AIMC Topic: Gene Expression Regulation

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Novel biomarker genes which distinguish between smokers and chronic obstructive pulmonary disease patients with machine learning approach.

BMC pulmonary medicine Feb 3, 2020
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is combination of progressive lung diseases. The diagnosis of COPD is generally based on the pulmonary function testing, however, difficulties underlie in prognosis of smokers or early stage of...
Pulmonary Disease, Chronic Obstructive Male Middle Aged Lung Biomarkers Female Adult Epithelial Cells Cigarette Smoking Gene Expression Regulation Smokers Gene Expression Profiling Case-Control Studies Logistic Models Humans Machine Learning
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miRgo: integrating various off-the-shelf tools for identification of microRNA-target interactions by heterogeneous features and a novel evaluation indicator.

Scientific reports Jan 30, 2020
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and biological processes through binding to messenger RNAs. Predicting the relationship between miRNAs and their targets is crucial for research and clinical applications. Man...
Models, Theoretical Support Vector Machine Humans MicroRNAs Models, Statistical Computational Biology Gene Expression Regulation
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DeepMiR2GO: Inferring Functions of Human MicroRNAs Using a Deep Multi-Label Classification Model.

International journal of molecular sciences Nov 30, 2019
MicroRNAs (miRNAs) are a highly abundant collection of functional non-coding RNAs involved in cellular regulation and various complex human diseases. Although a large number of miRNAs have been identified, most of their physiological functions remain...
Neural Networks, Computer Cardiovascular Diseases Neoplasms Gene Regulatory Networks Humans Gene Expression Regulation Gene Ontology MicroRNAs Schizophrenia Datasets as Topic
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Molecular basis of degenerative spinal disorders from a proteomic perspective (Review).

Molecular medicine reports Nov 12, 2019
Intervertebral disc degeneration (IDD) and ligamentum flavum hypertrophy (LFH) are major causes of degenerative spinal disorders. Comparative and proteomic analysis was used to identify differentially expressed proteins (DEPs) in IDD and LFH discs co...
Humans Proteomics Ligamentum Flavum Gene Expression Regulation Intervertebral Disc Degeneration Gene Ontology
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Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data.

PloS one Nov 8, 2019
Several studies have reported mitochondrial dysfunction in rheumatoid arthritis (RA). Many nuclear DNA (nDNA) encoded proteins translocate to mitochondria, but their participation in the dysfunction of this cell organelle during RA is quite unclear. ...
Apoptosis Oxidative Phosphorylation Reactive Oxygen Species Models, Biological Mitochondria Arthritis, Rheumatoid Gene Ontology Gene Expression Regulation Inflammation Mitochondrial Proteins Humans Synovial Membrane Gene Expression Profiling Protein Interaction Maps
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D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference.

Genes Oct 14, 2019
Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels, but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene e...
Gene Expression Regulation Promoter Regions, Genetic Deep Learning Computational Biology Humans Linear Models Sequence Analysis, DNA DNA Methylation Machine Learning CpG Islands Gene Expression Gene Expression Profiling
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Analysis of defective pathways and drug repositioning in Multiple Sclerosis via machine learning approaches.

Computers in biology and medicine Oct 9, 2019
BACKGROUND: Although some studies show that there could be a genetic predisposition to develop Multiple Sclerosis (MS), attempts to find genetic signatures related to MS diagnosis and development are extremely rare.
Oligonucleotide Array Sequence Analysis Databases, Nucleic Acid Models, Immunological Female Male Signal Transduction Multiple Sclerosis Gene Expression Regulation Drug Repositioning Metabolic Networks and Pathways Humans Machine Learning Retrospective Studies
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Designing Eukaryotic Gene Expression Regulation Using Machine Learning.

Trends in biotechnology Aug 17, 2019
Controlling the expression of genes is one of the key challenges of synthetic biology. Until recently fine-tuned control has been out of reach, particularly in eukaryotes owing to their complexity of gene regulation. With advances in machine learning...
Machine Learning Algorithms Genetic Variation Models, Genetic Eukaryotic Cells Synthetic Biology Gene Expression Regulation Flow Cytometry Eukaryota Genetic Engineering
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Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response.

BMC biology Jul 30, 2019
BACKGROUND: Identification of functional non-coding variants and their mechanistic interpretation is a major challenge of modern genomics, especially for precision medicine. Transcription factor (TF) binding profiles and epigenomic landscapes in refe...
Female Male Protein Binding Humans Machine Learning Gene Expression Regulation Polymorphism, Single Nucleotide Models, Genetic Transcription Factors
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Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network.

International journal of molecular sciences Jul 12, 2019
Transcription factor binding sites (TFBSs) play an important role in gene expression regulation. Many computational methods for TFBS prediction need sufficient labeled data. However, many transcription factors (TFs) lack labeled data in cell types. W...
Binding Sites Transcription Factors Neural Networks, Computer Gene Expression Regulation Algorithms ROC Curve Organ Specificity Deep Learning Protein Binding Computational Biology
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