Semi-supervised learning improves regulatory sequence prediction with unlabeled sequences [PDF]
BMC Bioinformatics, 2023 Motivation Genome-wide association studies have systematically identified thousands of single nucleotide polymorphisms (SNPs) associated with complex genetic diseases.
Raphaël Mourad
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Cross-species regulatory sequence activity prediction. [PDF]
PLoS Computational Biology, 2020 Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis.
David R Kelley
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Formation of regulatory modules by local sequence duplication. [PDF]
PLoS Computational Biology, 2011 Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites?
Armita Nourmohammad, Michael Lässig
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Boolean network model predicts cell cycle sequence of fission yeast. [PDF]
PLoS ONE, 2008 A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology.
Maria I Davidich, Stefan Bornholdt
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Extensive Association of Common Disease Variants with Regulatory Sequence. [PDF]
PLoS ONE, 2016 Overlap between non-coding DNA regulatory sequences and common variant associations can help to identify specific cell and tissue types that are relevant for particular diseases.
Michal Mokry +4 more
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Enhanced regulatory sequence prediction using gapped k-mer features. [PDF]
PLoS Computational Biology, 2014 Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer ...
Mahmoud Ghandi +3 more
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The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity. [PDF]
PLoS Genetics, 2015 Noncoding sequence contains pathogenic mutations. Yet, compared with mutations in protein-coding sequence, pathogenic regulatory mutations are notoriously difficult to recognize.
Slavé Petrovski +8 more
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The impact of different negative training data on regulatory sequence predictions. [PDF]
PLoS ONE, 2020 Regulatory regions, like promoters and enhancers, cover an estimated 5-15% of the human genome. Changes to these sequences are thought to underlie much of human phenotypic variation and a substantial proportion of genetic causes of disease.
Louisa-Marie Krützfeldt +2 more
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Regulatory sequence-based discovery of anti-defense genes in archaeal viruses [PDF]
Nature CommunicationsIn silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait.
Yuvaraj Bhoobalan-Chitty +6 more
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Nucleosome positioning sequence patterns as packing or regulatory. [PDF]
PLoS Computational Biology, 2020 Nucleosome positioning DNA sequence patterns (NPS)-usually distributions of particular dinucleotides or other sequence elements in nucleosomal DNA-at least partially determine chromatin structure and arrangements of nucleosomes that in turn affect gene ...
Erinija Pranckeviciene +3 more
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