AIMC Topic: Signal Transduction

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The reactome pathway knowledgebase 2022.

Nucleic acids research Jan 7, 2022
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired dise...
Signal Transduction Proteins Knowledge Bases Host-Pathogen Interactions Humans Software COVID-19 Antiviral Agents Genome, Human Data Curation
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Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

Proceedings of the National Academy of Sciences of the United States of America Jan 4, 2022
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-at...
Humans Machine Learning Signal Transduction Lipids Molecular Dynamics Simulation Cell Membrane Protein Multimerization Proto-Oncogene Proteins p21(ras)
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Predicting Residence Time of GPCR Ligands with Machine Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Drug-target residence time, the duration of binding at a given protein target, has been shown in some protein families to be more significant for conferring efficacy than binding affinity. To carry out efficient optimization of residence time in drug...
Protein Binding Signal Transduction Receptors, G-Protein-Coupled Kinetics Ligands Humans Machine Learning
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Detection of subtype-specific breast cancer surface protein biomarkers via a novel transcriptomics approach.

Bioscience reports Dec 22, 2021
BACKGROUND: Cell-surface proteins have been widely used as diagnostic and prognostic markers in cancer research and as targets for the development of anticancer agents. So far, very few attempts have been made to characterize the surfaceome of patien...
Prognosis Female Breast Neoplasms Biomarkers, Tumor Gene Expression Profiling Humans Machine Learning Gene Expression Regulation, Neoplastic Transcriptome Signal Transduction Case-Control Studies Databases, Genetic Protein Interaction Maps Predictive Value of Tests Gene Regulatory Networks
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XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data.

Briefings in bioinformatics Nov 5, 2021
The lack of explainability is one of the most prominent disadvantages of deep learning applications in omics. This 'black box' problem can undermine the credibility and limit the practical implementation of biomedical deep learning models. Here we pr...
Genomics Computational Biology Signal Transduction Databases, Genetic Gene Expression Profiling Deep Learning ROC Curve Gene Regulatory Networks Cluster Analysis Area Under Curve Humans Machine Learning Algorithms Female Reproducibility of Results Biomarkers, Tumor Male Neoplasms
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Bioinformatics and machine learning methodologies to identify the effects of central nervous system disorders on glioblastoma progression.

Briefings in bioinformatics Sep 2, 2021
Glioblastoma (GBM) is a common malignant brain tumor which often presents as a comorbidity with central nervous system (CNS) disorders. Both CNS disorders and GBM cells release glutamate and show an abnormality, but differ in cellular behavior. So, t...
Molecular Sequence Annotation Gene Ontology Atlases as Topic Glutamic Acid Machine Learning Datasets as Topic Central Nervous System Brain Neoplasms Proportional Hazards Models Gene Expression Profiling Kaplan-Meier Estimate Gene Regulatory Networks Humans Computational Biology Gene Expression Regulation, Neoplastic Signal Transduction Neoplasm Proteins Glioblastoma
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Identification of pan-cancer Ras pathway activation with deep learning.

Briefings in bioinformatics Jul 20, 2021
The identification of hidden responders is often an essential challenge in precision oncology. A recent attempt based on machine learning has been proposed for classifying aberrant pathway activity from multiomic cancer data. However, we note several...
Humans Neoplasms Deep Learning Programming Languages RNA-Seq Gene Dosage Signal Transduction ras Proteins Neoplasm Proteins Mutation
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[Consensus ensemble neural network multitarget model of RAGE inhibitory activity of chemical compounds].

Biomeditsinskaia khimiia May 1, 2021
RAGE signal transduction via the RAGE-NF-κB signaling pathway is one of the mechanisms of inflammatory reactions that cause severe complications in diabetes mellitus. RAGE inhibitors are promising pharmacological compounds that require the developmen...
Neural Networks, Computer Molecular Docking Simulation Consensus Signal Transduction NF-kappa B
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High-dimensional profiling clusters asthma severity by lymphoid and non-lymphoid status.

Cell reports Apr 13, 2021
Clinical definitions of asthma fail to capture the heterogeneity of immune dysfunction in severe, treatment-refractory disease. Applying mass cytometry and machine learning to bronchoalveolar lavage (BAL) cells, we find that corticosteroid-resistant ...
Proteomics Interleukin-7 Asthma Signal Transduction Receptors, IgE CD4-Positive T-Lymphocytes Severity of Illness Index Immunity, Innate Humans Adrenal Cortex Hormones Gene Expression Regulation Gene Expression Profiling CD8-Positive T-Lymphocytes Machine Learning Interferon-gamma Case-Control Studies Anti-Asthmatic Agents Interleukin-10 Adaptive Immunity Bronchoalveolar Lavage Fluid Macrophages Immunologic Memory
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CODEX, a neural network approach to explore signaling dynamics landscapes.

Molecular systems biology Apr 1, 2021
Current studies of cell signaling dynamics that use live cell fluorescent biosensors routinely yield thousands of single-cell, heterogeneous, multi-dimensional trajectories. Typically, the extraction of relevant information from time series data reli...
Dose-Response Relationship, Radiation Drosophila Radiation, Ionizing Extracellular Signal-Regulated MAP Kinases Intercellular Signaling Peptides and Proteins Humans Tumor Suppressor Protein p53 Neural Networks, Computer Databases as Topic Movement Cell Line Fluorescent Dyes Machine Learning Proto-Oncogene Proteins c-akt Algorithms Transforming Growth Factor beta Animals Light Signal Transduction
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