AIMC Topic: Transcriptome

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A neural network based model effectively predicts enhancers from clinical ATAC-seq samples.

Scientific reports Oct 30, 2018
Enhancers are cis-acting sequences that regulate transcription rates of their target genes in a cell-specific manner and harbor disease-associated sequence variants in cognate cell types. Many complex diseases are associated with enhancer malfunction...
Neural Networks, Computer Sensitivity and Specificity Gene Expression Profiling Humans Sequence Analysis, DNA Cell Line High-Throughput Nucleotide Sequencing Transcriptome ROC Curve Computational Biology Transposases Binding Sites Enhancer Elements, Genetic
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Comparative Evaluation of Machine Learning Strategies for Analyzing Big Data in Psychiatry.

International journal of molecular sciences Oct 29, 2018
The requirement of innovative big data analytics has become a critical success factor for research in biological psychiatry. Integrative analyses across distributed data resources are considered essential for untangling the biological complexity of m...
Schizophrenia Data Mining Humans Machine Learning Algorithms Transcriptome Big Data
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Heterogeneous Domain Adaptation for IHC Classification of Breast Cancer Subtypes.

IEEE/ACM transactions on computational biology and bioinformatics Oct 24, 2018
Increasingly, multiple parallel omics datasets are collected from biological samples. Integrating these datasets for classification is an open area of research. Additionally, whilst multiple datasets may be available for the training samples, future ...
Algorithms Female Breast Neoplasms Humans Transcriptome Computational Biology Machine Learning Immunohistochemistry
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Drug Repurposing Prediction for Immune-Mediated Cutaneous Diseases using a Word-Embedding-Based Machine Learning Approach.

The Journal of investigative dermatology Oct 17, 2018
Immune-mediated diseases affect more than 20% of the population, and many autoimmune diseases affect the skin. Drug repurposing (or repositioning) is a cost-effective approach for finding drugs that can be used to treat diseases for which they are cu...
Transcriptome Cohort Studies ROC Curve Humans Machine Learning Algorithms Skin Diseases PubMed Immune System Diseases Computational Biology Drug Repositioning Skin
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Deep learning-based transcriptome data classification for drug-target interaction prediction.

BMC genomics Sep 24, 2018
BACKGROUND: The ability to predict the interaction of drugs with target proteins is essential to research and development of drug. However, the traditional experimental paradigm is costly, and previous in silico prediction paradigms have been impeded...
Humans Machine Learning Algorithms Databases, Factual Computer Simulation Drug Discovery Gene Expression Profiling Transcriptome Models, Theoretical Proteins Drug Interactions Molecular Targeted Therapy
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Universal method for robust detection of circadian state from gene expression.

Proceedings of the National Academy of Sciences of the United States of America Sep 10, 2018
Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessment of physiological time using transcriptional biomarkers found in human blood can significantly imp...
Genes Circadian Rhythm Sleep Circadian Clocks Humans Models, Statistical Machine Learning Gene Expression Biomarkers Reproducibility of Results Gene Expression Profiling Transcriptome
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Classification of lung adenocarcinoma transcriptome subtypes from pathological images using deep convolutional networks.

International journal of computer assisted radiology and surgery Aug 29, 2018
PURPOSE: Convolutional neural networks have become rapidly popular for image recognition and image analysis because of its powerful potential. In this paper, we developed a method for classifying subtypes of lung adenocarcinoma from pathological imag...
Adenocarcinoma of Lung Humans Image Processing, Computer-Assisted Neural Networks, Computer Biopsy Transcriptome
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MCRiceRepGP: a framework for the identification of genes associated with sexual reproduction in rice.

The Plant journal : for cell and molecular biology Aug 16, 2018
Rice is an important cereal crop, being a staple food for over half of the world's population, and sexual reproduction resulting in grain formation underpins global food security. However, despite considerable research efforts, many of the genes, esp...
Reproduction Genome-Wide Association Study Machine Learning Oryza Genome, Plant Transcriptome Genes, Plant
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Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis.

BioMed research international Aug 14, 2018
Osteoarthritis (OA) is one of the most common diseases worldwide, but the pathogenic genes and pathways are largely unclear. The aim of this study was to screen and verify hub genes involved in OA and explore potential molecular mechanisms. The expre...
Computational Biology Transcriptome China Osteoarthritis Humans Gene Regulatory Networks Gene Ontology Gene Expression Profiling
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Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis.

International journal of molecular sciences Aug 10, 2018
Toxicity prediction is very important to public health. Among its many applications, toxicity prediction is essential to reduce the cost and labor of a drug's preclinical and clinical trials, because a lot of drug evaluations (cellular, animal, and c...
Humans Machine Learning Natural Language Processing Animals Gene Expression Profiling Transcriptome
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