AIMC Topic: Organ Specificity

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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 Machine Learning Single-Cell Analysis Sequence Analysis, RNA B-Lymphocytes Cells, Cultured Organ Specificity T-Lymphocytes Transcriptome
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Multiview confocal super-resolution microscopy.

Nature Nov 26, 2021
Confocal microscopy remains a major workhorse in biomedical optical microscopy owing to its reliability and flexibility in imaging various samples, but suffers from substantial point spread function anisotropy, diffraction-limited resolution, depth-d...
Animals Deep Learning Cell Line, Tumor Humans Myoblasts Organ Specificity Drosophila melanogaster Caenorhabditis elegans Single-Cell Analysis Mice Microscopy, Confocal Tissue Fixation Imaginal Discs
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Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors.

Nature communications Nov 18, 2021
Metastatic cancer is associated with poor patient prognosis but its spatiotemporal behavior remains unpredictable at early stage. Here we develop MetaNet, a computational framework that integrates clinical and sequencing data from 32,176 primary and ...
Organ Specificity High-Throughput Nucleotide Sequencing Neoplasm Metastasis Kaplan-Meier Estimate Biomarkers, Tumor Neoplasms Disease Progression Genomics Computational Biology Mutation Machine Learning Prognosis Risk Factors Humans
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Mapping single-cell data to reference atlases by transfer learning.

Nature biotechnology Aug 30, 2021
Large single-cell atlases are now routinely generated to serve as references for analysis of smaller-scale studies. Yet learning from reference data is complicated by batch effects between datasets, limited availability of computational resources and...
SARS-CoV-2 Animals Deep Learning Reference Standards Single-Cell Analysis Organ Specificity Humans Mice Datasets as Topic COVID-19
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In silico saturation mutagenesis of cancer genes.

Nature Jul 28, 2021
Despite the existence of good catalogues of cancer genes, identifying the specific mutations of those genes that drive tumorigenesis across tumour types is still a largely unsolved problem. As a result, most mutations identified in cancer genes acros...
Computer Simulation Precision Medicine Oncogenes Reproducibility of Results Probability Humans Mutation Mutagenesis Machine Learning Cell Transformation, Neoplastic Organ Specificity Neoplasms Models, Genetic
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Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images.

The American journal of pathology Jun 12, 2021
With applications in object detection, image feature extraction, image classification, and image segmentation, artificial intelligence is facilitating high-throughput analysis of image data in a variety of biomedical imaging disciplines, ranging from...
Humans Artificial Intelligence Animals Deep Learning Cells Image Processing, Computer-Assisted Microscopy Organ Specificity
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A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets.

Genes Jun 10, 2021
Technology to generate single cell RNA-sequencing (scRNA-seq) datasets and tools to annotate them have advanced rapidly in the past several years. Such tools generally rely on existing transcriptomic datasets or curated databases of cell type definin...
Organ Specificity Molecular Sequence Annotation RNA-Seq Databases, Genetic Natural Language Processing Humans Single-Cell Analysis
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Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities.

Genome biology May 3, 2021
A complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease status, or gene expression. Technological advances in single-cell profiling have enabled researchers to assay mul...
Machine Learning Chromatin Assembly and Disassembly Gene Expression Profiling Gene Expression Regulation Organ Specificity Chromatin Transcriptome Single-Cell Analysis Computational Biology
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Artificial Intelligence & Tissue Biomarkers: Advantages, Risks and Perspectives for Pathology.

Cells Apr 2, 2021
Tissue Biomarkers are information written in the tissue and used in Pathology to recognize specific subsets of patients with diagnostic, prognostic or predictive purposes, thus representing the key elements of Personalized Medicine. The advent of Art...
Pathology Humans Animals Artificial Intelligence Risk Software Organ Specificity Biomarkers
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Verifying explainability of a deep learning tissue classifier trained on RNA-seq data.

Scientific reports Jan 29, 2021
For complex machine learning (ML) algorithms to gain widespread acceptance in decision making, we must be able to identify the features driving the predictions. Explainability models allow transparency of ML algorithms, however their reliability with...
Genotype Algorithms Organ Specificity Deep Learning RNA-Seq Humans Neural Networks, Computer Machine Learning
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