AI Medical Compendium Journal:
Journal of bioinformatics and computational biology

Showing 61 to 70 of 73 articles

Integrating pharmacophore model and deep learning for activity prediction of molecules with BRCA1 gene.

Journal of bioinformatics and computational biology Feb 1, 2024
In this paper, we propose a novel approach for predicting the activity/inactivity of molecules with the BRCA1 gene by combining pharmacophore modeling and deep learning techniques. Initially, we generated 3D pharmacophore fingerprints using a pharmac...
Drug Discovery Genes, BRCA1 Reproducibility of Results Deep Learning Pharmacophore
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Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks.

Journal of bioinformatics and computational biology Feb 1, 2020
Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics due to rapid viral evolution. Vaccines are used to prevent influenza infections but the composition of the influenza vaccines have to be upd...
Influenza Vaccines Mutation Rate Viral Proteins Computational Biology Epitopes Influenza, Human Humans Influenza A Virus, H3N2 Subtype Neural Networks, Computer Interrupted Time Series Analysis
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PVsiRNAPred: Prediction of plant exclusive virus-derived small interfering RNAs by deep convolutional neural network.

Journal of bioinformatics and computational biology Dec 1, 2019
Plant exclusive virus-derived small interfering RNAs (vsiRNAs) regulate various biological processes, especially important in antiviral immunity. The identification of plant vsiRNAs is important for understanding the biogenesis and function mechanism...
Plants Computational Biology Neural Networks, Computer Host-Pathogen Interactions Databases, Genetic Plant Viruses Algorithms RNA, Small Interfering ROC Curve
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Min3: Predict microRNA target gene using an improved binding-site representation method and support vector machine.

Journal of bioinformatics and computational biology Oct 1, 2019
MicroRNAs are single-stranded noncoding RNAs known to down-regulate target genes at the protein or mRNA level. Computational prediction of targets is essential for elucidating the detailed functions of microRNA. However, prediction specificity and se...
Software Computational Biology RNA, Messenger Humans MicroRNAs HeLa Cells Gene Knockdown Techniques Binding Sites Models, Genetic Support Vector Machine Databases, Genetic Gene Knockout Techniques 3' Untranslated Regions
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Graph kernels combined with the neural network on protein classification.

Journal of bioinformatics and computational biology Oct 1, 2019
At present, most of the researches on protein classification are based on graph kernels. The essence of graph kernels is to extract the substructure and use the similarity of substructures as the kernel values. In this paper, we propose a novel graph...
Computer Graphics Proteins Algorithms Databases, Protein Reproducibility of Results Neural Networks, Computer Protein Conformation Computational Biology
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Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles.

Journal of bioinformatics and computational biology Jun 1, 2019
Deep learning technologies are permeating every field from image and speech recognition to computational and systems biology. However, the application of convolutional neural networks (CCNs) to "omics" data poses some difficulties, such as the proces...
Cluster Analysis Random Allocation Algorithms Reproducibility of Results Transcriptome Protein Interaction Maps Lung Neoplasms Support Vector Machine Humans Neural Networks, Computer Machine Learning
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Predicting drug synergy for precision medicine using network biology and machine learning.

Journal of bioinformatics and computational biology Apr 1, 2019
Identification of effective drug combinations for patients is an expensive and time-consuming procedure, especially for experiments. To accelerate the synergistic drug discovery process, we present a new classification model to identify more effecti...
Drug Synergism Humans Gene Ontology Machine Learning Databases, Pharmaceutical Precision Medicine Protein Interaction Maps Computational Biology Reproducibility of Results Transcriptome
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Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method.

Journal of bioinformatics and computational biology Feb 1, 2019
Molecular recognition features (MoRFs) are key functional regions of intrinsically disordered proteins (IDPs), which play important roles in the molecular interaction network of cells and are implicated in many serious human diseases. Identifying MoR...
Intrinsically Disordered Proteins Binding Sites Membrane Proteins Databases, Protein Amino Acid Sequence Deep Learning Protein Binding Computational Biology Humans Neural Networks, Computer
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Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins.

Journal of bioinformatics and computational biology Feb 1, 2019
Deep learning has been increasingly and widely used to solve numerous problems in various fields with state-of-the-art performance. It can also be applied in bioinformatics to reduce the requirement for feature extraction and reach high performance. ...
Humans Neural Networks, Computer Deep Learning Computational Biology Binding Sites Databases, Protein rab GTP-Binding Proteins Amino Acids Guanosine Triphosphate Amino Acid Sequence
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Gene multifunctionality scoring using gene ontology.

Journal of bioinformatics and computational biology Oct 1, 2018
Multifunctional genes are important genes because of their essential roles in human cells. Studying and analyzing multifunctional genes can help understand disease mechanisms and drug discovery. We propose a computational method for scoring gene mult...
Genetic Association Studies Gene Ontology Computational Biology Humans Proteins Biomedical Research Evolution, Molecular Algorithms PubMed Protein Interaction Maps Reproducibility of Results Genome, Human Genetic Predisposition to Disease
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