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Terminitor: Cleavage Site Prediction Using Deep Learning Models

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/wrna.116openalex-snapshot

Signals for pre‐mRNA cleavage and polyadenylation

inferredcites →https://doi.org/10.1007/s00018-012-0990-9openalex-snapshot

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

inferredcites →https://doi.org/10.1016/j.molcel.2014.02.007openalex-snapshot

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

inferredcites →https://doi.org/10.1016/j.tcb.2015.10.012openalex-snapshot

Evolution and Biological Roles of Alternative 3′UTRs

inferredcites →https://doi.org/10.1038/emboj.2010.42openalex-snapshot

A functional human Poly(A) site requires only a potent DSE and an A‐rich upstream sequence

inferredcites →https://doi.org/10.1038/nbt1239openalex-snapshot

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

inferredcites →https://doi.org/10.1038/ncomms6274openalex-snapshot

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types

inferredcites →https://doi.org/10.1038/srep05406openalex-snapshot

3′UTR shortening identifies high-risk cancers with targeted dysregulation of the ceRNA network

inferredcites →https://doi.org/10.1073/pnas.1400447111openalex-snapshot

Defining a personal, allele-specific, and single-molecule long-read transcriptome

inferredcites →https://doi.org/10.1073/pnas.68.6.1336openalex-snapshot

Polyadenylic Acid Sequences in the Heterogeneous Nuclear RNA and Rapidly-Labeled Polyribosomal RNA of HeLa Cells: Possible Evidence for a Precursor Relationship

inferredcites →https://doi.org/10.1080/15476286.2017.1306171openalex-snapshot

Cleavage and polyadenylation: Ending the message expands gene regulation

inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

inferredcites →https://doi.org/10.1093/bib/bbw068openalex-snapshot

Deep learning in bioinformatics

inferredcites →https://doi.org/10.1093/bioinformatics/bti310openalex-snapshot

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btr602openalex-snapshot

Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences

inferredcites →https://doi.org/10.1093/bioinformatics/bty029openalex-snapshot

APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data

inferredcites →https://doi.org/10.1093/bioinformatics/bty752openalex-snapshot

DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions

inferredcites →https://doi.org/10.1093/bioinformatics/bty991openalex-snapshot

DeeReCT-PolyA: a robust and generic deep learning method for PAS identification

inferredcites →https://doi.org/10.1093/bioinformatics/btz283openalex-snapshot

DeepPASTA: deep neural network based polyadenylation site analysis

inferredcites →https://doi.org/10.1093/database/bau076openalex-snapshot

APADB: a database for alternative polyadenylation and microRNA regulation events

inferredcites →https://doi.org/10.1093/database/baw093openalex-snapshot

The Ensembl gene annotation system

inferredcites →https://doi.org/10.1093/nar/28.1.352openalex-snapshot

dbSNP: a database of single nucleotide polymorphisms

inferredcites →https://doi.org/10.1093/nar/gki158openalex-snapshot

A large-scale analysis of mRNA polyadenylation of human and mouse genes

inferredcites →https://doi.org/10.1093/nar/gkj144openalex-snapshot

The UCSC Genome Browser Database: update 2006

inferredcites →https://doi.org/10.1093/nar/gkl919openalex-snapshot

Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis

inferredcites →https://doi.org/10.1093/nar/gku1076openalex-snapshot

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

inferredcites →https://doi.org/10.1093/nar/gkx1000openalex-snapshot

PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes

inferredcites →https://doi.org/10.1101/701607openalex-snapshot

RNA-Bloom provides lightweight reference-free transcriptome assembly for single cells

inferredcites →https://doi.org/10.1101/gad.1298605openalex-snapshot

Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition

inferredcites →https://doi.org/10.1101/gad.229328.113openalex-snapshot

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

inferredcites →https://doi.org/10.1101/gr.132563.111openalex-snapshot

A quantitative atlas of polyadenylation in five mammals

inferredcites →https://doi.org/10.1101/gr.202432.115openalex-snapshot

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

inferredcites →https://doi.org/10.1142/9789814644730_0034openalex-snapshot

KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES

inferredcites →https://doi.org/10.1186/gb-2005-6-12-r100openalex-snapshot

Biased alternative polyadenylation in human tissues

inferredcites →https://doi.org/10.1186/gb-2011-12-2-r16openalex-snapshot

Genomewide characterization of non-polyadenylated RNAs

inferredcites →https://doi.org/10.1186/s12864-017-4033-7openalex-snapshot

Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

inferredcites →https://doi.org/10.1186/s12864-018-4903-7openalex-snapshot

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

inferredcites →https://doi.org/10.1186/s13059-018-1414-4openalex-snapshot

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data

inferredcites →https://doi.org/10.1186/s13756-018-0352-yopenalex-snapshot

Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014

inferredcites →https://doi.org/10.1261/rna.048355.114openalex-snapshot

PAT-seq: a method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome

inferredcites →https://doi.org/10.1261/rna.2581711openalex-snapshot

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

inferredcites →https://doi.org/10.1371/journal.pone.0031129openalex-snapshot

Shortening of 3′UTRs Correlates with Poor Prognosis in Breast and Lung Cancer

inferredcites →https://doi.org/10.1371/journal.pone.0170914openalex-snapshot

Prediction of Poly(A) Sites by Poly(A) Read Mapping

inferredcites →https://doi.org/10.4161/rna.6.5.9554openalex-snapshot

An up-close look at the pre-mRNA 3’-end processing complex

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00204-9openalex-snapshot

Bioinformatic Analysis of Alternative Splicing

inferred← citeshttps://doi.org/10.1016/j.gpb.2022.09.005openalex-snapshot

A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-Seq, and Single-Cell RNA-Seq

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