TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-08-25
DOI
10.1093/nar/gkaa722
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Genome-wide analysis identifies cis-acting elements regulating mRNA polyadenylation and translation during vertebrate oocyte maturation
- (2020) Fei Yang et al. RNA
- Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
- (2020) Matthew T Parker et al. eLife
- Emerging Roles of RNA 3′-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders
- (2020) Jamie Nourse et al. Biomolecules
- Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes
- (2019) Ruijia Wang et al. Cell Reports
- Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution
- (2019) Congting Ye et al. RNA Biology
- Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination
- (2019) Kinga Kamieniarz-Gdula et al. MOLECULAR CELL
- Alternative cleavage and polyadenylation of genes associated with protein turnover and mitochondrial function are deregulated in Parkinson’s, Alzheimer’s and ALS disease
- (2019) Radhika Patel et al. BMC Medical Genomics
- Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation
- (2019) Tingting Weng et al. JOURNAL OF CLINICAL INVESTIGATION
- pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
- (2019) Federico Marini et al. BMC BIOINFORMATICS
- A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation
- (2019) Nicholas Bogard et al. CELL
- Alternative cleavage and polyadenylation in health and disease
- (2019) Andreas J. Gruber et al. NATURE REVIEWS GENETICS
- APAatlas: decoding alternative polyadenylation across human tissues
- (2019) Wei Hong et al. NUCLEIC ACIDS RESEARCH
- Building online genomics applications using BioPyramid
- (2018) Liam Stephenson et al. BIOINFORMATICS
- Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling
- (2018) Justin Brumbaugh et al. CELL
- Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation
- (2018) Eric R. Gamazon et al. NATURE GENETICS
- Alternative polyadenylation in the regulation and dysregulation of gene expression
- (2018) Rachael Emily Turner et al. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
- VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation
- (2018) Yanan Yue et al. Cell Discovery
- Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia
- (2018) Shih-Han Lee et al. NATURE
- The UCSC Genome Browser database: 2019 update
- (2018) Maximilian Haeussler et al. NUCLEIC ACIDS RESEARCH
- dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications
- (2018) Kai-Yao Huang et al. NUCLEIC ACIDS RESEARCH
- The Gene Ontology Resource: 20 years and still GOing strong
- (2018) NUCLEIC ACIDS RESEARCH
- Transcriptome 3′end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma
- (2018) Anton Ogorodnikov et al. Nature Communications
- Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues
- (2017) Alejandro Reyes et al. NUCLEIC ACIDS RESEARCH
- PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes
- (2017) Ruijia Wang et al. NUCLEIC ACIDS RESEARCH
- sCLIP—an integrated platform to study RNA–protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs
- (2017) Yulia Kargapolova et al. NUCLEIC ACIDS RESEARCH
- A pathology atlas of the human cancer transcriptome
- (2017) Mathias Uhlen et al. SCIENCE
- Role of miRNAs and alternative mRNA 3′-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy
- (2016) R. Soetanto et al. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms
- Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control
- (2016) Wencheng Li et al. BMC BIOLOGY
- SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export
- (2016) Michaela Müller-McNicoll et al. GENES & DEVELOPMENT
- A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- (2016) Andreas J. Gruber et al. GENOME RESEARCH
- Alternative polyadenylation of mRNA precursors
- (2016) Bin Tian et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end
- (2016) Anton Ogorodnikov et al. PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY
- Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut
- (2016) N. J. Proudfoot SCIENCE
- The FAIR Guiding Principles for scientific data management and stewardship
- (2016) Mark D. Wilkinson et al. Scientific Data
- A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation
- (2015) Shengdong Ke et al. GENES & DEVELOPMENT
- Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation
- (2015) Jonathan Neve et al. GENOME RESEARCH
- Regulation of alternative splicing inDrosophilaby 56 RNA binding proteins
- (2015) Angela N. Brooks et al. GENOME RESEARCH
- Coordination of RNA Polymerase II Pausing and 3’ end processing factor recruitment with alternative polyadenylation
- (2015) Becky Fusby et al. MOLECULAR AND CELLULAR BIOLOGY
- Orchestrating high-throughput genomic analysis with Bioconductor
- (2015) Wolfgang Huber et al. NATURE METHODS
- Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
- (2015) Nuala A. O'Leary et al. NUCLEIC ACIDS RESEARCH
- Promoting an open research culture
- (2015) B. A. Nosek et al. SCIENCE
- RBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3′ UTRs
- (2014) Dafne Campigli Di Giammartino et al. GENES & DEVELOPMENT
- Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease
- (2014) Ranjan Batra et al. MOLECULAR CELL
- CFIm25 links alternative polyadenylation to glioblastoma tumour suppression
- (2014) Chioniso P. Masamha et al. NATURE
- Policy: NIH plans to enhance reproducibility
- (2014) Francis S. Collins et al. NATURE
- A recently evolved class of alternative 3′-terminal exons involved in cell cycle regulation by topoisomerase inhibitors
- (2014) Martin Dutertre et al. Nature Communications
- Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types
- (2014) Zheng Xia et al. Nature Communications
- APADB: a database for alternative polyadenylation and microRNA regulation events
- (2014) S. Muller et al. Database-The Journal of Biological Databases and Curation
- Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
- (2013) B. J. Raney et al. BIOINFORMATICS
- CPEB1 coordinates alternative 3′-UTR formation with translational regulation
- (2013) Felice-Alessio Bava et al. NATURE
- Alternative cleavage and polyadenylation: extent, regulation and function
- (2013) Ran Elkon et al. NATURE REVIEWS GENETICS
- CBC–ARS2 stimulates 3′-end maturation of multiple RNA families and favors cap-proximal processing
- (2013) Marie Hallais et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Human TREX component Thoc5 affects alternative polyadenylation site choice by recruiting mammalian cleavage factor I
- (2013) J. Katahira et al. NUCLEIC ACIDS RESEARCH
- Software for Computing and Annotating Genomic Ranges
- (2013) Michael Lawrence et al. PLoS Computational Biology
- The Poly(A)-Binding Protein Nuclear 1 Suppresses Alternative Cleavage and Polyadenylation Sites
- (2012) Mathias Jenal et al. CELL
- Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins
- (2012) Alfredo Castello et al. CELL
- A quantitative atlas of polyadenylation in five mammals
- (2012) Adnan Derti et al. GENOME RESEARCH
- Mediator Complex Regulates Alternative mRNA Processing via the MED23 Subunit
- (2012) Yan Huang et al. MOLECULAR CELL
- The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts
- (2012) Alexander G. Baltz et al. MOLECULAR CELL
- Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing
- (2012) Mainul Hoque et al. NATURE METHODS
- An in-depth map of polyadenylation sites in cancer
- (2012) Yuefeng Lin et al. NUCLEIC ACIDS RESEARCH
- RNA polymerase II kinetics inpolopolyadenylation signal selection
- (2011) Pedro A B Pinto et al. EMBO JOURNAL
- p38 MAPK Controls Prothrombin Expression by Regulated RNA 3′ End Processing
- (2011) Sven Danckwardt et al. MOLECULAR CELL
- Induction of Antagonistic Soluble Decoy Receptor Tyrosine Kinases by Intronic PolyA Activation
- (2011) Sandra Vorlová et al. MOLECULAR CELL
- A germline variant in the TP53 polyadenylation signal confers cancer susceptibility
- (2011) Simon N Stacey et al. NATURE GENETICS
- Reproducible Research in Computational Science
- (2011) R. D. Peng SCIENCE
- Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation
- (2010) Fatih Ozsolak et al. CELL
- Leo1 Subunit of the Yeast Paf1 Complex Binds RNA and Contributes to Complex Recruitment
- (2010) Jessica L. Dermody et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation
- (2010) Daisuke Kaida et al. NATURE
- Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation
- (2010) Stefania Millevoi et al. NUCLEIC ACIDS RESEARCH
- Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
- (2010) Daniele Merico et al. PLoS One
- Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression
- (2010) Carol S. Lutz et al. Wiley Interdisciplinary Reviews-RNA
- Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells
- (2009) Christine Mayr et al. CELL
- Biased Chromatin Signatures around Polyadenylation Sites and Exons
- (2009) Noah Spies et al. MOLECULAR CELL
- Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex
- (2009) Yongsheng Shi et al. MOLECULAR CELL
- 3′ end mRNA processing: molecular mechanisms and implications for health and disease
- (2008) Sven Danckwardt et al. EMBO JOURNAL
- Regulation of alternative polyadenylation by genomic imprinting
- (2008) A. J. Wood et al. GENES & DEVELOPMENT
- Alternative isoform regulation in human tissue transcriptomes
- (2008) Eric T. Wang et al. NATURE
- HITS-CLIP yields genome-wide insights into brain alternative RNA processing
- (2008) Donny D. Licatalosi et al. NATURE
- Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites
- (2008) R. Sandberg et al. SCIENCE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started