AIMC Topic: Regulatory Sequences, Nucleic Acid

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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 ...
DNA DNA-Binding Proteins Transcription Factors Regulatory Elements, Transcriptional Regulatory Sequences, Nucleic Acid Binding Sites Gene Expression Regulation Neural Networks, Computer Computational Biology Algorithms Humans
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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...
Sequence Analysis, DNA Hep G2 Cells Models, Genetic DNA RNA Proteins Protein Binding Sequence Analysis, RNA Genomics Machine Learning Software Regulatory Sequences, Nucleic Acid K562 Cells Neural Networks, Computer Humans
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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...
Neural Networks, Computer Humans Regulatory Sequences, Nucleic Acid Genomics Genome, Human Software Chromatin Sequence Analysis, DNA
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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...
Regulatory Sequences, Nucleic Acid Temozolomide Antineoplastic Agents, Alkylating Tumor Suppressor Proteins Glioblastoma Computational Biology Neural Networks, Computer Dacarbazine Brain Neoplasms Magnetic Resonance Imaging DNA Repair Enzymes DNA Methylation Databases, Genetic Humans Drug Resistance, Neoplasm DNA Modification Methylases
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