ArticleBMC bioinformatics2019
IRESpy: an XGBoost model for prediction of internal ribosome entry sites.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 71 citations in OpenAlex.
- DB-IRES: a deep learning model based on ensemble learning for predicting internal ribosome entry sites.BMC bioinformatics · 2026Article
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- IRES-TrAPPr reveals novel insights into viral and cellular mRNA translation.bioRxiv : the preprint server for biology · 2026Article
- Unbiased profiling of translational landscape reveals TNFR2 as a translation-dependent vulnerability in colorectal cancer.Journal of experimental & clinical cancer research : CR · 2026Article
- An efficient method for network traffic anomaly detection based on SHAP and deep learning.PloS one · 2026Article
- IRESeek: structure-informed deep learning method for accurate identification of internal ribosome entry sites in circular RNAs.NAR genomics and bioinformatics · 2025Article
- A foundation language model to decipher diverse regulation of RNAs.Genome biology · 2025Article
- Micropeptides Encoded by Noncoding RNAs: Biological Functions and Roles in Diseases.Research (Washington, D.C.) · 2025Review
- Article
- Long non-coding RNA-encoded micropeptides: functions, mechanisms and implications.Cell death discovery · 2024Review
- DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs.Briefings in bioinformatics · 2024Article
- A 5' UTR Language Model for Decoding Untranslated Regions of mRNA and Function Predictions.Nature machine intelligence · 2024Article
- The regulatory role and clinical application prospects of circRNA in the occurrence and development of CNS tumors.CNS neuroscience & therapeutics · 2024Review
- Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene.Viruses · 2024Article
- PML Body Biogenesis: A Delicate Balance of Interactions.International journal of molecular sciences · 2023Review
- RNA isoform expression landscape of the human dorsal root ganglion (DRG) generated from long read sequencing.bioRxiv : the preprint server for biology · 2023Article
- Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-RelatedNon-coding RNA · 2023Article
- Decoding of translation-regulating entities reveals heterogeneous translation deficiency patterns in cellular senescence.Aging cell · 2023Article
- Emerging roles and potential clinical applications of translatable circular RNAs in cancer and other human diseases.Genes & diseases · 2023Review
- LBCE-XGB: A XGBoost Model for Predicting Linear B-Cell Epitopes Based on BERT Embeddings.Interdisciplinary sciences, computational life sciences · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInternal ribosome entry sites (IRES) are segments of mRNA found in untranslated regions that can recruit the ribosome and initiate translation independently of the 5' cap-dependent translation initiation mechanism. IRES usually function when 5' cap-dependent translation initiation has been blocked or repressed. They have been widely found to play important roles in viral infections and cellular processes. However, a limited number of confirmed IRES have been reported due to the requirement for highly labor intensive, slow, and low efficiency laboratory experiments. Bioinformatics tools have been developed, but there is no reliable online tool.
resultsThis paper systematically examines the features that can distinguish IRES from non-IRES sequences. Sequence features such as kmer words, structural features such as Q
conclusionsIRESpy is a fast, reliable, high-throughput IRES online prediction tool. It provides a publicly available tool for all IRES researchers, and can be used in other genomics applications such as gene annotation and analysis of differential gene expression.
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Registered trials
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.