AIMC Topic: Gene Regulatory Networks

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A Bi-Objective RNN Model to Reconstruct Gene Regulatory Network: A Modified Multi-Objective Simulated Annealing Approach.

IEEE/ACM transactions on computational biology and bioinformatics Nov 9, 2017
Gene Regulatory Network (GRN) is a virtual network in a cellular context of an organism, comprising a set of genes and their internal relationships to regulate protein production rate (gene expression level) of each other through coded proteins. Comp...
Gene Expression Profiling Gene Regulatory Networks Computational Biology Databases, Genetic Neural Networks, Computer Algorithms
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Predicting pathogenic genes for primary myelofibrosis based on a system‑network approach.

Molecular medicine reports Oct 20, 2017
The aim of the present study was to predict pathogenic genes for primary myelofibrosis (PMF) using a system‑network approach by combining protein‑protein interaction (PPI) network and gene expression data with known pathogenic genes. PMF gene express...
Neural Networks, Computer Gene Expression Profiling Gene Regulatory Networks Genetic Predisposition to Disease Humans Genetic Association Studies Models, Biological Computational Biology Primary Myelofibrosis Signal Transduction
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Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer.

Clinical cancer research : an official journal of the American Association for Cancer Research Oct 5, 2017
Identifying robust survival subgroups of hepatocellular carcinoma (HCC) will significantly improve patient care. Currently, endeavor of integrating multi-omics data to explicitly predict HCC survival from multiple patient cohorts is lacking. To fill ...
Computational Biology Proteomics Metabolomics Liver Neoplasms Gene Regulatory Networks Genomics Algorithms Proportional Hazards Models Prognosis Humans Transcriptome Biomarkers, Tumor Deep Learning Gene Expression Profiling Reproducibility of Results
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Gene2DisCo: Gene to disease using disease commonalities.

Artificial intelligence in medicine Sep 4, 2017
OBJECTIVE: Finding the human genes co-causing complex diseases, also known as "disease-genes", is one of the emerging and challenging tasks in biomedicine. This process, termed gene prioritization (GP), is characterized by a scarcity of known disease...
Area Under Curve Genetic Markers Data Mining Genetic Predisposition to Disease Models, Genetic Databases, Genetic Linear Models Toxicogenetics Humans Machine Learning Algorithms ROC Curve Gene Regulatory Networks
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Finding disagreement pathway signatures and constructing an ensemble model for cancer classification.

Scientific reports Aug 30, 2017
Cancer classification based on molecular level is a relatively routine research procedure with advances in high-throughput molecular profiling techniques. However, the number of genes typically far exceeds the number of the sample size in gene expres...
Gene Expression Regulation, Neoplastic Signal Transduction Support Vector Machine Oligonucleotide Array Sequence Analysis Taxoids Neoplasm Proteins Datasets as Topic Antineoplastic Agents Atlases as Topic Gene Expression Profiling Anthracyclines Gene Regulatory Networks Humans Neoplasms
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Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks.

Scientific reports Aug 1, 2017
Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed g...
Computational Biology Machine Learning Neoplasms Gene Regulatory Networks Humans
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Reconstructing Genetic Regulatory Networks Using Two-Step Algorithms with the Differential Equation Models of Neural Networks.

Interdisciplinary sciences, computational life sciences Jul 26, 2017
BACKGROUND: The identification of genetic regulatory networks (GRNs) provides insights into complex cellular processes. A class of recurrent neural networks (RNNs) captures the dynamics of GRN. Algorithms combining the RNN and machine learning scheme...
Databases, Genetic Area Under Curve Gene Regulatory Networks Saccharomyces cerevisiae Neural Networks, Computer Models, Genetic Algorithms Escherichia coli Computer Simulation Cell Cycle SOS Response, Genetics
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Reduced- and Full-Order Observers for Delayed Genetic Regulatory Networks.

IEEE transactions on cybernetics Jul 21, 2017
This paper is centered upon the state estimation for delayed genetic regulatory networks. Our aim is at estimating the concentrations of mRNAs and proteins by designing reduced-order and full-order state observers based on available network outputs. ...
RNA, Messenger Models, Statistical Neural Networks, Computer Algorithms Reproducibility of Results Gene Regulatory Networks
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Employing decomposable partially observable Markov decision processes to control gene regulatory networks.

Artificial intelligence in medicine Jul 18, 2017
OBJECTIVE: Formulate the induction and control of gene regulatory networks (GRNs) from gene expression data using Partially Observable Markov Decision Processes (POMDPs).
Gene Expression Regulation, Neoplastic Humans Databases, Genetic Gene Expression Profiling Markov Chains Artificial Intelligence Gene Regulatory Networks Transcriptome Computational Biology Melanoma Skin Neoplasms
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Combining Supervised and Unsupervised Learning for Improved miRNA Target Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Jul 13, 2017
MicroRNAs (miRNAs) are short non-coding RNAs which bind to mRNAs and regulate their expression. MiRNAs have been found to be associated with initiation and progression of many complex diseases. Investigating miRNAs and their targets can thus help dev...
Computational Biology RNA, Messenger Sequence Analysis, RNA Support Vector Machine MicroRNAs Unsupervised Machine Learning Gene Expression Profiling Transcriptome Gene Regulatory Networks Supervised Machine Learning
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