Detecting and quantifying the translated transcriptome with Ribo-seq data [PDF]
, 2018 Die Untersuchung der posttranskriptionellen Genregulation erfordert eine eingehende Kenntnis vieler molekularer Prozesse, die auf RNA wirken, von der Prozessierung im Nukleus bis zur Translation und der Degradation im Zytoplasma.
Calviello, Lorenzo
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Trips-Viz: a transcriptome browser for exploring Ribo-Seq data. [PDF]
Nucleic Acids Res, 2019 Ribosome profiling (Ribo-Seq) is a technique that allows for the isolation and sequencing of mRNA fragments protected from nuclease digestion by actively translating ribosomes.
Kiniry SJ +3 more
europepmc +6 more sources
A Multi-Tissue Yak (Bos grunniens) ceRNA Atlas with Ribo-Seq–Informed lncRNA Curation and Candidate Prioritization [PDF]
AnimalsThe yak (Bos grunniens) thrives under chronic hypoxia and cold on the Qinghai–Tibet Plateau, yet a cross-tissue view of post-transcriptional regulation in this species remains limited.
Zhenlin Zhu, Biao Li, Mingfeng Jiang
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Integrative analysis of RNA-seq and Ribo-seq reveals that lncRNA regulates chicken myogenesis through encoding peptide [PDF]
Journal of Animal Science and BiotechnologyBackground Long noncoding RNAs (lncRNAs) participate in various critical regulatory steps during myogenesis. LncRNAs can encode small peptides, which can regulate gene expression through multiple mechanisms, thereby participating in key biological ...
Yufang Niu +12 more
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Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions [PDF]
Nature CommunicationsThe mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1 is crucial for climate and environmental research due to its ability to produce methane. Here, we establish a Ribo-seq protocol for M.
Muhammad Aammar Tufail +11 more
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Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq [PDF]
eLife, 2014 Thousands of small Open Reading Frames (smORFs) with the potential to encode small peptides of fewer than 100 amino acids exist in our genomes. However, the number of smORFs actually translated, and their molecular and functional roles are still unclear.
Juan Pablo Couso (4460890) +6 more
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What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome? [PDF]
Molecular and Cellular Proteomics, 2023 Jennifer Abelin +2 more
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A tool for analyzing and visualizing ribo-seq data at the isoform level. [PDF]
BMC Bioinformatics, 2021 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 study translational regulation.
Wu WS +5 more
europepmc +6 more sources
STATR: A simple analysis pipeline of Ribo-Seq in bacteria. [PDF]
J Microbiol, 2020 Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances in next-generation sequencing (NGS), the abundance of
Choe D, Palsson B, Cho BK.
europepmc +3 more sources
Establishment of the Ribo-Seq method and Exploration of the Translatome in Chlamydomonas reinhardtii [PDF]
Translation is a ubiquitous, yet enigmatic process central to all cellular life on earth. Despite being a subject of research for many decades, its enormous complexity makes it difficult to study translation.
Gotsmann, Vincent Leon
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