AIMC Topic: Databases, Nucleic Acid

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Deep learning architectures for prediction of nucleosome positioning from sequences data.

BMC bioinformatics Nov 20, 2018
BACKGROUND: Nucleosomes are DNA-histone complex, each wrapping about 150 pairs of double-stranded DNA. Their function is fundamental for one of the primary functions of Chromatin i.e. packing the DNA into the nucleus of the Eukaryote cells. Several b...
Neural Networks, Computer Reproducibility of Results Animals Humans Saccharomyces cerevisiae Databases, Nucleic Acid Nucleosomes Deep Learning ROC Curve Base Sequence
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Computational characterization and identification of human polycystic ovary syndrome genes.

Scientific reports Aug 28, 2018
Human polycystic ovary syndrome (PCOS) is a highly heritable disease regulated by genetic and environmental factors. Identifying PCOS genes is time consuming and costly in wet-lab. Developing an algorithm to predict PCOS candidates will be helpful. I...
Polycystic Ovary Syndrome Databases, Nucleic Acid Humans Machine Learning Female Gene Regulatory Networks
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Towards better prediction of Mycobacterium tuberculosis lineages from MIRU-VNTR data.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Jun 28, 2018
The determination of lineages from strain-based molecular genotyping information is an important problem in tuberculosis. Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is a commonly used molecular genotyp...
Tuberculosis Genetic Variation Mycobacterium tuberculosis Machine Learning Phylogeny Computational Biology Interspersed Repetitive Sequences Minisatellite Repeats Molecular Epidemiology Databases, Nucleic Acid New York City Humans
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GeNets: a unified web platform for network-based genomic analyses.

Nature methods Jun 18, 2018
Functional genomics networks are widely used to identify unexpected pathway relationships in large genomic datasets. However, it is challenging to compare the signal-to-noise ratios of different networks and to identify the optimal network with which...
Machine Learning RNA Nucleic Acid Amplification Techniques Databases, Nucleic Acid DNA Software Internet Genomics
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HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy.

RNA biology Jun 6, 2018
LncRNA plays an important role in many biological and disease progression by binding to related proteins. However, the experimental methods for studying lncRNA-protein interactions are time-consuming and expensive. Although there are a few models des...
Sequence Analysis, RNA Support Vector Machine RNA, Long Noncoding Models, Biological Databases, Nucleic Acid Humans RNA-Binding Proteins
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Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data.

PLoS computational biology Apr 10, 2018
Artificial neural networks (ANN) are computing architectures with many interconnections of simple neural-inspired computing elements, and have been applied to biomedical fields such as imaging analysis and diagnosis. We have developed a new ANN frame...
High-Throughput Nucleotide Sequencing Survival Analysis Proportional Hazards Models Kaplan-Meier Estimate Databases, Nucleic Acid Computational Biology Sequence Analysis, RNA Metabolic Networks and Pathways Gene Expression Profiling Gene Regulatory Networks Humans Neural Networks, Computer Female Prognosis Male Neoplasms
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Graphical classification of DNA sequences of HLA alleles by deep learning.

Human cell Jan 11, 2018
Alleles of human leukocyte antigen (HLA)-A DNAs are classified and expressed graphically by using artificial intelligence "Deep Learning (Stacked autoencoder)". Nucleotide sequence data corresponding to the length of 822 bp, collected from the Immuno...
Humans Base Sequence Artificial Intelligence Databases, Nucleic Acid Sequence Analysis, DNA HLA-A Antigens Alleles
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A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data.

PloS one Feb 15, 2017
Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribut...
Databases, Nucleic Acid Gene Expression Regulation, Bacterial Gene Ontology Transcriptome Salmonella enteritidis Humans Alzheimer Disease
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Random Subspace Aggregation for Cancer Prediction with Gene Expression Profiles.

BioMed research international Nov 24, 2016
. Precisely predicting cancer is crucial for cancer treatment. Gene expression profiles make it possible to analyze patterns between genes and cancers on the genome-wide scale. Gene expression data analysis, however, is confronted with enormous chall...
Gene Expression Regulation, Neoplastic Animals Humans Models, Genetic Databases, Nucleic Acid Neoplasms Predictive Value of Tests Gene Expression Profiling Machine Learning
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Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

PloS one Aug 4, 2016
MOTIVATION: First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and...
Supervised Machine Learning Zebrafish Base Sequence Escherichia coli Animals Caenorhabditis elegans Databases, Nucleic Acid Zea mays Computational Biology
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