AIMC Topic: Computational Biology

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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...
Databases, Protein Amino Acid Sequence Intrinsically Disordered Proteins Binding Sites Protein Binding Computational Biology Membrane Proteins Humans Neural Networks, Computer Deep Learning
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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. ...
Amino Acids Amino Acid Sequence Binding Sites Deep Learning Computational Biology rab GTP-Binding Proteins Databases, Protein Humans Guanosine Triphosphate Neural Networks, Computer
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Prediction of drug synergy score using ensemble based differential evolution.

IET systems biology Feb 1, 2019
Prediction of drug synergy score is an ill-posed problem. It plays an efficient role in the medical field for inhibiting specific cancer agents. An efficient regression-based machine learning technique has an ability to minimise the drug synergy pred...
Computational Biology Support Vector Machine Drug Synergism Time Factors
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An account of in silico identification tools of secreted effector proteins in bacteria and future challenges.

Briefings in bioinformatics Jan 18, 2019
Bacterial pathogens secrete numerous effector proteins via six secretion systems, type I to type VI secretion systems, to adapt to new environments or to promote virulence by bacterium-host interactions. Many computational approaches have been used i...
Markov Chains Bacterial Secretion Systems Host Microbial Interactions Computational Biology Support Vector Machine Bayes Theorem Bacterial Proteins Models, Biological Virulence Algorithms Databases, Factual Computer Simulation Humans Neural Networks, Computer Machine Learning
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Facilitating prediction of adverse drug reactions by using knowledge graphs and multi-label learning models.

Briefings in bioinformatics Jan 18, 2019
Timely identification of adverse drug reactions (ADRs) is highly important in the domains of public health and pharmacology. Early discovery of potential ADRs can limit their effect on patient lives and also make drug development pipelines more robus...
Humans Machine Learning Computer Simulation Knowledge Bases Adverse Drug Reaction Reporting Systems Databases, Pharmaceutical Computational Biology Models, Statistical Drug-Related Side Effects and Adverse Reactions
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LigVoxel: inpainting binding pockets using 3D-convolutional neural networks.

Bioinformatics (Oxford, England) Jan 15, 2019
MOTIVATION: Structure-based drug discovery methods exploit protein structural information to design small molecules binding to given protein pockets. This work proposes a purely data driven, structure-based approach for imaging ligands as spatial fie...
Protein Binding Computational Biology Proteins Neural Networks, Computer Ligands Software Protein Conformation Drug Discovery Binding Sites
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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Nucleic acids research Jan 8, 2019
The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detaile...
Genetic Variation Humans Biological Ontologies Phenotype Rare Diseases Genetic Predisposition to Disease Internet Congenital Abnormalities Computational Biology Whole Genome Sequencing Databases, Genetic Knowledge Bases
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ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

Nucleic acids research Jan 8, 2019
The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product...
Gene Ontology Sequence Analysis, Protein Proteins Internet Information Storage and Retrieval User-Computer Interface Computational Biology Databases, Genetic Humans Animals
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PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs.

Nucleic acids research Jan 8, 2019
One important aspect of precision medicine aims to deliver the right medicine to the right patient at the right dose at the right time based on the unique 'omics' features of each individual patient, thus maximizing drug efficacy and minimizing adver...
Precision Medicine Reproducibility of Results Pharmacogenetics Computational Biology Internet Knowledge Bases Humans Genetic Variation Information Storage and Retrieval Disease
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New Computational Tool Based on Machine-learning Algorithms for the Identification of Rhinovirus Infection-Related Genes.

Combinatorial chemistry & high throughput screening Jan 1, 2019
BACKGROUND: Human rhinovirus has different identified serotypes and is the most common cause of cold in humans. To date, many genes have been discovered to be related to rhinovirus infection. However, the pathogenic mechanism of rhinovirus is difficu...
Suppressor of Cytokine Signaling 1 Protein Computational Biology Membrane Proteins Humans Support Vector Machine Picornaviridae Infections Gene Expression Profiling
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