AIMC Topic: Computational Biology

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A Deep Learning-Based Chemical System for QSAR Prediction.

IEEE journal of biomedical and health informatics
Research on quantitative structure-activity relationships (QSAR) provides an effective approach to determine new hits and promising lead compounds during drug discovery. In the past decades, various works have gained good performance for QSAR with th...

Exploration and Evaluation of Machine Learning-Based Models for Predicting Enzymatic Reactions.

Journal of chemical information and modeling
Unannotated gene sequences in databases are increasing due to sequencing advances. Therefore, computational methods to predict functions of unannotated genes are needed. Moreover, novel enzyme discovery for metabolic engineering applications further ...

Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction.

Scientific reports
Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel netw...

Exploring the Consistency of the Quality Scores with Machine Learning for Next-Generation Sequencing Experiments.

BioMed research international
BACKGROUND: Next-generation sequencing enables massively parallel processing, allowing lower cost than the other sequencing technologies. In the subsequent analysis with the NGS data, one of the major concerns is the reliability of variant calls. Alt...

Computational Identification and Analysis of Ubiquinone-Binding Proteins.

Cells
Ubiquinone is an important cofactor that plays vital and diverse roles in many biological processes. Ubiquinone-binding proteins (UBPs) are receptor proteins that dock with ubiquinones. Analyzing and identifying UBPs via a computational approach will...

Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression.

Scientific reports
Welding generates and releases fumes that are hazardous to human health. Welding fumes (WFs) are a complex mix of metallic oxides, fluorides and silicates that can cause or exacerbate health problems in exposed individuals. In particular, WF inhalati...

New criteria and new methodological tools for devising criteria sets of inflammatory rheumatic diseases.

Clinical and experimental rheumatology
Rheumatologists use classification criteria to separate patients with inflammatory rheumatic diseases (IRD). They change over time, and the concepts of the diseases also change. The paradigm is currently moving as the goal of classification in the fu...

Coding with transient trajectories in recurrent neural networks.

PLoS computational biology
Following a stimulus, the neural response typically strongly varies in time and across neurons before settling to a steady-state. While classical population coding theory disregards the temporal dimension, recent works have argued that trajectories o...

Machine learning and ligand binding predictions: A review of data, methods, and obstacles.

Biochimica et biophysica acta. General subjects
Computational predictions of ligand binding is a difficult problem, with more accurate methods being extremely computationally expensive. The use of machine learning for drug binding predictions could possibly leverage the use of biomedical big data ...

RefDNN: a reference drug based neural network for more accurate prediction of anticancer drug resistance.

Scientific reports
Cancer is one of the most difficult diseases to treat owing to the drug resistance of tumour cells. Recent studies have revealed that drug responses are closely associated with genomic alterations in cancer cells. Numerous state-of-the-art machine le...