Analysis of Ribosome Profiling Data.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1975-9_9
Abstract: Ribosome profiling methods are based on high-throughput sequencing of ribosome-protected mRNA footprints and allow to study in detail translational changes. Bioinformatic and statistical tools are necessary to analyze sequencing data. Here, we describe our developed… read more here.
Keywords: methodology; profiling data; ribosome profiling; biology ... See more keywords
mQC: A post-mapping data exploration tool for ribosome profiling
Sign Up to like & getrecommendations! Published in 2019 at "Computer methods and programs in biomedicine"
DOI: 10.1016/j.cmpb.2018.10.018
Abstract: BACKGROUND AND OBJECTIVE Ribosome profiling is a recent next generation sequencing technique enabling the genome-wide study of gene expression in biomedical research at the translation level. Too often, researchers precipitously start trying to test their… read more here.
Keywords: profiling data; ribosome profiling; exploration; tool ... See more keywords
Bayesian Modeling of Spatial Molecular Profiling Data via Gaussian Process.
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab455
Abstract: MOTIVATION The location, timing, and abundance of gene expression (both mRNA and proteins) within a tissue define the molecular mechanisms of cell functions. Recent technology breakthroughs in spatial molecular profiling, including imaging-based technologies and sequencing-based… read more here.
Keywords: profiling data; modeling spatial; bayesian modeling; molecular profiling ... See more keywords
De novo annotation and characterization of the translatome with ribosome profiling data
Sign Up to like & getrecommendations! Published in 2018 at "Nucleic Acids Research"
DOI: 10.1093/nar/gky179
Abstract: Abstract By capturing and sequencing the RNA fragments protected by translating ribosomes, ribosome profiling provides snapshots of translation at subcodon resolution. The growing needs for comprehensive annotation and characterization of the context-dependent translatomes are calling… read more here.
Keywords: profiling data; novo annotation; annotation characterization; ribosome profiling ... See more keywords
A tool for analyzing and visualizing ribo-seq data at the isoform level
Sign Up to like & getrecommendations! Published in 2021 at "BMC Bioinformatics"
DOI: 10.1186/s12859-021-04192-7
Abstract: Background Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to… read more here.
Keywords: isoform level; profiling data; ribosome profiling; level ... See more keywords
riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
Sign Up to like & getrecommendations! Published in 2018 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1006169
Abstract: Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in… read more here.
Keywords: ribowaltz; profiling data; ribosome site; ribosome profiling ... See more keywords
Analysis of expression profiling data suggests explanation for difficulties in finding biomarkers for nasal polyps.
Sign Up to like & getrecommendations! Published in 2020 at "Rhinology"
DOI: 10.4193/rhin19.407
Abstract: BACKGROUND Identification of clinically useful biomarkers for Nasal Polyposis in chronic rhinosinusitis (CRSwNP) has proven dif-ficult. We analyzed gene expression profiling data to find explanations for this. METHODS We analyzed mRNA expression profiling data, GSE36830,… read more here.
Keywords: expression; profiling data; expression profiling; biomarkers nasal ... See more keywords