AIMC Topic: RNA-Seq

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Unsupervised learning of cross-modal mappings in multi-omics data for survival stratification of gastric cancer.

Future oncology (London, England) Dec 2, 2021
This study presents a survival stratification model based on multi-omics integration using bidirectional deep neural networks (BiDNNs) in gastric cancer. Based on the survival-related representation features yielded by BiDNNs through integrating tr...
Aged Stomach Neoplasms Biomarkers, Tumor Male Middle Aged Humans Female DNA Methylation Cluster Analysis Unsupervised Machine Learning Datasets as Topic Kaplan-Meier Estimate Risk Assessment RNA-Seq Epigenomics Follow-Up Studies
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Robotic high-throughput biomanufacturing and functional differentiation of human pluripotent stem cells.

Stem cell reports Dec 2, 2021
Efficient translation of human induced pluripotent stem cells (hiPSCs) requires scalable cell manufacturing strategies for optimal self-renewal and functional differentiation. Traditional manual cell culture is variable and labor intensive, posing ch...
Neurons Hepatocytes Myocytes, Cardiac Automation Zika Virus Infection Human Embryonic Stem Cells Reference Standards Embryoid Bodies Cell Culture Techniques Cells, Cultured Cell Lineage Single-Cell Analysis Induced Pluripotent Stem Cells Humans RNA-Seq Robotics Cell Differentiation
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Genes and regulatory mechanisms associated with experimentally-induced bovine respiratory disease identified using supervised machine learning methodology.

Scientific reports Nov 25, 2021
Bovine respiratory disease (BRD) is a multifactorial disease involving complex host immune interactions shaped by pathogenic agents and environmental factors. Advancements in RNA sequencing and associated analytical methods are improving our understa...
Animals Lung Gene Expression Profiling Computational Biology Transcriptome Databases, Genetic Cattle Supervised Machine Learning RNA-Seq Host-Pathogen Interactions Gene Regulatory Networks Bovine Respiratory Disease Complex
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The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy.

BMC cancer Nov 5, 2021
BACKGROUND: Viral infections are prevalent in human cancers and they have great diagnostic and theranostic values in clinical practice. Recently, their potential of shaping the tumor immune microenvironment (TIME) has been related to the immunotherap...
Genetic Variation High-Throughput Nucleotide Sequencing Genome, Viral Tumor Virus Infections Kaplan-Meier Estimate Papillomaviridae Oncogenic Viruses Humans DNA, Viral Machine Learning Papillomavirus Infections Epstein-Barr Virus Infections Stomach Neoplasms Squamous Cell Carcinoma of Head and Neck Herpesvirus 4, Human Biomarkers, Tumor Tumor Microenvironment Head and Neck Neoplasms Mutation Neoplasms Support Vector Machine Leukocytes Transcriptome RNA-Seq Immunotherapy
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Construction and external validation of a 5-gene random forest model to diagnose non-obstructive azoospermia based on the single-cell RNA sequencing of testicular tissue.

Aging Nov 4, 2021
Non-obstructive azoospermia (NOA) is among the most severe factors for male infertility, but our understandings of the latent biological mechanisms remain insufficient. The single-cell RNA sequencing (scRNA-seq) data of 432 testicular cells isolated ...
Single-Cell Analysis Protein Interaction Maps RNA-Seq Azoospermia Adult Male Transcriptome Diagnosis, Computer-Assisted Humans Machine Learning
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MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity.

Nature methods Nov 1, 2021
Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID ...
Humans Neoplasms RNA-Seq Gene Expression Regulation, Neoplastic Cell Proliferation Knowledge Bases Software Reproducibility of Results Tumor Microenvironment Biomarkers, Tumor Tumor Cells, Cultured Cell Culture Techniques Spheroids, Cellular
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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.

Nature methods Oct 28, 2021
Charting an organs' biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehe...
Regulatory Sequences, Nucleic Acid Software Chromatin Brain Male RNA-Seq Female Gene Expression Profiling Mice Animals Transcriptome Mice, Inbred C57BL Deep Learning Gene Expression Regulation Single-Cell Analysis
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Classification and Functional Analysis between Cancer and Normal Tissues Using Explainable Pathway Deep Learning through RNA-Sequencing Gene Expression.

International journal of molecular sciences Oct 26, 2021
Deep learning has proven advantageous in solving cancer diagnostic or classification problems. However, it cannot explain the rationale behind human decisions. Biological pathway databases provide well-studied relationships between genes and their pa...
Humans Deep Learning Neural Networks, Computer RNA-Seq Neoplasms Gene Regulatory Networks Diagnosis, Computer-Assisted Gene Expression Regulation, Neoplastic Databases, Nucleic Acid
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Improved prediction of smoking status via isoform-aware RNA-seq deep learning models.

PLoS computational biology Oct 11, 2021
Most predictive models based on gene expression data do not leverage information related to gene splicing, despite the fact that splicing is a fundamental feature of eukaryotic gene expression. Cigarette smoking is an important environmental risk fac...
Protein Isoforms Exons ROC Curve Humans RNA-Seq Male Female Computational Biology Middle Aged Aged Models, Statistical Gene Expression Profiling Smoking Deep Learning
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DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data.

Nature communications Oct 6, 2021
Feature selection (marker gene selection) is widely believed to improve clustering accuracy, and is thus a key component of single cell clustering pipelines. Existing feature selection methods perform inconsistently across datasets, occasionally even...
Arthritis, Rheumatoid Sequence Analysis, RNA Cluster Analysis Gene Expression Genes, Mitochondrial Chromatin Immunoprecipitation Sequencing Software Algorithms Research Design Humans Single-Cell Analysis Machine Learning RNA-Seq
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