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Kleat: cleavage site analysis of transcriptomes

Inanç Birol, Anthony Raymond, Readman Chiu, Ka Ming Nip, Shaun D Jackman, Maayan Kreitzman, T Roderick Docking, Catherine A Ennis, A Gordon Robertson, Aly Karsan
2015 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Here we describe KLEAT, an analysis tool that uses de novo assembly of RNA-seq data to characterize cleavage sites on 3' UTRs.  ...  We also compare the performance of KLEAT with other popular RNA-seq analysis pipelines that reconstruct 3' UTR ends, and show that it performs favourably, based on an ROC-like curve.  ...  The content of this work is solely the responsibility of the authors and does not necessarily represent the official views of any of our funding agencies.  ... 
pmid:25592595 pmcid:PMC4350765 fatcat:kr2ejglwdjfqhpp7whcf3hbiby

Termin(A)ntor: Polyadenylation Site Prediction using deep learning models [article]

Chen Yang, Chenkai Li, Ka Ming Nip, Rene L Warren, Inanc Birol
2019 bioRxiv   pre-print
State-of-the-art polyadenylation site detection tools are influenced either by library preparation or manually selected features.  ...  To help decipher its underlying mechanism and understand its impact, it is desirable to comprehensively profile 3-prime-untranslated region cleavage and associated polyadenylation sites.  ...  cleavage site (CS) [6] .  ... 
doi:10.1101/710699 fatcat:v3vprv6lbvehfhzg7rcgdgiz4u

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

Thomas Bonfert, Caroline C. Friedel, Bin Tian
2017 PLoS ONE  
This is further illustrated by a re-analysis of the HSV-1 data where both high PPV and sensitivity are achieved, highlighting the value of poly(A) read mapping for host-pathogen transcriptomics.  ...  Our mapping-based approach is furthermore compared against an alternative approach based on transcriptome assembly presented recently (KLEAT [31]).  ...  Clustering of poly(A) sites was performed as there is some heterogeneity in the cleavage position downstream of individual polyadenylation signals [38] .  ... 
doi:10.1371/journal.pone.0170914 pmid:28135292 pmcid:PMC5279776 fatcat:np3cdo6enfftva4suuxlizyg3u

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine

Joel T Dudley, Jennifer Listgarten, Oliver Stegle, Steven E Brenner, Leopold Parts
2015 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
models of individual health.  ...  Personalized medicine stands to benefit from inclusion of rich new sources and dimensions of data.  ...  In our session, Birol et al. describe KLEAT, a novel analysis tool that uses de novo assembly of RNA-sequencing data to search for and prioritize cleavage sites in poly(A) tails.  ... 
pmid:25592594 pmcid:PMC5893135 fatcat:yqpzm6gmcnf4tbdo7e4i6ah7gu

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

Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila Reynolds (+1 others)
2018 BMC Genomics  
Results: We built a cloud-based targeted de novo transcript assembly and analysis pipeline that incorporates our previously developed cleavage site prediction tool, KLEAT.  ...  By comparing the frequencies of predicted cleavage sites between normal and tumor sample groups, we identified 77 events (i.e. gene-cancer type pairs) of tumor-specific APA regulation in 13 cancer types  ...  The analysis scripts are available at https://github.com/bcgsc/tasrkleat-TCGA-analysis-scripts A copy of all reference data and metadata, as well as files reporting identified and post-processed CSs, and  ... 
doi:10.1186/s12864-018-4903-7 pmid:30005633 pmcid:PMC6045855 fatcat:bmedberi5bcy7bng4vh4wgylpi

Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies

Hsin-Sung Yeh, Wei Zhang, Jeongsik Yong
2017 BMB Reports  
Alternations in usage of polyadenylation sites during transcription termination yield transcript isoforms from a gene.  ...  Recent findings of transcriptome-wide alternative polyadenylation (APA) as a molecular response to changes in biology position APA not only as a molecular event of early transcriptional termination but  ...  KLEAT (39) An analysis tool that uses de novo assembly of RNA-seq data to characterize cleavage sites on 3'UTRs through direct observation of poly(A) tails.  ... 
doi:10.5483/bmbrep.2017.50.4.019 pmid:28148393 pmcid:PMC5437964 fatcat:nyjrp2w5mvap7pes3ohppt73dq

Detection of Differentially Expressed Cleavage Site Intervals Within 3′ Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs

Benjamin J. Harrison, Juw Won Park, Cynthia Gomes, Jeffrey C. Petruska, Matthew R. Sapio, Michael J. Iadarola, Julia H. Chariker, Eric C. Rouchka
2019 Frontiers in Genetics  
We therefore developed a method, CSI-UTR, that models 3'UTR structure as tandem segments between functional alternative-polyadenylation sites (termed cleavage site intervals-CSIs).  ...  CSI-UTR analysis is UTR-annotation independent and can interrogate legacy data generated from standard RNA-Seq libraries. CSI-UTR identified a set of CSIs in human and rodent transcriptomes.  ...  bosTau4, canFam2, Galgal3, dm3, ce10 No No KLEAT Identifies polyA cleavage sites Any with aligned BAM file and gene GTF file No No GETUTR Identifies polyA cleavage sites hg19 No No  ... 
doi:10.3389/fgene.2019.00182 pmid:30915105 pmcid:PMC6422928 fatcat:we5p4pmhbjcu5blo6ojpln2bsa

Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods

Krzysztof J. Szkop, Irene Nobeli
2017 Bioessays  
RNA-seq Abbreviations APA, alternative poly-adenylation; PCS, poly-adenylation and cleavage site; RNA-seq, RNA sequencing; TSS, transcription start site; UTR, untranslated region.  ...  Subtitle Computational methods to discover and quantify isoforms with alternative untranslated regions Keywords Alternative poly-adenylation; alternative transcription start site; untranslated region;  ...  Conflict of interest The authors declare they have no conflict of interest in the production of this manuscript.  ... 
doi:10.1002/bies.201700090 pmid:29052251 fatcat:gdsprlpb5ncirksexutxmpwmje

Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence

Ryan Lusk, Evan Stene, Farnoush Banaei-Kashani, Boris Tabakoff, Katerina Kechris, Laura M. Saba
2021 Nature Communications  
The average precision of the aptardi model is twice that of a standard transcriptome assembler.  ...  Here, we introduce aptardi (alternative polyadenylation transcriptome analysis from RNA-Seq data and DNA sequence information), which leverages both DNA sequence and RNA sequencing in a machine learning  ...  This research was supported by the following US National Institutes of Health (NIH) grants: NIAAA F31AA027430, NIAAA R24AA013162, and NIDA P30DA044223.  ... 
doi:10.1038/s41467-021-21894-x pmid:33712618 fatcat:7rndrz264vdnzfjbhhl3qwxp4u

Profiling Alternative 3′ Untranslated Regions in Sorghum using RNA-seq Data

Min Tu, Yin Li
2020 Frontiers in Genetics  
Transcriptome-wide studies of 3' untranslated regions (3'UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing  ...  In the present study, we profiled the alternative 3'UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188.  ...  RESULTS Transcriptome-Wide Identification of Alternative 3 UTRs in Sorghum Using RNA-seq Data We performed a transcriptome-wide analysis of alternative 3 UTRs using the sorghum internode RNA-seq datasets  ... 
doi:10.3389/fgene.2020.556749 pmid:33193635 pmcid:PMC7649775 fatcat:chnajh7kznatlij4owkncuzwx4

Computational modelling, simulation, and prediction of biological sequences

Chen Yang
2021
RNA sequencing has become the established sequencing method of choice for a wide range of transcriptome projects.  ...  analysis.  ...  The importance of profiling 3' UTR cleavage and polyadenylation sites APA, together with alternative splicing, has considerable impact on the modulation of gene expression and contributes to transcriptome  ... 
doi:10.14288/1.0400046 fatcat:zy6kktcif5fi7lvcwopz7xvbge

The developemnt of computational approaches for systems genetics and alternative polyadenylation studies and their application in studying genetic predisposition to alcohol related phenotypes [article]

Ryan Lusk
2022
REVIEW OF THE LITERATURE AND STATEMENT OF PURPOSE .  ...  I appreciate you serving a chair of my committee and organizing the meetings.  ...  In terms of research, she is a brilliant scientist, and I am privileged to have had the opportunity to learn from her.  ... 
doi:10.25677/qz8w-5332 fatcat:vvrl7cuhejbofk4a7suf4z35p4