AIMC Topic: Sequence Analysis, DNA

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Res2s2aM: Deep residual network-based model for identifying functional noncoding SNPs in trait-associated regions.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2019
Noncoding single nucleotide polymorphisms (SNPs) and their target genes are important components of the heritability of diseases and other polygenic traits. Identifying these SNPs and target genes could potentially reveal new molecular mechanisms and...
Humans Neural Networks, Computer Algorithms Deep Learning Models, Genetic Sequence Analysis, DNA Molecular Sequence Annotation Databases, Nucleic Acid Genome-Wide Association Study Polymorphism, Single Nucleotide Computational Biology
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Discovering epistatic feature interactions from neural network models of regulatory DNA sequences.

Bioinformatics (Oxford, England) Sep 1, 2018
MOTIVATION: Transcription factors bind regulatory DNA sequences in a combinatorial manner to modulate gene expression. Deep neural networks (DNNs) can learn the cis-regulatory grammars encoded in regulatory DNA sequences associated with transcription...
DNA High-Throughput Nucleotide Sequencing Binding Sites Chromatin Genomics Neural Networks, Computer Transcription Factors Protein Binding Sequence Analysis, DNA
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GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS.

Bioinformatics (Oxford, England) Sep 1, 2018
SUMMARY: Exome sequencing approach is extensively used in research and diagnostic laboratories to discover pathological variants and study genetic architecture of human diseases. However, a significant proportion of identified genetic variants are ac...
Sequence Analysis, DNA High-Throughput Nucleotide Sequencing INDEL Mutation Genomics Deep Learning Polymorphism, Single Nucleotide
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pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion.

Bioinformatics (Oxford, England) Jul 1, 2018
MOTIVATION: Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrat...
Humans Software Computational Biology Sequence Analysis, DNA Bayes Theorem Information Storage and Retrieval Phenotype Animals Genomics Biological Ontologies
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Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data.

Bioinformatics (Oxford, England) May 15, 2018
MOTIVATION: Correct and rapid determination of Mycobacterium tuberculosis (MTB) resistance against available tuberculosis (TB) drugs is essential for the control and management of TB. Conventional molecular diagnostic test assumes that the presence o...
Ofloxacin Rifampin Streptomycin Moxifloxacin Antitubercular Agents Tuberculosis, Multidrug-Resistant Ciprofloxacin Pyrazinamide Isoniazid Mycobacterium tuberculosis Ethambutol Machine Learning Microbial Sensitivity Tests Sequence Analysis, DNA Humans
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Deep learning of genomic variation and regulatory network data.

Human molecular genetics May 1, 2018
The human genome is now investigated through high-throughput functional assays, and through the generation of population genomic data. These advances support the identification of functional genetic variants and the prediction of traits (e.g. deleter...
Humans Software Genomics Deep Learning High-Throughput Nucleotide Sequencing Sequence Analysis, DNA Gene Regulatory Networks Genome, Human Exome
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Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.

GigaScience May 1, 2018
Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex elec...
Base Pairing Nanopores Escherichia coli Sequence Analysis, DNA Signal Processing, Computer-Assisted Neural Networks, Computer Machine Learning Probability Software Nucleotides Reproducibility of Results Base Sequence Mycobacterium tuberculosis
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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...
Regulatory Sequences, Nucleic Acid Humans Protein Binding DNA Neural Networks, Computer Sequence Analysis, DNA Sequence Analysis, RNA Genomics RNA Machine Learning Hep G2 Cells Models, Genetic K562 Cells Software Proteins
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Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations.

Bioinformatics (Oxford, England) Mar 15, 2018
MOTIVATION: As whole-genome tumor sequence and biological annotation datasets grow in size, number and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergenc...
Mutation Supervised Machine Learning Male Neoplasms Sequence Analysis, DNA Humans Software Female
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Machine learning annotation of human branchpoints.

Bioinformatics (Oxford, England) Mar 15, 2018
MOTIVATION: The branchpoint element is required for the first lariat-forming reaction in splicing. However current catalogues of human branchpoints remain incomplete due to the difficulty in experimentally identifying these splicing elements. To addr...
Introns Humans RNA Splicing Genetic Variation Sensitivity and Specificity Machine Learning Genome, Human Sequence Analysis, DNA Software Molecular Sequence Annotation
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