ArticleBiology direct2006
Method of predicting splice sites based on signal interactions.
Article in Biology direct, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- BlendSplice: A Frequency-Blended Generative Framework forComputational and structural biotechnology journal · 2026Article
- The Influence of a Genetic Variant inInternational journal of molecular sciences · 2024Article
- Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup.American journal of human genetics · 2023Article
- APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP.medRxiv : the preprint server for health sciences · 2023Article
- Mechanical Stress and Single Nucleotide Variants Regulate Alternative Splicing of the MYLK Gene.American journal of respiratory cell and molecular biology · 2017Article
- Article
- Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.Genomics, proteomics & bioinformatics · 2013Article
- Origin and evolution of spliceosomal introns.Biology direct · 2012Review
- A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements.BMC bioinformatics · 2010Article
- Computational prediction of splicing regulatory elements shared by Tetrapoda organisms.BMC genomics · 2009Article
- Human Splicing Finder: an online bioinformatics tool to predict splicing signals.Nucleic acids research · 2009Article
- An exon-based comparative variant analysis pipeline to study the scale and role of frameshift and nonsense mutation in the human-chimpanzee divergence.Comparative and functional genomics · 2009Article
- Clustering ionic flow blockade toggles with a mixture of HMMs.BMC bioinformatics · 2008Article
- A luteinizing hormone receptor intronic variant is significantly associated with decreased risk of Alzheimer's disease in males carrying an apolipoprotein E epsilon4 allele.BMC medical genetics · 2008Article
- Aberrant RNA splicing and its functional consequences in cancer cells.Disease models & mechanismsReview
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundPredicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan.
resultsAccording to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE) and Intronic (ISE) Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments.
conclusionDesigned methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. REVIEWERS: This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.
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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.