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Databases, Nucleic Acid

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SCMAG: A Semisupervised Single-Cell Clustering Method Based on Matrix Aggregation Graph Convolutional Neural Network.

Computational and mathematical methods in medicine 34646337
Clustering analysis is one of the most important technologies for single-cell data mining. It is widely used in the division of different gene sequences, the identification of functional genes, and the detection of new cell types. Although the tradit...
Algorithms Cluster Analysis Computational Biology Data Mining Databases, Nucleic Acid Humans Neural Networks, Computer RNA-Seq Single-Cell Analysis Supervised Machine Learning
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Analysis of DNA Sequence Classification Using CNN and Hybrid Models.

Computational and mathematical methods in medicine 34306171
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 Computational Biology COVID-19 Databases, Nucleic Acid Deep Learning DNA, Viral High-Throughput Nucleotide Sequencing Humans Neural Networks, Computer Pandemics SARS-CoV-2 Sequence Analysis, DNA
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High-throughput developability assays enable library-scale identification of producible protein scaffold variants.

Proceedings of the National Academy of Sciences of the United States of America 34078670
Proteins require high developability-quantified by expression, solubility, and stability-for robust utility as therapeutics, diagnostics, and in other biotechnological applications. Measuring traditional developability metrics is low throughput in na...
Databases, Nucleic Acid Gene Library High-Throughput Screening Assays Machine Learning Proteins
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Benchmarking and Testing Machine Learning Approaches with BARRA:CuRDa, a for Cancer Research.

Journal of computational biology : a journal of computational molecular cell biology 34264745
Algorithms Artificial Intelligence Benchmarking Data Visualization Databases, Nucleic Acid Humans Machine Learning Neoplasms Principal Component Analysis RNA-Seq Sequence Analysis, RNA
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eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping.

Nucleic acids research 34104972
Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the d...
Databases, Nucleic Acid Exons Internet Introns Machine Learning Oligonucleotides, Antisense RNA Splicing Sequence Analysis Software
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GATNNCDA: A Method Based on Graph Attention Network and Multi-Layer Neural Network for Predicting circRNA-Disease Associations.

International journal of molecular sciences 34445212
Circular RNAs (circRNAs) are a new class of endogenous non-coding RNAs with covalent closed loop structure. Researchers have revealed that circRNAs play an important role in human diseases. As experimental identification of interactions between circR...
Breast Neoplasms Carcinoma, Hepatocellular Computational Biology Databases, Nucleic Acid Female Humans Liver Neoplasms Neural Networks, Computer RNA, Circular RNA, Neoplasm
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Classification and Functional Analysis between Cancer and Normal Tissues Using Explainable Pathway Deep Learning through RNA-Sequencing Gene Expression.

International journal of molecular sciences 34768960
Deep learning has proven advantageous in solving cancer diagnostic or classification problems. However, it cannot explain the rationale behind human decisions. Biological pathway databases provide well-studied relationships between genes and their pa...
Databases, Nucleic Acid Deep Learning Diagnosis, Computer-Assisted Gene Expression Regulation, Neoplastic Gene Regulatory Networks Humans Neoplasms Neural Networks, Computer RNA-Seq
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Table2Vec-automated universal representation learning of enterprise data DNA for benchmarkable and explainable enterprise data science.

Scientific reports 34907319
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...
Databases, Nucleic Acid Machine Learning Sequence Analysis, DNA Software
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Biological features between miRNAs and their targets are unveiled from deep learning models.

Scientific reports 34893648
MicroRNAs (miRNAs) are ~ 22 nucleotide ubiquitous gene regulators. They modulate a broad range of essential cellular processes linked to human health and diseases. Consequently, identifying miRNA targets and understanding how they function are critic...
Algorithms Base Pairing Computational Biology Databases, Nucleic Acid Deep Learning Gene Expression Regulation Gene Regulatory Networks Humans MicroRNAs Models, Biological Mutagenesis RNA Interference RNA, Messenger
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GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks.

Journal of computational biology : a journal of computational molecular cell biology 35050715
We propose GRNUlar, a novel deep learning framework for supervised learning of gene regulatory networks (GRNs) from single-cell RNA-Sequencing (scRNA-Seq) data. Our framework incorporates two intertwined models. First, we leverage the expressive abil...
Algorithms Animals Bias Computational Biology Computer Simulation Databases, Nucleic Acid Deep Learning Escherichia coli Gene Regulatory Networks Humans Mice Neural Networks, Computer RNA-Seq Saccharomyces cerevisiae Single-Cell Analysis Supervised Machine Learning
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