AIMC Topic: Base Sequence

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gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning.

Scientific reports Apr 21, 2020
The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromoso...
Machine Learning Software Nucleotide Motifs Consensus Sequence Gammaproteobacteria Replication Origin Phylogeny Models, Genetic Base Sequence
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Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction.

Nature communications Mar 26, 2020
The diversity in our genome is crucial to understanding the demographic history of worldwide populations. However, we have yet to know whether subtle genetic differences within a population can be disentangled, or whether they have an impact on compl...
Genetics, Population Base Sequence Multifactor Dimensionality Reduction Multifactorial Inheritance Risk Factors Genetic Predisposition to Disease Principal Component Analysis Asian People Humans Biological Specimen Banks Phenotype Japan
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Exploring the Consistency of the Quality Scores with Machine Learning for Next-Generation Sequencing Experiments.

BioMed research international Feb 25, 2020
BACKGROUND: Next-generation sequencing enables massively parallel processing, allowing lower cost than the other sequencing technologies. In the subsequent analysis with the NGS data, one of the major concerns is the reliability of variant calls. Alt...
High-Throughput Nucleotide Sequencing Linear Models Base Sequence Algorithms Reproducibility of Results Computational Biology Genome, Human Humans Machine Learning Software
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Deep neural networks for human microRNA precursor detection.

BMC bioinformatics Jan 13, 2020
BACKGROUND: MicroRNAs (miRNAs) play important roles in a variety of biological processes by regulating gene expression at the post-transcriptional level. So, the discovery of new miRNAs has become a popular task in biological research. Since the expe...
Machine Learning Deep Learning Databases, Genetic Humans Neural Networks, Computer Protein Structure, Secondary MicroRNAs Base Sequence RNA Precursors
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SpliceFinder: ab initio prediction of splice sites using convolutional neural network.

BMC bioinformatics Dec 27, 2019
BACKGROUND: Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on splice sites with important biological fun...
Animals Computational Biology Databases, Genetic Neural Networks, Computer Software Algorithms RNA Splice Sites Base Sequence Genome RNA Splicing Humans
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A generative model for constructing nucleic acid sequences binding to a protein.

BMC genomics Dec 27, 2019
BACKGROUND: Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the development of several computational...
Base Sequence Nucleic Acid Conformation Transcription Factors Proteins DNA Algorithms Aptamers, Nucleotide Protein Binding Humans Neural Networks, Computer
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Fast and accurate microRNA search using CNN.

BMC bioinformatics Dec 27, 2019
BACKGROUND: There are many different types of microRNAs (miRNAs) and elucidating their functions is still under intensive research. A fundamental step in functional annotation of a new miRNA is to classify it into characterized miRNA families, such a...
Neural Networks, Computer Algorithms MicroRNAs Probability Nucleotide Motifs Base Sequence RNA, Transfer Base Pairing
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In vitro selection of DNA aptamers and their integration in a competitive voltammetric biosensor for azlocillin determination in waste water.

Analytica chimica acta Dec 16, 2019
The uncontrolled usage of veterinary antibiotics has led to their widespread pollution in waterways and milk products. Potential impact of antibiotic residues on the environment and human health such as increased antibiotic resistance of microorganis...
Electrochemical Techniques Limit of Detection Biosensing Techniques Azlocillin Base Sequence Water Pollutants, Chemical Wastewater Drinking Water DNA Anti-Bacterial Agents Aptamers, Nucleotide
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DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network.

BMC bioinformatics Dec 12, 2019
BACKGROUND: Calling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling single nucleotide polymorphisms (...
Sequence Deletion Machine Learning Software Genomics High-Throughput Nucleotide Sequencing Base Sequence Chromosomes, Human Humans Neural Networks, Computer
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Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage.

BMC bioinformatics Dec 11, 2019
BACKGROUND: In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the read...
Base Sequence Genome, Mitochondrial Macropodidae Animals Nucleotides High-Throughput Nucleotide Sequencing Machine Learning Algorithms
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