ArticleNucleic acids research2018
Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 53 citations in OpenAlex.
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- Proteogenomics Reveals Microproteins in Activated T Cells.Molecular & cellular proteomics : MCP · 2025Article
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data.Nature communications · 2024Article
- Review
- ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events.BMC bioinformatics · 2023Article
- A hidden translatome in tumors-the coding lncRNAs.Science China. Life sciences · 2023Review
- Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task.PLoS computational biology · 2023Article
- RNA binding protein TIAR modulates HBV replication by tipping the balance of pgRNA translation.Signal transduction and targeted therapy · 2023Article
- Review
- Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World.International journal of molecular sciences · 2023Review
- slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.Briefings in bioinformatics · 2023Article
- Discovering microproteins: making the most of ribosome profiling data.RNA biology · 2023Review
- Review
- Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames.Briefings in bioinformatics · 2022Article
- Small open reading frames in plant research: from prediction to functional characterization.3 Biotech · 2022Review
- MVIP: multi-omics portal of viral infection.Nucleic acids research · 2022Article
- RiboPlotR: a visualization tool for periodic Ribo-seq reads.Plant methods · 2021Article
- RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints.Life (Basel, Switzerland) · 2021Article
- ORFik: a comprehensive R toolkit for the analysis of translation.BMC bioinformatics · 2021Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frames (ORFs) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes and precisely locate their footprint denoted as Periodic Footprint P-site (PF P-site). Such high-resolution footprint is found to capture the full track of actively elongating ribosomes, from which translational landscape can be explicitly characterized. We compare RiboWave with several published methods, like RiboTaper, ORFscore and RibORF, and found that RiboWave outperforms them in both accuracy and usage when defining actively translated ORFs. Moreover, we show that PF P-site derived by RiboWave shows superior performance in characterizing the dynamics and complexity of cellular translatome by accurately estimating the abundance of protein levels, assessing differential translation and identifying dynamic translation frameshift.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.