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. Mit dem Aufkommen von RNA-seq-Technologien können wir nun jeden dieser Schritte mit hohem Durchsatz und Auflösung verfolgen.
Calviello, Lorenzo
openaire +3 more sources
The use of Benzonase to produce ribosome footprints simplifies translational levels quantification by Ribo-seq. [PDF]
NAR Genom BioinformABSTRACT Gene expression quantification through genomics methods is crucial for understanding diverse biological contexts. Among these methods, ribosome profiling (Ribo-seq) stands out as a valuable tool for uncovering post-transcriptional gene expression regulation by providing a comprehensive view of the translatome.
Eastman G, Bloom GS, Sotelo-Silveira JR.
europepmc +3 more sources
DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data. [PDF]
BMC Bioinformatics, 2019 Abstract Background Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mapped reads to similar isoforms.
Cui H, Hu H, Zeng J, Chen T.
europepmc +5 more sources
Data-driven design of LNA-blockers for efficient contaminant removal in Ribo-Seq libraries. [PDF]
Sci RepSummary Ribo-Seq libraries often contain a high amount of non-coding RNA fragments, which can significantly reduce the information output of these experiments. Contaminants can comprise up to 90% of a Ribo-Seq library, showing high sequence variability and diverse fragmentation, which hinders the effectiveness of rRNA depletion kits ...
Ricciardi DA, Peter FE, Böhmer M.
europepmc +3 more sources
Riborex: fast and flexible identification of differential translation from Ribo-seq data. [PDF]
Bioinformatics, 2017 Abstract Motivation Global analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample.
Li W +4 more
europepmc +4 more sources
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.
Aspden, JL +6 more
core +6 more sources
Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases. [PDF]
Cells, 2022 RNA-seq has been widely used as a high-throughput method to characterize transcript dynamic changes in a broad context, such as development and diseases.
Bagheri A +3 more
europepmc +2 more sources
Identifying and Visualizing Novel Small Open Reading Frames (sORFs) Via Ribo-Seq, Transcriptome Assembly, and ggRibo [PDF]
Methods in Molecular BiologyHsin-Yen Larry Wu, Polly Yingshan Hsu
exaly +2 more sources
The Translatome Map: RNC-Seq vs. Ribo-Seq for Profiling of HBE, A549, and MCF-7 Cell Lines [PDF]
International Journal of Molecular SciencesAnna Kozlova +2 more
exaly +2 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. The development of the Ribo-Seq technique, a combination of classical ribosome profiling and next generation sequencing, enabled scientists to ...
Gotsmann, Vincent Leon
openaire +3 more sources