AIMC Topic: Gene Expression Profiling

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SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles.

Nucleic acids research May 7, 2019
Characterization of individual cell types is fundamental to the study of multicellular samples. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task....
Single-Cell Analysis Mice Humans Sequence Analysis, RNA Gene Expression Regulation, Neoplastic Animals Gene Expression Profiling Transcriptome High-Throughput Nucleotide Sequencing Software Datasets as Topic Cell Lineage RNA, Small Cytoplasmic Cluster Analysis Pancreatic Neoplasms Supervised Machine Learning
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Machine learning approaches to decipher hormone and HER2 receptor status phenotypes in breast cancer.

Briefings in bioinformatics Mar 22, 2019
Breast cancer prognosis and administration of therapies are aided by knowledge of hormonal and HER2 receptor status. Breast cancer lacking estrogen receptors, progesterone receptors and HER2 receptors are difficult to treat. Regarding large data repo...
Humans Gene Expression Profiling Computational Biology Receptor, ErbB-2 Receptors, Estrogen Receptors, Progesterone Prognosis Machine Learning Breast Neoplasms Female Algorithms Biomarkers, Tumor Phenotype
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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...
Humans Picornaviridae Infections Gene Expression Profiling Computational Biology Membrane Proteins Support Vector Machine Suppressor of Cytokine Signaling 1 Protein
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Enrichment of Up-regulated and Down-regulated Gene Clusters Using Gene Ontology, miRNAs and lncRNAs in Colorectal Cancer.

Combinatorial chemistry & high throughput screening Jan 1, 2019
AIM AND OBJECTIVE: It is interesting to find the gene signatures of cancer stages based on the omics data. The aim of study was to evaluate and to enrich the array data using gene ontology and ncRNA databases in colorectal cancer.
Gene Ontology Humans Gene Expression Profiling Colorectal Neoplasms Multigene Family Down-Regulation Databases, Genetic Gene Regulatory Networks High-Throughput Screening Assays Up-Regulation MicroRNAs RNA, Long Noncoding
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Screening key lncRNAs for human lung adenocarcinoma based on machine learning and weighted gene co-expression network analysis.

Cancer biomarkers : section A of Disease markers Jan 1, 2019
BACKGROUND: Lung adenocarcinoma (LUAD) accounts for a significant proportion of lung cancer and there have been few diagnostic and therapeutic targets for LUAD due to the lack of specific biomarker. The aim of this study was to identify key long non-...
Humans Machine Learning Gene Expression Profiling Gene Regulatory Networks Female Male RNA, Long Noncoding Adenocarcinoma of Lung
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Recognition of Lung Adenocarcinoma-specific Gene Pairs Based on Genetic Algorithm and Establishment of a Deep Learning Prediction Model.

Combinatorial chemistry & high throughput screening Jan 1, 2019
AIM AND OBJECTIVE: Lung cancer is a disease with a dismal prognosis and is the major cause of cancer deaths in many countries. Nonetheless, rapid technological developments in genome science guarantees more effective prevention and treatment strategi...
Cluster Analysis Models, Biological Algorithms Adenocarcinoma of Lung Deep Learning Humans Gene Expression Profiling Lung Neoplasms
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Exploring microRNA Regulation of Cancer with Context-Aware Deep Cancer Classifier.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2019
BACKGROUND: MicroRNAs (miRNAs) are small, non-coding RNA that regulate gene expression through post-transcriptional silencing. Differential expression observed in miRNAs, combined with advancements in deep learning (DL), have the potential to improve...
MicroRNAs High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Gene Ontology Databases, Nucleic Acid Deep Learning Computational Biology Sequence Analysis, RNA Gene Expression Regulation, Neoplastic Neoplasms Gene Expression Profiling Diagnosis, Computer-Assisted Female Male Humans Neural Networks, Computer
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Using Drug Expression Profiles and Machine Learning Approach for Drug Repurposing.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2019
The cost of new drug development has been increasing, and repurposing known medications for new indications serves as an important way to hasten drug discovery. One promising approach to drug repositioning is to take advantage of machine learning (ML...
Gene Expression Profiling Transcriptome Deep Learning Genomics Machine Learning Algorithms Reproducibility of Results Supervised Machine Learning Gene Expression Regulation Databases, Pharmaceutical Computational Biology Drug Repositioning Workflow Humans Neural Networks, Computer
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EBIC: an evolutionary-based parallel biclustering algorithm for pattern discovery.

Bioinformatics (Oxford, England) Nov 1, 2018
MOTIVATION: Biclustering algorithms are commonly used for gene expression data analysis. However, accurate identification of meaningful structures is very challenging and state-of-the-art methods are incapable of discovering with high accuracy differ...
Algorithms Artificial Intelligence Gene Expression Profiling Software Cluster Analysis
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Discriminating early- and late-stage cancers using multiple kernel learning on gene sets.

Bioinformatics (Oxford, England) Jul 1, 2018
MOTIVATION: Identifying molecular mechanisms that drive cancers from early to late stages is highly important to develop new preventive and therapeutic strategies. Standard machine learning algorithms could be used to discriminate early- and late-sta...
Sequence Analysis, RNA Support Vector Machine Humans Male Metabolic Networks and Pathways Machine Learning Neoplasm Staging Neoplasms Female Genome, Human Gene Expression Profiling
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