Active Ribosome Profiling with RiboLace
Cell Reports, 2018 Summary: Ribosome profiling, or Ribo-seq, is based on large-scale sequencing of RNA fragments protected from nuclease digestion by ribosomes. Thanks to its unique ability to provide positional information about ribosomes flowing along transcripts, this ...
Massimiliano Clamer +2 more
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Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data
Frontiers in Molecular Biosciences, 2021 Quantitative prediction on protein synthesis requires accurate translation initiation and codon translation rates. Ribosome profiling data, which provide steady-state distribution of relative ribosome occupancies along a transcript, can be used to ...
Vandana Yadav +2 more
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Ribosome profiling: a powerful tool in oncological research [PDF]
Biomarker ResearchNeoplastic cells need to adapt their gene expression pattern to survive in an ever-changing or unfavorable tumor microenvironment. Protein synthesis (or mRNA translation), an essential part of gene expression, is dysregulated in cancer.
Dan Su +9 more
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Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts [PDF]
Nature CommunicationsRibosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis.
Kotaro Tomuro +9 more
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Common cell lysis procedures distort ribosome profiling analyses of gene expression [PDF]
Genome BiologyRibosome profiling is a powerful technique used to study gene expression on a transcriptome-wide scale. It involves sequencing of mRNA fragments protected by ribosomes from ribonuclease digestion. The initial steps commonly involve cell lysis followed by
Aoife O’Connell +6 more
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Genome-wide assessment of differential translations with ribosome profiling data
Nature Communications, 2016 The global measurement of ribosome occupancy on mRNAs is commonly used as a proxy in estimating rates of protein synthesis. Here the authors describe Xtail, a computational approach that facilitates the extraction of accurate quantitative insight from ...
Zhengtao Xiao, Xuerui Yang, Zou Qin
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Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection [PDF]
Microbiology SpectrumBacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage–host molecular interactions and ultimately determine the outcome of the infection.
Patrick B. F. O’Connor +5 more
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Principles, challenges, and advances in ribosome profiling: from bulk to low-input and single-cell analysis [PDF]
Advanced Biotechnology, 2023 Yuanhui Mao, Wang Qiuyi, Mao Yuanhui
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A tool for analyzing and visualizing ribo-seq data at the isoform level
BMC Bioinformatics, 2021 Background Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases.
Wei-Sheng Wu +5 more
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Genome-wide Survey of Ribosome Collision
Cell Reports, 2020 Summary: Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the ...
Peixun Han +10 more
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