AIMC Topic: Signal Transduction

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Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer.

Genome medicine Mar 11, 2021
BACKGROUND: Contemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application of deep learning in healthcare remains limited since deep learning methods are often considered as ...
Protein Interaction Maps Gene Regulatory Networks Gene Expression Regulation, Neoplastic Neural Networks, Computer Signal Transduction Algorithms Humans Neoplasm Metastasis Female Breast Neoplasms
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Expanding the drug discovery space with predicted metabolite-target interactions.

Communications biology Mar 5, 2021
Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite-host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potenti...
Transcriptome Protein Interaction Maps Bacteria Signal Transduction Databases, Factual Inflammatory Bowel Diseases Drug Discovery Gene Expression Profiling Gastrointestinal Agents Data Mining Ligands Humans Molecular Targeted Therapy Gastrointestinal Microbiome Machine Learning Host-Pathogen Interactions Metabolomics Cells, Cultured Metabolome Anti-Inflammatory Agents
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Modulation of the dynamics of cerebellar Purkinje cells through the interaction of excitatory and inhibitory feedforward pathways.

PLoS computational biology Feb 10, 2021
The dynamics of cerebellar neuronal networks is controlled by the underlying building blocks of neurons and synapses between them. For which, the computation of Purkinje cells (PCs), the only output cells of the cerebellar cortex, is implemented thro...
Animals Signal Transduction Neuronal Plasticity Models, Neurological Humans Neural Networks, Computer Computer Simulation Neural Pathways Normal Distribution Synaptic Transmission Interneurons Action Potentials Neurons Cerebellum Synapses Purkinje Cells Excitatory Postsynaptic Potentials Cerebellar Cortex
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Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference.

PloS one Feb 8, 2021
In order to increase statistical power for learning a causal network, data are often pooled from multiple observational and interventional experiments. However, if the direct effects of interventions are uncertain, multi-experiment data pooling can r...
Biomedical Research Humans Protein Interaction Maps Models, Theoretical Computational Biology Neural Networks, Computer CD4-Positive T-Lymphocytes Signal Transduction Machine Learning
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Integrative transcriptomic, proteomic, and machine learning approach to identifying feature genes of atrial fibrillation using atrial samples from patients with valvular heart disease.

BMC cardiovascular disorders Jan 28, 2021
BACKGROUND: Atrial fibrillation (AF) is the most common arrhythmia with poorly understood mechanisms. We aimed to investigate the biological mechanism of AF and to discover feature genes by analyzing multi-omics data and by applying a machine learnin...
Oligonucleotide Array Sequence Analysis Genetic Association Studies Proteomics Signal Transduction Databases, Genetic Bayes Theorem Transcriptome Atrial Fibrillation Case-Control Studies Heart Atria Female Humans Protein Interaction Maps Heart Valve Diseases Male Machine Learning Gene Regulatory Networks Middle Aged Gene Expression Profiling
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Characterization of Antiphospholipid Syndrome Atherothrombotic Risk by Unsupervised Integrated Transcriptomic Analyses.

Arteriosclerosis, thrombosis, and vascular biology Dec 24, 2020
OBJECTIVE: Our aim was to characterize distinctive clinical antiphospholipid syndrome phenotypes and identify novel microRNA (miRNA)-mRNA-intracellular signaling regulatory networks in monocytes linked to cardiovascular disease. Approach and Results:...
Gene Expression Regulation Oligonucleotide Array Sequence Analysis Antiphospholipid Syndrome Risk Assessment Gene Expression Profiling Risk Factors Cluster Analysis Humans Transcriptome Adult Protein Interaction Maps MicroRNAs Case-Control Studies Male Unsupervised Machine Learning Cells, Cultured Gene Regulatory Networks Middle Aged Thrombosis Female Monocytes Signal Transduction
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Development of a hybrid model for a partially known intracellular signaling pathway through correction term estimation and neural network modeling.

PLoS computational biology Dec 14, 2020
Developing an accurate first-principle model is an important step in employing systems biology approaches to analyze an intracellular signaling pathway. However, an accurate first-principle model is difficult to be developed since it requires in-dept...
Least-Squares Analysis NF-kappa B Algorithms Signal Transduction Apoptosis Neural Networks, Computer Lipopolysaccharides
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Neuronal differentiation strategies: insights from single-cell sequencing and machine learning.

Development (Cambridge, England) Dec 8, 2020
Neuronal replacement therapies rely on the differentiation of specific cell types from embryonic or induced pluripotent stem cells, or on the direct reprogramming of differentiated adult cells via the expression of transcription factors or signaling...
Humans Machine Learning Animals Single-Cell Analysis Signal Transduction Cellular Reprogramming Cell Differentiation Neurons Induced Pluripotent Stem Cells Neural Stem Cells Embryonic Stem Cells
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Machine-Learning and Chemicogenomics Approach Defines and Predicts Cross-Talk of Hippo and MAPK Pathways.

Cancer discovery Nov 18, 2020
Hippo pathway dysregulation occurs in multiple cancers through genetic and nongenetic alterations, resulting in translocation of YAP to the nucleus and activation of the TEAD family of transcription factors. Unlike other oncogenic pathways such as RA...
Humans Signal Transduction Machine Learning MAP Kinase Signaling System Genomics Cheminformatics Computational Biology Hippo Signaling Pathway
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Learning to encode cellular responses to systematic perturbations with deep generative models.

NPJ systems biology and applications Nov 6, 2020
Cellular signaling systems play a vital role in maintaining homeostasis when a cell is exposed to different perturbations. Components of the systems are organized as hierarchical networks, and perturbing different components often leads to transcript...
Deep Learning Cells Systems Biology Signal Transduction Models, Biological
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