312841
Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs. PMID:23303783
Reprogramming of the microRNA transcriptome mediates resistance to rapamycin. PMID:23300087
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PMID:23284279
Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression. PMID:23268654
Evolutionary relationships between miRNA genes and their activity. PMID:23259970
HIV-1 suppressive sequences are modulated by Rev transport of unspliced RNA and are required for efficient HIV-1 production. PMID:23251516
Complex role of microRNAs in HTLV-1 infections. PMID:23251140
miRNA-mediated risk for schizophrenia in 22q11.2 deletion syndrome. PMID:23248646
FMRP targets distinct mRNA sequence elements to regulate protein expression. PMID:23235829
Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression. PMID:23233736
Up-regulation of Imp3 confers in vivo tumorigenicity on murine osteosarcoma cells. PMID:23226335
Systematic screens of proteins binding to synthetic microRNA precursors. PMID:23221640
Toward a genome-wide landscape of translational control. PMID:23209130
Predicting sRNAs and their targets in bacteria. PMID:23200137
Finding microRNA targets in plants: current status and perspectives. PMID:23200136
One decade of development and evolution of microRNA target prediction algorithms. PMID:23200135
Translational control by 3'-UTR-binding proteins. PMID:23196851
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. PMID:23193281
A microRNA encoded by Kaposi sarcoma-associated herpesvirus promotes B-cell expansion in vivo. PMID:23185331
SomamiR: a database for somatic mutations impacting microRNA function in cancer. PMID:23180788
An HMGA2-IGF2BP2 axis regulates myoblast proliferation and myogenesis. PMID:23177649
Identifying miRNAs, targets and functions. PMID:23175680
Noncanonical microRNAs and endogenous siRNAs in normal and psoriatic human skin. PMID:23175445
MicroRNA-mediated restriction of HIV-1 in resting CD4+ T cells and monocytes. PMID:23170164
Insect microRNAs: biogenesis, expression profiling and biological functions. PMID:23165178
Changes in microRNA expression in the MG-63 osteosarcoma cell line compared with osteoblasts. PMID:23162647
Identification of proteins binding coding and non-coding human RNAs using protein microarrays. PMID:23157412
Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. PMID:23142080
The functions of microRNAs in pluripotency and reprogramming. PMID:23131918
MicroRNA sequence profiles of human kidney allografts with or without tubulointerstitial fibrosis. PMID:23131772
The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA function. PMID:23125361
Alternative polyadenylation: new insights from global analyses. PMID:23097429
Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes. PMID:23091610
Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs): post-transcriptional drivers of cancer progression? PMID:23069990
Genome-wide approaches to dissect the roles of RNA binding proteins in translational control: implications for neurological diseases. PMID:23060744
MicroRNA-target interactions: new insights from genome-wide approaches. PMID:23050973
Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome. PMID:23049969
MicroRNAs and HIV-1: complex interactions. PMID:23043098
POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster. PMID:23034181
Molecular network analysis of human microRNA targetome: from cancers to Alzheimer's disease. PMID:23034144
Probing Evolutionary Biography of MicroRNAs and Associated Factors. PMID:23024606
Site identification in high-throughput RNA-protein interaction data. PMID:23024010
Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression. PMID:22995832
Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. PMID:22991471
P-value-based regulatory motif discovery using positional weight matrices. PMID:22990209
IGF2BP1: a post-transcriptional "driver" of tumor cell migration. PMID:22983196
Structural analysis of the quaking homodimerization interface. PMID:22982292
Identification of novel targets for miR-29a using miRNA proteomics. PMID:22952654
Posttranscriptional regulation of gene expression-adding another layer of complexity to the DNA damage response. PMID:22936947
Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas. PMID:22927820
Genome-wide identification of miRNA targets by PAR-CLIP. PMID:22926237
Analysis of the accessibility of CLIP bound sites reveals that nucleation of the miRNA:mRNA pairing occurs preferentially at the 3'-end of the seed match. PMID:22915600
MicroRNAs and autoimmunity. PMID:22902047
Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets. PMID:22888400
Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing. PMID:22885844
Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. PMID:22885304
Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. PMID:22871084
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. PMID:22863408
Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. PMID:22858678
Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types. PMID:22849433
A new module in neural differentiation control: two microRNAs upregulated by retinoic acid, miR-9 and -103, target the differentiation inhibitor ID2. PMID:22848373
An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. PMID:22844237
Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data. PMID:22844102
Association of Argonaute proteins and microRNAs can occur after cell lysis. PMID:22836356
RNA sequencing: platform selection, experimental design, and data interpretation. PMID:22830413
MicroRNAs and esophageal cancer. PMID:22811805
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. PMID:22806141
The greatest catch: big game fishing for mRNA-bound proteins. PMID:22805650
Dysregulation of uterine signaling pathways in progesterone receptor-Cre knockout of dicer. PMID:22798293
DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. PMID:22796965
MicroRNA-27b is a regulatory hub in lipid metabolism and is altered in dyslipidemia. PMID:22777896
Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. PMID:22759612
High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries. PMID:22751203
From cis-regulatory elements to complex RNPs and back. PMID:22751153
Perspectives on the ARE as it turns 25 years old. PMID:22733578
The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PMID:22723874
Cytoplasmic RNA-binding proteins and the control of complex brain function. PMID:22723494
MicroRNA and cutaneous melanoma: from discovery to prognosis and therapy. PMID:22693259
Global patterns of tissue-specific alternative polyadenylation in Drosophila. PMID:22685694
An oxygen-regulated switch in the protein synthesis machinery. PMID:22678294
The hallmarks of cancer: a long non-coding RNA point of view. PMID:22664915
MicroRNAs in renal development. PMID:22660936
The let-7-Imp axis regulates ageing of the Drosophila testis stem-cell niche. PMID:22660319
The microRNA-17-92 family of microRNA clusters in development and disease. PMID:22647363
Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. PMID:22645572
Next generation quantitative genetics in plants. PMID:22645550
MicroRNA-206 regulates cell movements during zebrafish gastrulation by targeting prickle1a and regulating c-Jun N-terminal kinase 2 phosphorylation. PMID:22615492
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. PMID:22574288
miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets. PMID:22566243
Kaposi's Sarcoma-Associated Herpesvirus microRNAs. PMID:22563327
Embryonic stem cell miRNAs and their roles in development and disease. PMID:22561239
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. PMID:22539649
Base pairing between hepatitis C virus RNA and microRNA 122 3' of its seed sequence is essential for genome stabilization and production of infectious virus. PMID:22532678
Computational inference of mRNA stability from histone modification and transcriptome profiles. PMID:22495509
Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site. PMID:22467831
Small non-coding RNAs mount a silent revolution in gene expression. PMID:22464106
Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. PMID:22457636
Impact of microRNA regulation on variation in human gene expression. PMID:22456605
RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. PMID:22454234
The regulation of mRNA stability in mammalian cells: 2.0. PMID:22452843
Misregulated RNA processing in amyotrophic lateral sclerosis. PMID:22444279
microPIR: an integrated database of microRNA target sites within human promoter sequences. PMID:22439011
MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. PMID:22411466
Optimal use of conservation and accessibility filters in microRNA target prediction. PMID:22384176
Decoding the cardiac message: the 2011 Thomas W. Smith Memorial Lecture. PMID:22383710
Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PMID:22346748
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. PMID:22344696
An alternative mode of microRNA target recognition. PMID:22343717
Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments. PMID:22325809
Regulation of senescence by microRNA biogenesis factors. PMID:22306790
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
Systems Biology Reveals MicroRNA-Mediated Gene Regulation. PMID:22303325
The long and short of microRNAs in the kidney. PMID:22302196
The viral and cellular microRNA targetome in lymphoblastoid cell lines. PMID:22291592
A zipcode unzipped. PMID:22279044
Looking at Kaposi's Sarcoma-Associated Herpesvirus-Host Interactions from a microRNA Viewpoint. PMID:22275910
Regulation of IMP3 by EGFR signaling and repression by ERβ: implications for triple-negative breast cancer. PMID:22266872
Protein-RNA interactions: new genomic technologies and perspectives. PMID:22251872
Advances in microRNA experimental approaches to study physiological regulation of gene products implicated in CNS disorders. PMID:22245616
Inhibition of microRNA function by antimiR oligonucleotides. PMID:22230293
Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control. PMID:22215810
Identification of RNA-protein interaction networks using PAR-CLIP. PMID:22213601
Identification of evolutionarily conserved exons as regulated targets for the splicing activator tra2β in development. PMID:22194695
Predicting RNA-protein interactions using only sequence information. PMID:22192482
Upregulation of the cell-cycle regulator RGC-32 in Epstein-Barr virus-immortalized cells. PMID:22163048
RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. PMID:22162396
In vivo and transcriptome-wide identification of RNA binding protein target sites. PMID:22152485
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. PMID:22135297
miREE: miRNA recognition elements ensemble. PMID:22115078
Replication competent HIV-1 viruses that express intragenomic microRNA reveal discrete RNA-interference mechanisms that affect viral replication. PMID:22112720
Structural effects of linkage disequilibrium on the transcriptome. PMID:22109839
Ago-2-mediated slicer activity is essential for anti-flaviviral efficacy of RNAi. PMID:22102908
Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PMID:22102825
Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. PMID:22101243
Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. PMID:22100165
doRiNA: a database of RNA interactions in post-transcriptional regulation. PMID:22086949
RNA targets of wild-type and mutant FET family proteins. PMID:22081015
PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. PMID:22080514
New insights in the mechanism of microRNA-mediated target repression. PMID:22056803
Functional microRNA screening using a comprehensive lentiviral human microRNA expression library. PMID:22050702
A systematic screen for micro-RNAs regulating the canonical Wnt pathway. PMID:22043311
Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PMID:22028667
Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. PMID:22012620
An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. PMID:22000015
Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. PMID:21954178
The QKI-PLP pathway controls SIRT2 abundance in CNS myelin. PMID:21948283
HITS-CLIP: panoramic views of protein-RNA regulation in living cells. PMID:21935890
A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population. PMID:21917492
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. PMID:21911355
Viruses and microRNAs: RISCy interactions with serious consequences. PMID:21896651
Mechanisms of dendritic mRNA transport and its role in synaptic tagging. PMID:21878995
MicroRNAs coordinately regulate protein complexes. PMID:21867514
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. PMID:21851591
Understanding the transcriptome through RNA structure. PMID:21850044
QKI-mediated alternative splicing of the histone variant MacroH2A1 regulates cancer cell proliferation. PMID:21844227
The role of microRNAs in Epstein-Barr virus latency and lytic reactivation. PMID:21835261
Emerging roles for the Ro 60-kDa autoantigen in noncoding RNA metabolism. PMID:21823229
MicroRNA in TLR signaling and endotoxin tolerance. PMID:21822296
MicroRNA regulation by RNA-binding proteins and its implications for cancer. PMID:21822212
UneCLIPsing HuR nuclear function. PMID:21816340
PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. PMID:21788334
FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. PMID:21784246
RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. PMID:21775473
Viral miRNAs and immune evasion. PMID:21757042
Dicer recognizes the 5' end of RNA for efficient and accurate processing. PMID:21753850
Multilayer checkpoints for microRNA authenticity during RISC assembly. PMID:21738221
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. PMID:21723170
Inferring causative variants in microRNA target sites. PMID:21693556
Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. PMID:21685129
Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements. PMID:21674004
miR-122 activates hepatitis C virus translation by a specialized mechanism requiring particular RNA components. PMID:21653556
Experimental strategies for microRNA target identification. PMID:21652644
PUMILIO-2 is involved in the positive regulation of cellular proliferation in human adipose-derived stem cells. PMID:21649561
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. PMID:21633356
MicroRNAs in rheumatoid arthritis. PMID:21600203
MicroRNAs and their roles in mammalian stem cells. PMID:21576351
mTOR phosphorylates IMP2 to promote IGF2 mRNA translation by internal ribosomal entry. PMID:21576258
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. PMID:21572407
Toward a systematic understanding of mRNA 3' untranslated regions. PMID:21543795
The ribosomal protein RACK1 is required for microRNA function in both C. elegans and humans. PMID:21525958
Pre-mRNA splicing: where and when in the nucleus. PMID:21514162
MicroRNAs in NF-kappaB signaling. PMID:21502305
Zipcode binding protein 1 regulates the development of dendritic arbors in hippocampal neurons. PMID:21471362
The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. PMID:21460797
The impact of miRNA target sites in coding sequences and in 3'UTRs. PMID:21445367
The sufficient minimal set of miRNA seed types. PMID:21441577
miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. PMID:21441347
Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts. PMID:21415141
Interactome networks and human disease. PMID:21414488
MicroRNAs: Allies or foes in erythropoiesis? PMID:21412774
Viral microRNA target allows insight into the role of translation in governing microRNA target accessibility. PMID:21402938
Alternate modes of cognate RNA recognition by human PUMILIO proteins. PMID:21397187
Combined characterization of microRNA and mRNA profiles delineates early differentiation pathways of CD133+ and CD34+ hematopoietic stem and progenitor cells. PMID:21394831
Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. PMID:21390282
MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. PMID:21389147
A viral microRNA cluster strongly potentiates the transforming properties of a human herpesvirus. PMID:21379335
RNA-protein interactions in human health and disease. PMID:21333748
Post-transcriptional regulation of amyloid precursor protein by microRNAs and RNA binding proteins. PMID:21331224
Pharmacogenomics of the RNA world: structural RNA polymorphisms in drug therapy. PMID:21289622
Quantitative profiling of in vivo-assembled RNA-protein complexes using a novel integrated proteomic approach. PMID:21285413
Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. PMID:21282978
Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. PMID:21258322
Quaking regulates Hnrnpa1 expression through its 3' UTR in oligodendrocyte precursor cells. PMID:21253564
Understanding splicing regulation through RNA splicing maps. PMID:21232811
Genome-wide approaches in the study of microRNA biology. PMID:21197653
A two-step site and mRNA-level model for predicting microRNA targets. PMID:21194446
Widespread regulatory activity of vertebrate microRNA* species. PMID:21177881
A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1. PMID:21169991
A study of miRNAs targets prediction and experimental validation. PMID:21153515
Vigilance and validation: Keys to success in RNAi screening. PMID:21142076
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. PMID:21127008
miRNAs in human cancer. PMID:21125669
The RNA structurome: high-throughput probing. PMID:21116245
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. PMID:21087992
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. PMID:21037263
RBPDB: a database of RNA-binding specificities. PMID:21036867
Affinity purification of microRNA-133a with the cardiac transcription factor, Hand2. PMID:20974915
MicroRNA functions in stress responses. PMID:20965416
MiRonTop: mining microRNAs targets across large scale gene expression studies. PMID:20959382
Role of the RNA-binding protein IMP-2 in muscle cell motility. PMID:20956565
Quaking I controls a unique cytoplasmic pathway that regulates alternative splicing of myelin-associated glycoprotein. PMID:20956316
RNA regulation in neurologic disease and cancer. PMID:20948916
The piRNA pathway: a fly's perspective on the guardian of the genome. PMID:20934772
Desperately seeking microRNA targets. PMID:20924405
Context-dependent functions of specific microRNAs in neuronal development. PMID:20920300
The QKI-6 RNA binding protein localizes with the MBP mRNAs in stress granules of glial cells. PMID:20862255
Virally induced cellular microRNA miR-155 plays a key role in B-cell immortalization by Epstein-Barr virus. PMID:20844043
Analysis of microRNA knockouts in mice. PMID:20805106
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. PMID:20799968
Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs. PMID:20729470
The miR-15/107 group of microRNA genes: evolutionary biology, cellular functions, and roles in human diseases. PMID:20678503
The widespread regulation of microRNA biogenesis, function and decay. PMID:20661255
PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. PMID:20644507
Bound to the messenger. PMID:20524217
Signatures of RNA binding proteins globally coupled to effective microRNA target sites. PMID:20508147
A genome-wide map of conserved microRNA targets in C. elegans PubMed citations: 199.

199 articles citing: A genome-wide map of conserved microRNA targets in C. elegans

The FGFR4 Homolog KIN-9 Regulates Lifespan and Stress Responses in Caenorhabditis elegans. PMID:35821842
The signaling pathway of levamisole-sensitive-acetylcholine receptors involved in short-term forgetting of Caenorhabditis elegans. PMID:35585325
Network Approaches to Study Endogenous RNA Competition and Its Impact on Tissue-Specific microRNA Functions. PMID:35204832
Bioinformatics Prediction and Analysis of MicroRNAs and Their Targets as Biomarkers for Prostate Cancer: A Preliminary Study. PMID:34665432
Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma. PMID:34662337
miR-1 sustains muscle physiology by controlling V-ATPase complex assembly. PMID:34652942
MicroRNA Targeting. PMID:34432276
miR-1 coordinately regulates lysosomal v-ATPase and biogenesis to impact proteotoxicity and muscle function during aging. PMID:34311841
Comparison of the Therapeutic Effect of Allogeneic and Xenogeneic Small Extracellular Vesicles in Soft Tissue Repair. PMID:33061363
Role of miRNA-mRNA Interaction in Neural Stem Cell Differentiation of Induced Pluripotent Stem Cells. PMID:32977388
Intergenerational Pathogen-Induced Diapause in Caenorhabditis elegans Is Modulated by mir-243. PMID:32963007
Robust partitioning of microRNA targets from downstream regulatory changes. PMID:32821933
Serum-borne factors alter cerebrovascular endothelial microRNA expression following particulate matter exposure near an abandoned uranium mine on the Navajo Nation. PMID:32611356
MicroRNA-34a Acutely Regulates Synaptic Efficacy in the Adult Dentate Gyrus In Vivo. PMID:31754996
Dynamics of microRNA expression during mouse prenatal development. PMID:31645363
MiR-20b Down-Regulates Intestinal Ferroportin Expression In Vitro and In Vivo. PMID:31554201
Functional Screening Identifies MicroRNA Regulators of Corin Activity and Atrial Natriuretic Peptide Biogenesis. PMID:31548261
ALG-1 Influences Accurate mRNA Splicing Patterns in the Caenorhabditis elegans Intestine and Body Muscle Tissues by Modulating Splicing Factor Activities. PMID:31073019
miRNAs, target genes expression and morphological analysis on the heart in gestational protein-restricted offspring. PMID:31034522
Neurite-Enriched MicroRNA-218 Stimulates Translation of the GluA2 Subunit and Increases Excitatory Synaptic Strength. PMID:30671783
Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors. PMID:30531873
Coal combustion related fine particulate matter (PM2.5) induces toxicity in Caenorhabditis elegans by dysregulating microRNA expression. PMID:30090511
Trends in the development of miRNA bioinformatics tools. PMID:29982332
Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. PMID:29967059
Mechanistic Insights into MicroRNA-Mediated Gene Silencing. PMID:29959194
Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. PMID:29873777
Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. PMID:29846699
Systematic analysis of the molecular mechanism of microRNA-124 in hepatoblastoma cells. PMID:29344147
The role of microRNAs in chronic respiratory disease: recent insights. PMID:29148977
A small molecule drug promoting miRNA processing induces alternative splicing of MdmX transcript and rescues p53 activity in human cancer cells overexpressing MdmX protein. PMID:28973015
acn-1, a C. elegans homologue of ACE, genetically interacts with the let-7 microRNA and other heterochronic genes. PMID:28933985
Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network. PMID:28656148
Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues. PMID:28348061
MiRNATIP: a SOM-based miRNA-target interactions predictor. PMID:28185545
Novel blood-based microRNA biomarker panel for early diagnosis of chronic pancreatitis. PMID:28074846
Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita. PMID:27775666
MicroRNA let-7f-5p Inhibits Porcine Reproductive and Respiratory Syndrome Virus by Targeting MYH9. PMID:27686528
MicroRNA-140-5p targets insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1) to suppress cervical cancer growth and metastasis. PMID:27588393
miR-29 regulates Tet1 expression and contributes to early differentiation of mouse ESCs. PMID:27449105
Experimental procedures to identify and validate specific mRNA targets of miRNAs. PMID:27047316
Dual and Opposing Roles of MicroRNA-124 in Epilepsy Are Mediated through Inflammatory and NRSF-Dependent Gene Networks. PMID:26947066
A human 3'UTR clone collection to study post-transcriptional gene regulation. PMID:26645212
Bioinformatic tools for microRNA dissection. PMID:26578605
Micro(mi) RNA-34a targets protein phosphatase (PP)1γ to regulate DNA damage tolerance. PMID:26111201
Plasticity-related microRNA and their potential contribution to the maintenance of long-term potentiation. PMID:25755632
Specific microRNAs regulate heat stress responses in Caenorhabditis elegans. PMID:25746291
Competition between target sites of regulators shapes post-transcriptional gene regulation. PMID:25488579
DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. PMID:25416797
Hunting the needle in the haystack: a guide to obtain biologically meaningful microRNA targets. PMID:25383673
MicroRNAs as predictive biomarkers and therapeutic targets in prostate cancer. PMID:25374924
Computational Methods for MicroRNA Target Prediction. PMID:25153283
MicroRNA-8 promotes robust motor axon targeting by coordinate regulation of cell adhesion molecules during synapse development. PMID:25135978
OMIT: dynamic, semi-automated ontology development for the microRNA domain. PMID:25025130
Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism. PMID:24957527
ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. PMID:24829448
Next Generation Sequencing of miRNAs - Strategies, Resources and Methods. PMID:24710011
Characterizing dynamic regulatory programs in mouse lung development and their potential association with tumourigenesis via miRNA-TF-mRNA circuits. PMID:24564886
Identification of tissue microRNAs predictive of sunitinib activity in patients with metastatic renal cell carcinoma. PMID:24475095
NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo. PMID:24454279
MicroRNAs: fundamental regulators of gene expression in major affective disorders and suicidal behavior? PMID:24298237
The role of microRNAs in hepatocarcinogenesis: current knowledge and future prospects. PMID:24258409
A useful method of identifying of miRNAs which can down-regulate Zeb-2. PMID:24245745
Involvement of miRNAs in the differentiation of human glioblastoma multiforme stem-like cells. PMID:24155920
In-Silico Algorithms for the Screening of Possible microRNA Binding Sites and Their Interactions. PMID:24082822
Low expression of miR-196b enhances the expression of BCR-ABL1 and HOXA9 oncogenes in chronic myeloid leukemogenesis. PMID:23894305
Large-scale screens of miRNA-mRNA interactions unveiled that the 3'UTR of a gene is targeted by multiple miRNAs. PMID:23874542
Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans. PMID:23811144
Placental miRNA expression profiles are associated with measures of infant neurobehavioral outcomes. PMID:23783433
MicroRNA-regulated protein-protein interaction networks and their functions in breast cancer. PMID:23722663
A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer. PMID:23717626
The C. elegans gene pan-1 encodes novel transmembrane and cytoplasmic leucine-rich repeat proteins and promotes molting and the larva to adult transition. PMID:23682709
Advances in the techniques for the prediction of microRNA targets. PMID:23591837
A novel strategy for cell-autonomous gene knockdown in Caenorhabditis elegans defines a cell-specific function for the G-protein subunit GOA-1. PMID:23525334
Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans. PMID:23516374
Tertiary structure-based analysis of microRNA-target interactions. PMID:23417009
Genetic variations creating microRNA target sites in the FXN 3'-UTR affect frataxin expression in Friedreich ataxia. PMID:23382970
miRNAs and their putative roles in the development and progression of Parkinson's disease. PMID:23316214
Building a robust a-p axis. PMID:23204917
One decade of development and evolution of microRNA target prediction algorithms. PMID:23200135
Identifying miRNAs, targets and functions. PMID:23175680
Insect microRNAs: biogenesis, expression profiling and biological functions. PMID:23165178
OrbId: Origin-based identification of microRNA targets. PMID:23087843
Integration of SNP and mRNA arrays with microRNA profiling reveals that MiR-370 is upregulated and targets NF1 in acute myeloid leukemia. PMID:23077663
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PMID:23071454
Dose-dependent differential mRNA target selection and regulation by let-7a-7f and miR-17-92 cluster microRNAs. PMID:22995834
Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae. PMID:22953717
The microRNA mir-71 inhibits calcium signaling by targeting the TIR-1/Sarm1 adaptor protein to control stochastic L/R neuronal asymmetry in C. elegans. PMID:22876200
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? PMID:22767260
Extensive alternative polyadenylation during zebrafish development. PMID:22722342
miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets. PMID:22566243
Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis. PMID:22549745
MicroRNAs in inner ear biology and pathogenesis. PMID:22484222
The C. elegans microRNA mir-71 acts in neurons to promote germline-mediated longevity through regulation of DAF-16/FOXO. PMID:22482727
RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. PMID:22454234
Bioinformatic Resources of microRNA Sequences, Gene Targets, and Genetic Variation. PMID:22403585
miRNA-mediated relationships between Cis-SNP genotypes and transcript intensities in lymphocyte cell lines. PMID:22348086
Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data. PMID:22303397
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PMID:22125477
Gene-centered regulatory network mapping. PMID:22118281
Analysis of microRNA expression and function. PMID:22118279
miREE: miRNA recognition elements ensemble. PMID:22115078
Regulation of zinc-responsive Slc39a5 (Zip5) translation is mediated by conserved elements in the 3'-untranslated region. PMID:22113231
doRiNA: a database of RNA interactions in post-transcriptional regulation. PMID:22086949
Identifying targets of human micrornas with the LightSwitch Luciferase Assay System using 3'UTR-reporter constructs and a microRNA mimic in adherent cells. PMID:21988797
Seeing elegance in gene regulatory networks of the worm. PMID:21963133
A study of the evolution of human microRNAs by their apparent repression effectiveness on target genes. PMID:21957473
A set of miRNAs that involve in the pathways of drug resistance and leukemic stem-cell differentiation is associated with the risk of relapse and glucocorticoid response in childhood ALL. PMID:21926415
Uncovering new functions for microRNAs in Caenorhabditis elegans. PMID:21920301
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. PMID:21909094
Evidence for the complexity of microRNA-mediated regulation in ovarian cancer: a systems approach. PMID:21811625
Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. PMID:21810936
miRTar: an integrated system for identifying miRNA-target interactions in human. PMID:21791068
Immortalization of MEF is characterized by the deregulation of specific miRNAs with potential tumor suppressor activity. PMID:21765199
Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PMID:21694770
Tumour-suppressor microRNAs let-7 and mir-101 target the proto-oncogene MYCN and inhibit cell proliferation in MYCN-amplified neuroblastoma. PMID:21654684
DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. PMID:21551220
Brain expression quantitative trait locus mapping informs genetic studies of psychiatric diseases. PMID:21441974
Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. PMID:21402708
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PMID:21364759
Practical Aspects of microRNA Target Prediction. PMID:21342132
Association of a microRNA/TP53 feedback circuitry with pathogenesis and outcome of B-cell chronic lymphocytic leukemia. PMID:21205967
Genome-wide approaches in the study of microRNA biology. PMID:21197653
Widespread regulatory activity of vertebrate microRNA* species. PMID:21177881
Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. PMID:21085120
MicroRNA-210 regulates cancer cell proliferation through targeting fibroblast growth factor receptor-like 1 (FGFRL1). PMID:21044961
MicroRNA discovery and analysis of pinewood nematode Bursaphelenchus xylophilus by deep sequencing. PMID:20967259
Cardiovascular Disease, Single Nucleotide Polymorphisms; and the Renin Angiotensin System: Is There a MicroRNA Connection? PMID:20948563
A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype. PMID:20930125
MicroRNA targeting in mammalian genomes: genes and mechanisms. PMID:20836019
A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. PMID:20835247
A negative regulatory loop between microRNA and Hox gene controls posterior identities in Caenorhabditis elegans. PMID:20824072
MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. PMID:20809528
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. PMID:20799968
The nuclear receptor gene nhr-25 plays multiple roles in the Caenorhabditis elegans heterochronic gene network to control the larva-to-adult transition. PMID:20678979
Maternal cigarette smoking during pregnancy is associated with downregulation of miR-16, miR-21, and miR-146a in the placenta. PMID:20647767
MicroRNAs in cardiac remodeling and disease. PMID:20560042
microRNAs: a role in drug resistance in parasitic nematodes? PMID:20541972
The landscape of C. elegans 3'UTRs. PMID:20522740
eHive: an artificial intelligence workflow system for genomic analysis. PMID:20459813
MicroRNA-210 regulates mitochondrial free radical response to hypoxia and krebs cycle in cancer cells by targeting iron sulfur cluster protein ISCU. PMID:20436681
The conserved miR-51 microRNA family is redundantly required for embryonic development and pharynx attachment in Caenorhabditis elegans. PMID:20421599
High-throughput experimental studies to identify miRNA targets directly, with special focus on the mammalian brain. PMID:20380813
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. PMID:20371350
A dictionary on microRNAs and their putative target pathways. PMID:20299343
Got target? Computational methods for microRNA target prediction and their extension. PMID:20177143
MTar: a computational microRNA target prediction architecture for human transcriptome. PMID:20122191
MYCN-regulated microRNAs repress estrogen receptor-alpha (ESR1) expression and neuronal differentiation in human neuroblastoma. PMID:20080637
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. PMID:20062054
In silico method for systematic analysis of feature importance in microRNA-mRNA interactions. PMID:20015389
Computational approaches for microRNA studies: a review. PMID:20012966
Down-regulation of the cyclin E1 oncogene expression by microRNA-16-1 induces cell cycle arrest in human cancer cells. PMID:19944013
C. elegans sym-1 is a downstream target of the hunchback-like-1 developmental timing transcription factor. PMID:19923914
MicroRNAs in C. elegans Aging: Molecular Insurance for Robustness? PMID:19881908
Accurate microRNA target prediction correlates with protein repression levels. PMID:19765283
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PMID:19724645
MicroRNA-143 targets DNA methyltransferases 3A in colorectal cancer. PMID:19638978
Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PMID:19543383
Reexamining microRNA site accessibility in Drosophila: a population genomics study. PMID:19478854
DIANA-microT web server: elucidating microRNA functions through target prediction. PMID:19406924
The interplay between transcription factors and microRNAs in genome-scale regulatory networks. PMID:19274664
Microarray profiling of microRNAs expressed in testis tissues of developing primates. PMID:19242788
MicroRNAs: target recognition and regulatory functions. PMID:19167326
mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. PMID:19160516
Repression of C. elegans microRNA targets at the initiation level of translation requires GW182 proteins. PMID:19131968
Most mammalian mRNAs are conserved targets of microRNAs. PMID:18955434
A novel biochemical method to identify target genes of individual microRNAs: identification of a new Caenorhabditis elegans let-7 target. PMID:18824511
Browsing multidimensional molecular networks with the generic network browser (N-Browse). PMID:18819079
The let-7 microRNA interfaces extensively with the translation machinery to regulate cell differentiation. PMID:18818519
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. PMID:18794350
Mating induces an immune response and developmental switch in the Drosophila oviduct. PMID:18725632
In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs. PMID:18680611
microRNA control of cell-cell signaling during development and disease. PMID:18677099
The impact of microRNAs on protein output. PMID:18668037
A set of differentially expressed miRNAs, including miR-30a-5p, act as post-transcriptional inhibitors of BDNF in prefrontal cortex. PMID:18632683
Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. PMID:18559475
A matter of timing: microRNA-controlled temporal identities in worms and flies. PMID:18559473
The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. PMID:18510933
Molecular architecture of a miRNA-regulated 3' UTR. PMID:18463285
MiR-15a and miR-16-1 cluster functions in human leukemia. PMID:18362358
Sequence variation of MicroRNAs and their binding sites in Arabidopsis. PMID:18305205
Computational prediction of rice (Oryza sativa) miRNA targets. PMID:18267301
The expression of the Alzheimer's amyloid precursor protein-like gene is regulated by developmental timing microRNAs and their targets in Caenorhabditis elegans. PMID:18262516
microRNAs: a new emerging class of players for disease diagnostics and gene therapy. PMID:18088390
Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PMID:18085825
Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. PMID:18042455
Concise review: MicroRNA expression in multipotent mesenchymal stromal cells. PMID:17991914
UTRome.org: a platform for 3'UTR biology in C. elegans. PMID:17986455
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. PMID:17922911
MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. PMID:17890317
The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. PMID:17697356
Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes. PMID:17668390
MicroRNA regulation of human protein protein interaction network. PMID:17652130
Isolation of microRNA targets by miRNP immunopurification. PMID:17592038
Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes. PMID:17526642
Regulatory circuit of human microRNA biogenesis. PMID:17447837
MicroTar: predicting microRNA targets from RNA duplexes. PMID:17254305
Modularity and dynamics of cellular networks. PMID:17196032
Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression. PMID:17002790
RNAhybrid: microRNA target prediction easy, fast and flexible. PMID:16845047
DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation PubMed citations: 62.

62 articles citing: DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

CRAFT: a bioinformatics software for custom prediction of circular RNA functions. PMID:35106564
The Cellular and Viral circRNAome Induced by Respiratory Syncytial Virus Infection. PMID:34872355
Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression. PMID:34694601
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Illuminating lncRNA Function Through Target Prediction. PMID:34417758
Identification of circRNA-miRNA-mRNA networks contributes to explore underlying pathogenesis and therapy strategy of gastric cancer. PMID:34049561
BRIO: a web server for RNA sequence and structure motif scan. PMID:34038531
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans. PMID:33942874
Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer. PMID:33803328
Quaking 5 suppresses TGF-β-induced EMT and cell invasion in lung adenocarcinoma. PMID:33769671
Silencing of LINC00284 inhibits cell proliferation and migration in oral squamous cell carcinoma by the miR-211-3p/MAFG axis and FUS/KAZN axis. PMID:33618612
Validation of human microRNA target pathways enables evaluation of target prediction tools. PMID:33305319
Identifying Key MicroRNAs Targeted by Narenmandula in a Rodent Nephropathy Model. PMID:33299464
A survey on deep learning in DNA/RNA motif mining. PMID:33005921
RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins. PMID:32727537
PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction. PMID:32678300
DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage. PMID:32503257
Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures. PMID:32379750
Unveiling ncRNA regulatory axes in atherosclerosis progression. PMID:32009226
MicroRNA-744/transforming growth factor β1 relationship regulates liver cirrhosis. PMID:31643031
CRIP: predicting circRNA-RBP-binding sites using a codon-based encoding and hybrid deep neural networks. PMID:31537716
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. PMID:31510640
IRNdb: the database of immunologically relevant non-coding RNAs. PMID:31414702
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data. PMID:31238884
Discovering sequence and structure landscapes in RNA interaction motifs. PMID:31162604
Global identification of functional microRNA-mRNA interactions in Drosophila. PMID:30967537
beRBP: binding estimation for human RNA-binding proteins. PMID:30590704
RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics. PMID:30558267
Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. PMID:30527764
The biological functions of target genes in pan-cancers and cell lines were predicted by miR-375 microarray data from GEO database and bioinformatics. PMID:30379973
New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression. PMID:30374356
Target RNAs Strike Back on MicroRNAs. PMID:30333855
RBPvsMIR: A Computational Pipeline to Identify Competing miRNAs and RNA-Binding Protein Pairs Regulating the Shared Transcripts. PMID:30131454
Downregulation of miR‑486‑5p in papillary thyroid carcinoma tissue: A study based on microarray and miRNA sequencing. PMID:30015845
Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks. PMID:29970003
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. PMID:29800452
Widespread intronic polyadenylation diversifies immune cell transcriptomes. PMID:29712909
Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs. PMID:29670884
A Brief Review of RNA-Protein Interaction Database Resources. PMID:29657278
FUS Regulates Activity of MicroRNA-Mediated Gene Silencing. PMID:29499134
mirDIP 4.1-integrative database of human microRNA target predictions. PMID:29194489
Non-coding RNA networks in cancer. PMID:29170536
BEAM web server: a tool for structural RNA motif discovery. PMID:29095974
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data. PMID:28977546
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. PMID:28582575
Identification of molecular targets for esophageal carcinoma diagnosis using miRNA-seq and RNA-seq data from The Cancer Genome Atlas: a study of 187 cases. PMID:28415685
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. PMID:28334930
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. PMID:28053162
Bioinformatic tools for analysis of CLIP ribonucleoprotein data. PMID:28008714
Integrating Epigenomics into the Understanding of Biomedical Insight. PMID:27980397
YM500v3: a database for small RNA sequencing in human cancer research. PMID:27899625
A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. PMID:27580722
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. PMID:27087310
Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. PMID:27050392
Cis-acting elements in its 3' UTR mediate post-transcriptional regulation of KRAS. PMID:26930719
Meta-analysis of the differentially expressed microRNA profiles in nasopharyngeal carcinoma. PMID:26824418
Bioinformatics Resources for MicroRNA Discovery. PMID:26819547
A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing. PMID:26207626
Revealing protein-lncRNA interaction. PMID:26041786
Design and bioinformatics analysis of genome-wide CLIP experiments. PMID:25958398
Expression quantitative trait loci (eQTLs) in microRNA genes are enriched for schizophrenia and bipolar disorder association signals. PMID:25817407
http://dx.doi.org/10.1093/nar/

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version: FAIRsharing.org: doRiNA; doRiNA; DOI: https://doi.org/10.25504/FAIRsharing.z0ea6a; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: doRiNA; doRiNA; DOI: https://doi.org/10.25504/FAIRsharing.z0ea6a; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

micro rna
metasource: Fairsharing.org
version: FAIRsharing.org: doRiNA; doRiNA; DOI: https://doi.org/10.25504/FAIRsharing.z0ea6a; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

micro rna (mirna) target site
metasource: Fairsharing.org
version: FAIRsharing.org: doRiNA; doRiNA; DOI: https://doi.org/10.25504/FAIRsharing.z0ea6a; Last edited: Jan. 8, 2019, 1:13 p.m.; Last accessed: Jan 03 2022 7:09 p.m.

rna sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

mrna
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

micrornas
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

rna
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:07.319245

rpbs
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

biology
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

biomedicine
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

gene regulation
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:07.319245

genetics
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

systems biology
metasource: re3data.org
version: re3data.org: doRiNA; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3561S last accessed: 2022-11-04

exon gene expression micro rna micro rna (mirna) target site rna sequence mrna micrornas rna rpbs bioinformatics biomedicine gene regulation genetics systems biology

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POSTAR

pSILAC

DARNED

Human Transcriptional Regulation Interactions database

BPS

PROkariotIC Database Of Gene-Regulation

Gene Transcription Regulation Database

RNA Binding Protein Variant Database

RNApathwaysDB

RegulonDB

RAID

RNAJunction: A Database of RNA Junction and Kissing loop Structure

RRMdb

RMBase

MODOMICS

RNA FRABASE

RNA Modification Database

CoDNaS-RNA

The database of eukaryotic RNA binding proteins

miRFFLDB