AIMC Topic: Open Reading Frames
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Cucumber green mottle mosaic virus encodes additional small proteins with specific subcellular localizations and virulence function.
Science China. Life sciences
Apr 1, 2025
The vast majority of known viruses belong to the positive-sense single-stranded RNA (+ssRNA) class. Tobamoviruses are among the most destructive plant viruses and threaten global food security. It is generally accepted that +ssRNA viruses including t...
Deep learning to decode sites of RNA translation in normal and cancerous tissues.
Nature communications
Feb 2, 2025
The biological process of RNA translation is fundamental to cellular life and has wide-ranging implications for human disease. Accurate delineation of RNA translation variation represents a significant challenge due to the complexity of the process a...
SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.
NAR genomics and bioinformatics
Jan 7, 2025
Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotation of prokar...
Interpreting deep neural networks for the prediction of translation rates.
BMC genomics
Nov 9, 2024
BACKGROUND: The 5' untranslated region of mRNA strongly impacts the rate of translation initiation. A recent convolutional neural network (CNN) model accurately quantifies the relationship between massively parallel synthetic 5' untranslated regions ...
Functional annotation of enzyme-encoding genes using deep learning with transformer layers.
Nature communications
Nov 14, 2023
Functional annotation of open reading frames in microbial genomes remains substantially incomplete. Enzymes constitute the most prevalent functional gene class in microbial genomes and can be described by their specific catalytic functions using the ...
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning.
Genome biology
Jun 20, 2022
The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, which accurate...
The hunt for sORFs: A multidisciplinary strategy.
Experimental cell research
Mar 2, 2020
Growing evidence illustrates the shortcomings on the current understanding of the full complexity of the proteome. Previously overlooked small open reading frames (sORFs) and their encoded microproteins have filled important gaps, exerting their func...
MiPepid: MicroPeptide identification tool using machine learning.
BMC bioinformatics
Nov 8, 2019
BACKGROUND: Micropeptides are small proteins with length < = 100 amino acids. Short open reading frames that could produces micropeptides were traditionally ignored due to technical difficulties, as few small peptides had been experimentally confirme...
Prediction of plant lncRNA by ensemble machine learning classifiers.
BMC genomics
May 2, 2018
BACKGROUND: In plants, long non-protein coding RNAs are believed to have essential roles in development and stress responses. However, relative to advances on discerning biological roles for long non-protein coding RNAs in animal systems, this RNA cl...
Improved ontology for eukaryotic single-exon coding sequences in biological databases.
Database : the journal of biological databases and curation
Jan 1, 2018
Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryo...
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