AIMC Topic: Sequence Analysis, DNA

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Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.

American journal of human genetics Feb 9, 2017
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is...
Genotype Genetic Association Studies Sequence Analysis, DNA Male Polymorphism, Single Nucleotide Pedigree Exome Chromosomes, Human, X Genetic Loci Genome, Human Humans Software Female Machine Learning
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Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks.

PloS one Feb 3, 2017
Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functional motifs that provide gene-specific initiation of transcription. In this paper we utilize Convolu...
Computational Biology Sequence Analysis, DNA Neural Networks, Computer Animals Eukaryotic Cells Promoter Regions, Genetic Prokaryotic Cells Humans
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PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data.

Scientific reports Jan 4, 2017
The reliable detection of novel bacterial pathogens from next-generation sequencing data is a key challenge for microbial diagnostics. Current computational tools usually rely on sequence similarity and often fail to detect novel species when closely...
Humans Machine Learning Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Bacterial Infections Bacteria Computational Biology
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DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations.

BMC bioinformatics Dec 23, 2016
BACKGROUND: With the developments of DNA sequencing technology, large amounts of sequencing data have become available in recent years and provide unprecedented opportunities for advanced association studies between somatic point mutations and cancer...
Humans Neoplasms Computational Biology Neural Networks, Computer Point Mutation Sequence Analysis, DNA Genes, Neoplasm
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Genomic Islands: an overview of current software and future improvements.

Journal of integrative bioinformatics Dec 22, 2016
Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms....
Sequence Analysis, DNA Genome, Bacterial Software Genomic Islands Bacteria
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Gogadget: An R Package for Interpretation and Visualization of GO Enrichment Results.

Molecular informatics Dec 21, 2016
Gene expression profiling followed by gene ontology (GO) term enrichment analysis can generate long lists of significant GO terms. To interpret these results and get biological insight in the data, filtering and rearranging these long lists of GO ter...
Gene Expression Profiling Computational Biology Cluster Analysis Gene Ontology Software Sequence Analysis, DNA
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acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.

BMC bioinformatics Dec 20, 2016
BACKGROUND: A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put...
DNA Quality Control DNA Contamination Genome Sequence Analysis, DNA Cluster Analysis Machine Learning Single-Cell Analysis
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GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

BMC bioinformatics Sep 13, 2016
BACKGROUND: High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significa...
Gene Ontology Humans Sequence Analysis, DNA Databases, Factual Metabolomics Sequence Analysis, RNA
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Restarting and recentering genetic algorithm variations for DNA fragment assembly: The necessity of a multi-strategy approach.

Bio Systems Aug 10, 2016
DNA Fragment assembly - an NP-Hard problem - is one of the major steps in of DNA sequencing. Multiple strategies have been used for this problem, including greedy graph-based algorithms, deBruijn graphs, and the overlap-layout-consensus approach. Thi...
Artificial Intelligence Algorithms Humans DNA Animals DNA Fragmentation Sequence Analysis, DNA
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eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform.

Scientific reports Jul 29, 2016
Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods...
Databases, Nucleic Acid Software Sequence Analysis, DNA Polymorphism, Single Nucleotide Gene Ontology
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