AIMC Topic: Gene Expression Profiling

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Prediction of cancer dependencies from expression data using deep learning.

Molecular omics Nov 2, 2020
Detecting cancer dependencies is key to disease treatment. Recent efforts have mapped gene dependencies and drug sensitivities in hundreds of cancer cell lines. These data allow us to learn for the first time models of tumor vulnerabilities and apply...
Humans Deep Learning Computational Biology Neural Networks, Computer Gene Expression Regulation, Neoplastic Neoplasms Drug Resistance, Neoplasm Gene Expression Profiling Linear Models Transcriptome
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Development and Validation of a Gene Signature Classifier for Consensus Molecular Subtyping of Colorectal Carcinoma in a CLIA-Certified Setting.

Clinical cancer research : an official journal of the American Association for Cancer Research Oct 27, 2020
PURPOSE: Consensus molecular subtyping (CMS) of colorectal cancer has potential to reshape the colorectal cancer landscape. We developed and validated an assay that is applicable on formalin-fixed, paraffin-embedded (FFPE) samples of colorectal cance...
Risk Assessment Antineoplastic Agents Gene Expression Profiling Transcriptome Colorectal Neoplasms Biomarkers, Tumor Male Middle Aged Gene Expression Regulation, Neoplastic Support Vector Machine Drug Resistance, Neoplasm Prognosis Female Reproducibility of Results Humans
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A Comprehensive Analysis of MicroRNAs in Human Osteoporosis.

Frontiers in endocrinology Oct 21, 2020
MicroRNAs (miRNAs) are single-stranded RNA molecules that control gene expression in various processes, such as cancers, Alzheimer's disease, and bone metabolic diseases. However, the regulatory roles of miRNAs in osteoporosis have not been systemati...
Computational Biology Hindlimb Suspension Gene Expression Profiling Humans Protein Interaction Maps Databases, Genetic Gene Regulatory Networks Gene Ontology Osteoporosis Disease Models, Animal Mice Animals MicroRNAs Male
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Machine learning discriminates a movement disorder in a zebrafish model of Parkinson's disease.

Disease models & mechanisms Oct 16, 2020
Animal models of human disease provide an system that can reveal molecular mechanisms by which mutations cause pathology, and, moreover, have the potential to provide a valuable tool for drug development. Here, we have developed a zebrafish model of...
Dopaminergic Neurons Movement Disorders Gene Targeting Protein Deglycase DJ-1 Alleles Machine Learning Disease Models, Animal Animals Zebrafish Algorithms Parkinson Disease Gene Expression Profiling Base Sequence Brain Mutation Movement
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Spage2vec: Unsupervised representation of localized spatial gene expression signatures.

The FEBS journal Oct 11, 2020
Investigations of spatial cellular composition of tissue architectures revealed by multiplexed in situ RNA detection often rely on inaccurate cell segmentation or prior biological knowledge from complementary single-cell sequencing experiments. Here,...
Neural Networks, Computer Animals Gene Expression Profiling Transcriptome Gene Regulatory Networks Humans Somatosensory Cortex Cell Line Internet Gene Ontology CA1 Region, Hippocampal Mice Computational Biology Cluster Analysis Fibroblasts
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Artificial Intelligence Applied to Gene Expression Testing (IVIGET) to Predict Trivalent Inactivated Influenza Vaccine Immunogenicity in HIV Infected Children.

Frontiers in immunology Oct 5, 2020
The number of patients affected by chronic diseases with special vaccination needs is burgeoning. In this scenario, predictive markers of immunogenicity, as well as signatures of immune responses are typically missing even though it would especially ...
Child Computational Biology Humans Vaccination Artificial Intelligence Coinfection Reproducibility of Results Vaccines, Inactivated Influenza, Human Prognosis Gene Expression Profiling Influenza Vaccines Hemagglutination Inhibition Tests Transcriptome Influenza A Virus, H1N1 Subtype HIV Infections Immunogenicity, Vaccine
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An immune-related gene signature for determining Ewing sarcoma prognosis based on machine learning.

Journal of cancer research and clinical oncology Sep 23, 2020
PURPOSE: Ewing sarcoma (ES) is one of the most common malignant bone tumors in children and adolescents. The immune microenvironment plays an important role in the development of ES. Here, we developed an optimal signature for determining ES patient ...
Follow-Up Studies Lymphocytes, Tumor-Infiltrating Bone Neoplasms Sarcoma, Ewing Humans Male Machine Learning Gene Expression Profiling Prognosis Adolescent Gene Expression Regulation, Neoplastic Female Survival Rate Tumor Microenvironment Biomarkers, Tumor
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Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments.

BMC medical genomics Sep 18, 2020
BACKGROUND: Machine learning (ML) methods still have limited applicability in personalized oncology due to low numbers of available clinically annotated molecular profiles. This doesn't allow sufficient training of ML classifiers that could be used f...
Neoplasms Antineoplastic Agents Gene Expression Profiling Humans Machine Learning Treatment Outcome Progression-Free Survival
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Machine learning predicts stem cell transplant response in severe scleroderma.

Annals of the rheumatic diseases Sep 15, 2020
OBJECTIVE: The Scleroderma: Cyclophosphamide or Transplantation (SCOT) trial demonstrated clinical benefit of haematopoietic stem cell transplant (HSCT) compared with cyclophosphamide (CYC). We mapped PBC (peripheral blood cell) samples from the SCOT...
Gene Expression Profiling Transcriptome Treatment Outcome Immunosuppressive Agents Scleroderma, Diffuse Hematopoietic Stem Cell Transplantation Female Humans Cyclophosphamide Adult Machine Learning Male Middle Aged
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Representation of features as images with neighborhood dependencies for compatibility with convolutional neural networks.

Nature communications Sep 1, 2020
Deep learning with Convolutional Neural Networks has shown great promise in image-based classification and enhancement but is often unsuitable for predictive modeling using features without spatial correlations. We present a feature representation ap...
Bayes Theorem High-Throughput Nucleotide Sequencing Datasets as Topic Drug Resistance, Neoplasm Oligonucleotide Array Sequence Analysis Humans Cell Line, Tumor Biomarkers, Tumor Image Processing, Computer-Assisted Cell Proliferation Neoplasms Drug Screening Assays, Antitumor Antineoplastic Agents Gene Expression Profiling Deep Learning
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