AIMC Topic: Sequence Analysis, DNA

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Co-evolution based machine-learning for predicting functional interactions between human genes.

Nature communications Nov 9, 2021
Over the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary question...
Sequence Analysis, DNA Evolution, Molecular DNA Repair Humans Machine Learning Phylogeny
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Deep learning for cancer type classification and driver gene identification.

BMC bioinformatics Oct 25, 2021
BACKGROUND: Genetic information is becoming more readily available and is increasingly being used to predict patient cancer types as well as their subtypes. Most classification methods thus far utilize somatic mutations as independent features for cl...
Humans Sequence Analysis, DNA Neoplasms Exome Sequencing Deep Learning Oncogenes
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A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
Multi-drug resistance (MDR) has become one of the greatest threats to human health worldwide, and novel treatment methods of infections caused by MDR bacteria are urgently needed. Phage therapy is a promising alternative to solve this problem, to whi...
Algorithms DNA, Viral Sequence Analysis, DNA Bacteria Microbial Interactions Drug Resistance, Bacterial Bacteriophages Computational Biology Deep Learning DNA, Bacterial
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T Cell Epitope Prediction and Its Application to Immunotherapy.

Frontiers in immunology Sep 15, 2021
T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for ep...
Histocompatibility Antigens Class I Base Sequence Antigen Presentation Mass Spectrometry Models, Molecular Receptors, Antigen, T-Cell T-Cell Antigen Receptor Specificity Computational Biology Neoplasms Immunotherapy Epitopes, T-Lymphocyte Antigens, Neoplasm Peptides Humans Sequence Analysis, DNA Neural Networks, Computer
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iPromoter-ET: Identifying promoters and their strength by extremely randomized trees-based feature selection.

Analytical biochemistry Aug 10, 2021
Promoter is a region of DNA that determines the transcription of a particular gene. There are several σ factors in the RNA polymerase, which has the function of identifying the promoter and facilitating the binding of the RNA polymerase to the promot...
Nucleotides Promoter Regions, Genetic Support Vector Machine Sequence Analysis, DNA DNA
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Discovering differential genome sequence activity with interpretable and efficient deep learning.

PLoS computational biology Aug 9, 2021
Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Patt...
High-Throughput Nucleotide Sequencing Genome, Human Transcription Factors Sequence Analysis, DNA Humans Neural Networks, Computer Deep Learning
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iEnhancer-RD: Identification of enhancers and their strength using RKPK features and deep neural networks.

Analytical biochemistry Aug 5, 2021
Enhancers are regulatory elements involved in gene expression.It is a part of DNA, which can enhance the transcription rate of gene. However, the identification of enhancer by biological experimental methods is time-consuming and expensive. Therefore...
Humans DNA Enhancer Elements, Genetic Neural Networks, Computer Computational Biology Sequence Analysis, DNA
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A deep learning model for predicting next-generation sequencing depth from DNA sequence.

Nature communications Jul 19, 2021
Targeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, and more recently as a readout for DNA information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization...
DNA Probes Base Sequence Deep Learning Genomics Sequence Analysis, DNA Humans DNA Polymorphism, Single Nucleotide High-Throughput Nucleotide Sequencing
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Analysis of DNA Sequence Classification Using CNN and Hybrid Models.

Computational and mathematical methods in medicine Jul 15, 2021
In a general computational context for biomedical data analysis, DNA sequence classification is a crucial challenge. Several machine learning techniques have used to complete this task in recent years successfully. Identification and classification o...
Base Sequence Pandemics Databases, Nucleic Acid COVID-19 SARS-CoV-2 Humans DNA, Viral Deep Learning Neural Networks, Computer Sequence Analysis, DNA Computational Biology High-Throughput Nucleotide Sequencing
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Gene Position Index Mutation Detection Algorithm Based on Feedback Fast Learning Neural Network.

Computational intelligence and neuroscience Jul 6, 2021
In the detection of genome variation, the research on the internal correlation of reference genome is deepening; the detection of variation in genome sequence has become the focus of research, and it has also become an effective path to find new gene...
Neural Networks, Computer Software Algorithms Mutation Feedback Sequence Analysis, DNA Gene Order
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