Programming Languages with Applications to Biology and Security
Essays Dedicated to Pierpaolo Degano on the Occasion of His 65th Birthday
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78 Result(s)
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Article
Systems biology approaches to study the molecular effects of caloric restriction and polyphenols on aging processes
Worldwide population is aging, and a large part of the growing burden associated with age-related conditions can be prevented or delayed by promoting healthy lifestyle and normalizing metabolic risk factors. H...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome
The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota...
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Book
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Chapter
Pierpaolo Degano
This section contains the laudatio in honour of Pierpaolo Degano. It illustrates his distinguished career and his main scientific contributions.
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Chapter
\(\ell \) : An Imperative DSL to Stochastically Simulate Biological Systems
Language-based modelling of biological systems is a growing field of research. Many proofs of concept have been published in the last decade. We propose a domain specific language, imperative in style, to step...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Genetic associations with micronutrient levels identified in immune and gastrointestinal networks
The discovery of vitamins and clarification of their role in preventing frank essential nutrient deficiencies occurred in the early 1900s. Much vitamin research has understandably focused on public health and...
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Article
Methylation potential associated with diet, genotype, protein, and metabolite levels in the Delta Obesity Vitamin Study
Micronutrient research typically focuses on analyzing the effects of single or a few nutrients on health by analyzing a limited number of biomarkers. The observational study described here analyzed micronutri...
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Chapter and Conference Paper
Inference of Autism-Related Genes by Integrating Protein-Protein Interactions and miRNA-Target Interactions
Autism spectrum disorders (ASD) are a group of conditions characterized by impairments in social interaction and presence of repetitive behavior. These complex neurological diseases are among the fastest growi...
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Chapter and Conference Paper
Algorithmic Systems Ecology: Experiments on Multiple Interaction Types and Patches
Dynamic behavior in ecosystems can emerge as a result of multiple interactions of different types as well as movements of the ecosystem species between different patches. The extinction behaviors in ecosystem ...
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Article
Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life
Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum’s one gene—one polypeptide hypothesis, thereby reducing biological processes to s...
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Chapter
A Model Predicting Rolling Cells Percentage in Inflamed Brain Venules
We present a stochastic model of the lymphocytes recruitment in inflamed brain microvessels. The framework used is based on stochastic process algebras for mobile systems. The automatic tool used in the simula...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics
The representation of a biochemical system as a network is the precursor of any mathematical model of the processes driving the dynamics of that system. Pharmacokinetics uses mathematical models to describe th...
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Book and Conference Proceedings
Transactions on Computational Systems Biology XIV
Special Issue on Computational Models for Cell Processes
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Chapter and Conference Paper
A Rule-Based and Imperative Language for Biochemical Modeling and Simulation
We present COSBI LAB Language ( \(\mathcal{L}\) for short), a simple modeling language for biochemical systems. ...
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Chapter and Conference Paper
Composability: Perspectives in Ecological Modeling
The multiplicity of ecological interactions acting in parallel calls for novel computational approaches in modeling ecosystem dynamics. Composability, a key property of process algebra-based models can help to...
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Reference Work Entry In depth
Algorithmic Systems Biology — Computer Science Propels Systems Biology
The convergence between computer science and biology occurred in successive waves involving deeper and deeper concepts of computing. The current situation makes computer science a suitable candidate to become ...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins
Nutritional systems biology offers the potential for comprehensive predictions that account for all metabolic changes with the intricate biological organization and the multitudinous interactions between the c...
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Book
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Protocol
Network Inference from Time-Dependent Omics Data
We provide a commented overview of the available databases for the systematic collection of pathway information and biological models essential for the interpretation of Omics data. Then, we present both the s...
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Article
Calibration of dynamic models of biological systems with KInfer
Methods for parameter estimation that are robust to experimental uncertainties and to stochastic and biological noise and that require a minimum of a priori input knowledge are of key importance in computation...
