AIMC Topic: Regulatory Sequences, Nucleic Acid

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Convolutional neural network model to predict causal risk factors that share complex regulatory features.

Nucleic acids research Dec 16, 2019
Major progress in disease genetics has been made through genome-wide association studies (GWASs). One of the key tasks for post-GWAS analyses is to identify causal noncoding variants with regulatory function. Here, on the basis of >2000 functional fe...
Neural Networks, Computer Mental Disorders Risk Factors Humans Autoimmune Diseases Genome-Wide Association Study Genetic Predisposition to Disease Quantitative Trait Loci Regulatory Sequences, Nucleic Acid Polymorphism, Single Nucleotide
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TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes.

Nucleic acids research Aug 22, 2019
Genome-wide association studies (GWAS) associate single nucleotide polymorphisms (SNPs) to complex phenotypes. Most human SNPs fall in non-coding regions and are likely regulatory SNPs, but linkage disequilibrium (LD) blocks make it difficult to dist...
Humans Internet Regulatory Sequences, Nucleic Acid Supervised Machine Learning Genetic Predisposition to Disease Quantitative Trait Loci Gene Expression Regulation Phenotype Polymorphism, Single Nucleotide Linkage Disequilibrium Genome-Wide Association Study Computational Biology
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DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.

Nucleic acids research Jun 4, 2019
Interactions between regulatory elements are of crucial importance for the understanding of transcriptional regulation and the interpretation of disease mechanisms. Hi-C technique has been developed for genome-wide detection of chromatin contacts. Ho...
Deep Learning Genome-Wide Association Study Computational Biology Algorithms Cells, Cultured Regulatory Sequences, Nucleic Acid Chromatin Gene Expression Regulation Promoter Regions, Genetic High-Throughput Nucleotide Sequencing Humans
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DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants.

Nucleic acids research Jun 20, 2018
The complex system of gene expression is regulated by the cell type-specific binding of transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding and lead to human diseases remains a great challenge. To address ...
Gene Expression Regulation Binding Sites Regulatory Sequences, Nucleic Acid Regulatory Elements, Transcriptional Transcription Factors Humans Algorithms DNA Neural Networks, Computer Computational Biology DNA-Binding Proteins
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Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.

Bioinformatics (Oxford, England) Apr 15, 2018
MOTIVATION: Regulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries or polyadenylation site. Deep learning has become the a...
Neural Networks, Computer Machine Learning Protein Binding Genomics Software RNA Sequence Analysis, DNA Sequence Analysis, RNA Humans K562 Cells Hep G2 Cells Regulatory Sequences, Nucleic Acid Models, Genetic DNA Proteins
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Chromatin accessibility prediction via a hybrid deep convolutional neural network.

Bioinformatics (Oxford, England) Mar 1, 2018
MOTIVATION: A majority of known genetic variants associated with human-inherited diseases lie in non-coding regions that lack adequate interpretation, making it indispensable to systematically discover functional sites at the whole genome level and p...
Regulatory Sequences, Nucleic Acid Chromatin Sequence Analysis, DNA Genome, Human Neural Networks, Computer Humans Software Genomics
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MRI to MGMT: predicting methylation status in glioblastoma patients using convolutional recurrent neural networks.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2018
Glioblastoma Multiforme (GBM), a malignant brain tumor, is among the most lethal of all cancers. Temozolomide is the primary chemotherapy treatment for patients diagnosed with GBM. The methylation status of the promoter or the enhancer regions of the...
Tumor Suppressor Proteins Magnetic Resonance Imaging DNA Repair Enzymes Brain Neoplasms Temozolomide Computational Biology Regulatory Sequences, Nucleic Acid Humans Drug Resistance, Neoplasm DNA Methylation Antineoplastic Agents, Alkylating Dacarbazine Neural Networks, Computer Databases, Genetic Glioblastoma DNA Modification Methylases
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