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Article
Open AccessAn agent-based approach for modelling and simulation of glycoprotein VI receptor diffusion, localisation and dimerisation in platelet lipid rafts
Receptor diffusion plays an essential role in cellular signalling via the plasma membrane microenvironment and receptor interactions, but the regulation is not well understood. To aid in understanding of the k...
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Article
Open AccessMini-batch optimization enables training of ODE models on large-scale datasets
Quantitative dynamic models are widely used to study cellular signal processing. A critical step in modelling is the estimation of unknown model parameters from experimental data. As model sizes and datasets a...
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Article
Open AccessA framework for validating AI in precision medicine: considerations from the European ITFoC consortium
Artificial intelligence (AI) has the potential to transform our healthcare systems significantly. New AI technologies based on machine learning approaches should play a key role in clinical decision-making in ...
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Article
Open AccessA data- and model-driven approach for cancer treatment
All people are unique and so are their diseases. Our genomes, disease histories, behavior, and lifestyles are all different; therefore it is not too surprising that people often respond differently when admini...
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Article
Open AccessEin daten- und modellgesteuerter Ansatz zur Behandlung maligner Tumoren
Alle Menschen sind einzigartig und so sind es auch ihre Krankheiten. Genome, Erkrankungsverläufe, Verhalten und Lebensstile sind unterschiedlich; es ist daher nicht erstaunlich, dass Menschen auch auf dieselbe...
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Open AccessMolecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors
Colorectal carcinoma represents a heterogeneous entity, with only a fraction of the tumours responding to available therapies, requiring a better molecular understanding of the disease in precision oncology. T...
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Chapter
Modelling Molecular Mechanisms of Cancer Pathogenesis: Virtual Patients, Real Opportunities
A combination of decades of cancer research and trillions of dollars has helped to exponentially increase our understanding of the molecular processes involved in cancer pathogenesis [1, 2] and to develop new ...
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Article
Open AccessMulti-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes
Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, o...
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Chapter
Computational Tools and Resources for Integrative Modeling in Systems Biology
Mathematical modeling is key for systems level understanding of cellular processes. The development of mathematical models demands advanced computational tools that keep track of heterogeneous data of molecule...
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Article
Open AccessThe structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors
Current large-scale cancer sequencing projects have identified large numbers of somatic mutations covering an increasing number of different cancer tissues and patients. However, the characterization of these ...
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Protocol
Standards, Tools, and Databases for the Analysis of Yeast ‘Omics Data
One of the major objectives of systems biology is the development of mathematical models for the quantitative description of complex biological systems, such as living cells. Biological data and software tools...
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Chapter
Computational Tools and Resources for Systems Biology Approaches in Cancer
Systems biology focuses on the study of interacting components of biological systems rather than on the analysis of single genes or proteins and offers a new approach to understand complex disease mechanisms b...
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Article
Open AccessMonte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network
Gene Regulatory Networks (GRNs) control the differentiation, specification and function of cells at the genomic level. The levels of interactions within large GRNs are of enormous depth and complexity. Details...
