Viral Short ORFs and Their Possible Functions
Sign Up to like & getrecommendations! Published in 2018 at "Proteomics"
DOI: 10.1002/pmic.201700255
Abstract: Definition of functional genomic elements is one of the greater challenges of the genomic era. Traditionally, putative short open reading frames (sORFs) coding for less than 100 amino acids were disregarded due to computational and… read more here.
Keywords: viral short; orfs possible; ribosome profiling; short orfs ... See more keywords
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
Ribosome Profiling in Trypanosomatids.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-9210-2_5
Abstract: Ribosomes are the machinery responsible for reading mRNAs and translating them into proteins. The ribosome profiling approach is based on high-throughput sequencing of ribosome-protected mRNAs. RNAs not harboring ribosomes are removed by nuclease digestion leaving… read more here.
Keywords: biology; ribosome profiling; profiling trypanosomatids;
A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling.
Sign Up to like & getrecommendations! Published in 2021 at "Cell reports"
DOI: 10.1016/j.celrep.2021.108695
Abstract: Mycobacterium tuberculosis, which causes tuberculosis, can undergo prolonged periods of non-replicating persistence in the host. The mechanisms underlying this are not fully understood, but translational regulation is thought to play a role. A large proportion… read more here.
Keywords: ribosome profiling; tuberculosis; translation; nutrient starvation ... 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
Monitoring translation in synaptic fractions using a ribosome profiling strategy
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Neuroscience Methods"
DOI: 10.1016/j.jneumeth.2019.108456
Abstract: Highlights • Ribosome profiling in synaptosomes.• Transcriptome and translatome profiling from synaptic fractions.• Powerful tool to study local translation at the synapse. read more here.
Keywords: monitoring translation; translation synaptic; synaptic fractions; ribosome profiling ... See more keywords
High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress.
Sign Up to like & getrecommendations! Published in 2019 at "Molecular cell"
DOI: 10.1016/j.molcel.2018.12.009
Abstract: Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to differently sized… read more here.
Keywords: translation elongation; stress; ribosome profiling; elongation ... See more keywords
Hallmarks and Determinants of Oncogenic Translation Revealed by Ribosome Profiling in Models of Breast Cancer☆
Sign Up to like & getrecommendations! Published in 2020 at "Translational Oncology"
DOI: 10.1016/j.tranon.2019.12.002
Abstract: Gene expression is extensively and dynamically modulated at the level of translation. How cancer cells prioritize the translation of certain mRNAs over others from a pool of competing mRNAs remains an open question. Here, we… read more here.
Keywords: ribosome profiling; oncogenic translation; breast cancer; models breast ... See more keywords
Transcriptome-wide measurement of translation by ribosome profiling.
Sign Up to like & getrecommendations! Published in 2017 at "Methods"
DOI: 10.1016/j.ymeth.2017.05.028
Abstract: Translation is one of the fundamental processes of life. It comprises the assembly of polypeptides whose amino acid sequence corresponds to the codon sequence of an mRNA's ORF. Translation is performed by the ribosome; therefore,… read more here.
Keywords: ribosome profiling; wide measurement; translation; transcriptome wide ... See more keywords
Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-15634-w
Abstract: The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing), a… read more here.
Keywords: ribosome profiling; differential splicing; human mouse; level ... See more keywords
Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus
Sign Up to like & getrecommendations! Published in 2022 at "FEMS Yeast Research"
DOI: 10.1093/femsyr/foac024
Abstract: Abstract Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses,… read more here.
Keywords: development ribosome; kluyveromyces marxianus; ribosome profiling; translation ... See more keywords