AIMC Topic: Transcriptome

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Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Science (New York, N.Y.) May 13, 2022
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a ...
Humans Single-Cell Analysis Sequence Analysis, RNA B-Lymphocytes Organ Specificity Machine Learning Cells, Cultured T-Lymphocytes Transcriptome
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Gradient tree boosting and network propagation for the identification of pan-cancer survival networks.

STAR protocols Apr 23, 2022
Cancer survival prediction is typically done with uninterpretable machine learning techniques, e.g., gradient tree boosting. Therefore, additional steps are needed to infer biological plausibility of the predictions. Here, we describe a protocol that...
Neoplasms Transcriptome Protein Interaction Maps Humans Machine Learning
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Augmentation of Transcriptomic Data for Improved Classification of Patients with Respiratory Diseases of Viral Origin.

International journal of molecular sciences Feb 24, 2022
To better understand the molecular basis of respiratory diseases of viral origin, high-throughput gene-expression data are frequently taken by means of DNA microarray or RNA-seq technology. Such data can also be useful to classify infected individual...
Gene Expression Profiling Transcriptome RNA-Seq Gene Ontology Humans Neural Networks, Computer Machine Learning COVID-19 Algorithms Reproducibility of Results SARS-CoV-2
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Combining explainable machine learning, demographic and multi-omic data to inform precision medicine strategies for inflammatory bowel disease.

PloS one Feb 23, 2022
Inflammatory bowel diseases (IBDs), including ulcerative colitis and Crohn's disease, affect several million individuals worldwide. These diseases are heterogeneous at the clinical, immunological and genetic levels and result from complex host and en...
Mesalamine Pyrazoles Phenylurea Compounds Precision Medicine Naphthalenes Female Prednisolone Aged Anti-Inflammatory Agents, Non-Steroidal Young Adult Humans Adult Adolescent Crohn Disease Machine Learning Male Genomics Drug Evaluation, Preclinical Tumor Necrosis Factor-alpha Middle Aged Signal Transduction Transcriptome Colitis, Ulcerative
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Machine Learning Identifies Pan-Cancer Landscape of Nrf2 Oxidative Stress Response Pathway-Related Genes.

Oxidative medicine and cellular longevity Feb 17, 2022
BACKGROUND: Oxidative stress produced a large amount of reactive oxygen species (ROS), which played a pivotal role in balanced ability and determining cell fate. The activated Nrf2 signaling pathway that responds to the excessive ROS regulated the ex...
NF-E2-Related Factor 2 Neoplasms Transcriptome Prognosis Humans Survival Rate Gene Expression Regulation, Neoplastic Case-Control Studies Machine Learning Oxidative Stress Tumor Microenvironment Phenotype Signal Transduction Biomarkers, Tumor Reactive Oxygen Species Mutation Rate
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Construction of genetic classification model for coronary atherosclerosis heart disease using three machine learning methods.

BMC cardiovascular disorders Feb 12, 2022
BACKGROUND: Although the diagnostic method for coronary atherosclerosis heart disease (CAD) is constantly innovated, CAD in the early stage is still missed diagnosis for the absence of any symptoms. The gene expression levels varied during disease de...
Humans Machine Learning Phenotype Gene Expression Profiling Databases, Genetic Predictive Value of Tests Coronary Artery Disease Transcriptome Genetic Predisposition to Disease Models, Genetic Support Vector Machine
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Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks.

Nature communications Feb 3, 2022
Identifying the molecular systems and proteins that modify the progression of Alzheimer's disease and related dementias (ADRD) is central to drug target selection. However, discordance between mRNA and protein abundance, and the scarcity of proteomic...
Humans Alzheimer Disease Deep Learning Protein Biosynthesis Cognitive Dysfunction Aged Neural Networks, Computer Dementia Aged, 80 and over Brain RNA-Seq RNA, Messenger Male Female Proteomics Transcriptome Proteome Mass Spectrometry
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AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments.

PLoS computational biology Jan 26, 2022
In the integrative analyses of omics data, it is often of interest to extract data representation from one data type that best reflect its relations with another data type. This task is traditionally fulfilled by linear methods such as canonical corr...
Software Computer Simulation Transcriptome Deep Learning Computational Biology Databases, Genetic MicroRNAs Least-Squares Analysis
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Evaluation of deep convolutional neural networks for in situ hybridization gene expression image representation.

PloS one Jan 24, 2022
High resolution in situ hybridization (ISH) images of the brain capture spatial gene expression at cellular resolution. These spatial profiles are key to understanding brain organization at the molecular level. Previously, manual qualitative scoring ...
Male Middle Aged Transcriptome Case-Control Studies Schizophrenia Image Interpretation, Computer-Assisted Datasets as Topic Humans Brain In Situ Hybridization Neural Networks, Computer Female Machine Learning Young Adult Adult
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A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data.

Scientific reports Jan 18, 2022
The fast-advancing single cell RNA sequencing (scRNA-seq) technology enables researchers to study the transcriptome of heterogeneous tissues at a single cell level. The initial important step of analyzing scRNA-seq data is usually to accurately annot...
Sequence Analysis, RNA Gene Expression Profiling Transcriptome Single-Cell Analysis RNA-Seq Humans Neural Networks, Computer Animals
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