AIMC Topic: Computational Biology

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Inferring the Disease-Associated miRNAs Based on Network Representation Learning and Convolutional Neural Networks.

International journal of molecular sciences
Identification of disease-associated miRNAs (disease miRNAs) are critical for understanding etiology and pathogenesis. Most previous methods focus on integrating similarities and associating information contained in heterogeneous miRNA-disease networ...

Readmission prediction using deep learning on electronic health records.

Journal of biomedical informatics
Unscheduled 30-day readmissions are a hallmark of Congestive Heart Failure (CHF) patients that pose significant health risks and escalate care cost. In order to reduce readmissions and curb the cost of care, it is important to initiate targeted inter...

Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks.

PloS one
Protein-protein interaction network data provides valuable information that infers direct links between genes and their biological roles. This information brings a fundamental hypothesis for protein function prediction that interacting proteins tend ...

Time-Domain Analysis of Molecular Dynamics Trajectories Using Deep Neural Networks: Application to Activity Ranking of Tankyrase Inhibitors.

Journal of chemical information and modeling
Molecular dynamics simulations provide valuable insights into the behavior of molecular systems. Extending the recent trend of using machine learning techniques to predict physicochemical properties from molecular dynamics data, we propose to conside...

Analysis of Protein-Protein Functional Associations by Using Gene Ontology and KEGG Pathway.

BioMed research international
Protein-protein interaction (PPI) plays an extremely remarkable role in the growth, reproduction, and metabolism of all lives. A thorough investigation of PPI can uncover the mechanism of how proteins express their functions. In this study, we used g...

An Ensemble Classifier to Predict Protein-Protein Interactions by Combining PSSM-based Evolutionary Information with Local Binary Pattern Model.

International journal of molecular sciences
Protein plays a critical role in the regulation of biological cell functions. Among them, whether proteins interact with each other has become a fundamental problem, because proteins usually perform their functions by interacting with other proteins....

Predicting lncRNA-disease associations using network topological similarity based on deep mining heterogeneous networks.

Mathematical biosciences
A kind of noncoding RNA with length more than 200 nucleotides named long noncoding RNA (lncRNA) has gained considerable attention in recent decades. Many studies have confirmed that human genome contains many thousands of lncRNAs. LncRNAs play signif...

PhenPath: a tool for characterizing biological functions underlying different phenotypes.

BMC genomics
BACKGROUND: Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For...

Screening and Bioinformatics Analysis of IgA Nephropathy Gene Based on GEO Databases.

BioMed research international
PURPOSE: To identify novel biomarkers of IgA nephropathy (IgAN) through bioinformatics analysis and elucidate the possible molecular mechanism.

Prediction of ATP-binding sites in membrane proteins using a two-dimensional convolutional neural network.

Journal of molecular graphics & modelling
Membrane proteins, the most important drug targets, account for around 30% of total proteins encoded by the genome of living organisms. An important role of these proteins is to bind adenosine triphosphate (ATP), facilitating crucial biological proce...