AIMC Topic: Sequence Analysis, DNA

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A sequence-based two-layer predictor for identifying enhancers and their strength through enhanced feature extraction.

Journal of bioinformatics and computational biology Mar 9, 2022
Enhancers are short regulatory DNA fragments that are bound with proteins called activators. They are free-bound and distant elements, which play a vital role in controlling gene expression. It is challenging to identify enhancers and their strength ...
Computational Biology Sequence Analysis, DNA DNA Neural Networks, Computer
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DeLUCS: Deep learning for unsupervised clustering of DNA sequences.

PloS one Jan 21, 2022
We present a novel Deep Learning method for the Unsupervised Clustering of DNA Sequences (DeLUCS) that does not require sequence alignment, sequence homology, or (taxonomic) identifiers. DeLUCS uses Frequency Chaos Game Representations (FCGR) of prim...
Base Sequence Genome, Viral Genome, Mitochondrial Sequence Analysis, DNA Cluster Analysis Genome, Bacterial Humans Animals Deep Learning Neural Networks, Computer
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Table2Vec-automated universal representation learning of enterprise data DNA for benchmarkable and explainable enterprise data science.

Scientific reports Dec 14, 2021
Enterprise data typically involves multiple heterogeneous data sources and external data that respectively record business activities, transactions, customer demographics, status, behaviors, interactions and communications with the enterprise, and th...
Sequence Analysis, DNA Databases, Nucleic Acid Machine Learning Software
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GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies.

IEEE/ACM transactions on computational biology and bioinformatics Dec 8, 2021
Short-read DNA sequencing instruments can yield over 10 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using short reads ...
Programming Languages High-Throughput Nucleotide Sequencing Genome, Human Sequence Analysis, DNA Natural Language Processing Humans Deep Learning Genomics Algorithms
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BreakNet: detecting deletions using long reads and a deep learning approach.

BMC bioinformatics Dec 2, 2021
BACKGROUND: Structural variations (SVs) occupy a prominent position in human genetic diversity, and deletions form an important type of SV that has been suggested to be associated with genetic diseases. Although various deletion calling methods based...
Humans Genome Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Software Deep Learning
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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...
DNA Repair Sequence Analysis, DNA Evolution, Molecular Machine Learning Phylogeny Humans
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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...
Deep Learning Sequence Analysis, DNA Humans Exome Sequencing Oncogenes Neoplasms
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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...
Deep Learning Bacteria DNA, Bacterial DNA, Viral Computational Biology Algorithms Drug Resistance, Bacterial Bacteriophages Sequence Analysis, DNA Microbial Interactions
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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...
Models, Molecular Histocompatibility Antigens Class I Base Sequence Sequence Analysis, DNA Peptides Mass Spectrometry Receptors, Antigen, T-Cell Neoplasms Immunotherapy Computational Biology Antigen Presentation Humans Antigens, Neoplasm Epitopes, T-Lymphocyte T-Cell Antigen Receptor Specificity 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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