AIMC Topic: Base Sequence

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Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning.

Frontiers in immunology Feb 10, 2021
The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achie...
Amino Acid Sequence AIDS Serodiagnosis Oligonucleotides Hepatitis C Antibodies HIV Core Protein p24 Antigen-Antibody Reactions Hepatitis C Genetic Vectors DNA, Recombinant High-Throughput Nucleotide Sequencing Serologic Tests Hepatitis C Antigens HIV Antibodies HIV Envelope Protein gp160 HIV Infections DNA Barcoding, Taxonomic Humans Peptide Library Machine Learning Base Sequence Peptide Fragments Communicable Diseases Polymerase Chain Reaction Epitopes
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DNA sequences performs as natural language processing by exploiting deep learning algorithm for the identification of N4-methylcytosine.

Scientific reports Jan 8, 2021
N4-methylcytosine is a biochemical alteration of DNA that affects the genetic operations without modifying the DNA nucleotides such as gene expression, genomic imprinting, chromosome stability, and the development of the cell. In the proposed work, a...
Computer Simulation Deep Learning Natural Language Processing Base Sequence
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Deep learning for HGT insertion sites recognition.

BMC genomics Dec 29, 2020
BACKGROUND: Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT mechanisms. Recent studies in m...
Phylogeny Deep Learning Metagenomics Base Sequence Genome Gene Transfer, Horizontal
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Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure.

Nature communications Dec 1, 2020
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression leve...
Bacteria RNA, Messenger Evolution, Molecular Gene Expression Regulation Humans Animals Deep Learning Mice Base Sequence Saccharomyces cerevisiae Drosophila melanogaster Regulatory Sequences, Nucleic Acid
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Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools.

Scientific reports Nov 24, 2020
The outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cell...
HLA Antigens Alleles Histocompatibility Antigens Class I Base Sequence Peptides COVID-19 Vaccines Spike Glycoprotein, Coronavirus Computational Biology Histocompatibility Antigens Class II Humans Machine Learning COVID-19 SARS-CoV-2 Epitopes, T-Lymphocyte
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Transfer learning enables prediction of CYP2D6 haplotype function.

PLoS computational biology Nov 2, 2020
Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene whose protein product metabolizes more than 20% of clinically used drugs. Genetic variations in CYP2D6 are responsible for interindividual heterogeneity in drug response that can lead to drug ...
Computer Simulation Deep Learning Computational Biology DNA Humans Neural Networks, Computer Phenotype Pharmacogenomic Testing Cytochrome P-450 CYP2D6 Microsomes, Liver Haplotypes Base Sequence Polymorphism, Genetic Pharmaceutical Preparations Supervised Machine Learning Alleles
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m5CPred-SVM: a novel method for predicting m5C sites of RNA.

BMC bioinformatics Oct 30, 2020
BACKGROUND: As one of the most common post-transcriptional modifications (PTCM) in RNA, 5-cytosine-methylation plays important roles in many biological functions such as RNA metabolism and cell fate decision. Through accurate identification of 5-meth...
ROC Curve Mice Support Vector Machine Internet RNA Base Sequence Arabidopsis 5-Methylcytosine Humans Animals
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Identification and Classification of Enhancers Using Dimension Reduction Technique and Recurrent Neural Network.

Computational and mathematical methods in medicine Oct 18, 2020
Enhancers are noncoding fragments in DNA sequences, which play an important role in gene transcription and translation. However, due to their high free scattering and positional variability, the identification and classification of enhancers have a h...
Mathematical Concepts Base Composition Databases, Genetic Base Sequence Enhancer Elements, Genetic Algorithms Computational Biology Models, Genetic Humans Support Vector Machine Neural Networks, Computer Machine Learning
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Machine learning discriminates a movement disorder in a zebrafish model of Parkinson's disease.

Disease models & mechanisms Oct 16, 2020
Animal models of human disease provide an system that can reveal molecular mechanisms by which mutations cause pathology, and, moreover, have the potential to provide a valuable tool for drug development. Here, we have developed a zebrafish model of...
Movement Disorders Gene Targeting Protein Deglycase DJ-1 Zebrafish Base Sequence Machine Learning Movement Algorithms Dopaminergic Neurons Parkinson Disease Brain Mutation Animals Alleles Gene Expression Profiling Disease Models, Animal
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DeepC: predicting 3D genome folding using megabase-scale transfer learning.

Nature methods Oct 12, 2020
Predicting the impact of noncoding genetic variation requires interpreting it in the context of three-dimensional genome architecture. We have developed deepC, a transfer-learning-based deep neural network that accurately predicts genome folding from...
CCCTC-Binding Factor Models, Genetic Genomic Structural Variation Humans Base Sequence Neural Networks, Computer Genome, Human Computer Simulation Chromatin Genomics
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