Results 21 to 30 of about 16,252 (205)

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.
Andrews, Arava, Basrai, Bazzini, Boerjan, Brunner, Chew, Child, Chou, Crappe, Derrien, Djakovic, Duncan, Dunn, Eden, Falth, Frith, Fritsch, Galindo, Guttman, Hanada, Hanyu-Nakamura, Hemm, Ingolia, Ingolia, Ingolia, Kastenmayer, King, Kondo, Kozak, Krogh, Kulkarni, Kumar, Ladoukakis, Lemaitre, Magny, Pauli, Pueyo, Schmidt, Schneider, Siepel, Slavoff, Smith, Tripoli, Volders, Wilson   +45 more
core   +6 more sources

Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions [PDF]

Nature Communications
The 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, Britta Jordan, Lydia Hadjeras, Rick Gelhausen, Liam Cassidy, Tim Habenicht, Miriam Gutt, Lisa Hellwig, Rolf Backofen, Andreas Tholey, Cynthia M. Sharma, Ruth A. Schmitz   +11 more
doaj   +2 more sources

Abridged Ribosome Profiling for Accurate Bacterial Translation Measurements [PDF]

Methods and Protocols
Ribosome profiling, or Ribo-Seq, is a powerful tool for studying translation. It maps the positions of translating ribosomes on mRNAs, providing insights into actively expressed genes. Unlike mass spectrometry, Ribo-Seq is not affected by the same biases
Marc Follmer, Korbinian Pürckhauer, Klaus Neuhaus   +2 more
doaj   +2 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

What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome? [PDF]

Mol Cell Proteomics, 2023
Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of noncanonical sites of ribosome translation outside the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 noncanonical ORFs are translated, which, at first glance, has ...
Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Moritz RL, Deutsch EW, van Heesch S.   +9 more
europepmc   +5 more sources

Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq. [PDF]

Bioinformatics, 2021
Abstract Motivation Ribosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution.
Alkan F, Silva J, Pintó Barberà E, Faller WJ.   +3 more
europepmc   +4 more sources

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, Tsao YH, Shiue SC, Chen TY, Tseng YY, Tseng JT.   +5 more
europepmc   +5 more sources

Ribo-seq enlightens codon usage bias. [PDF]

DNA Res, 2017
Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of
Paulet D, David A, Rivals E.
europepmc   +5 more sources

Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq [PDF]

Briefings in Bioinformatics
Thomas F Martínez
exaly   +2 more sources

Accurate detection of short and long active ORFs using Ribo-seq data. [PDF]

Bioinformatics, 2020
Abstract Motivation Ribo-seq, a technique for deep-sequencing ribosome-protected mRNA fragments, has enabled transcriptome-wide monitoring of translation in vivo. It has opened avenues for re-evaluating the coding potential of open reading frames (ORFs), including many short ORFs that were previously ...
Choudhary S, Li W, D Smith A.
europepmc   +4 more sources