Page
%P
54 Result(s)
-
Chapter
From Microscopes to Macroscopes: Advancing Biomedical Research Through Systems Approaches
As a modeler my value to the experimentalist is often my way of thinking, the questions I ask them. Because mathematical modeling requires us to think carefully about what to measure and to be clear about assu...
-
Open Access This content is freely available online to anyone, anywhere at any time.
Article
COMODI: an ontology to characterise differences in versions of computational models in biology
Open model repositories provide ready-to-reuse computational models of biological systems. Models within those repositories evolve over time, leading to different model versions. Taken together, the underlying...
-
Open Access This content is freely available online to anyone, anywhere at any time.
Article
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Technical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysi...
-
Book
-
Protocol
RNA Systems Biology for Cancer: From Diagnosis to Therapy
It is due to the advances in high-throughput omics data generation that RNA species have re-entered the focus of biomedical research. International collaborate efforts, like the ENCODE and GENCODE projects, ha...
-
Protocol
Network-Assisted Disease Classification and Biomarker Discovery
Developing improved approaches for diagnosis, treatment, and prevention of diseases is a major goal of biomedical research. Therefore, the discovery of biomarker signatures from high-throughput “omics” data is...
-
Open Access This content is freely available online to anyone, anywhere at any time.
Article
Annotation-based feature extraction from sets of SBML models
Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concept...
-
Chapter
Explanation and Organizing Principles in Systems Biology
While explanation in biology is a well-established topic in philosophy of science, since the rise of new mechanistic approaches little has been said about explanation in Systems Biology. In this contribution, ...
-
Article
Coenzyme A-transferase-independent butyrate re-assimilation in Clostridium acetobutylicum—evidence from a mathematical model
The hetero-dimeric CoA-transferase CtfA/B is believed to be crucial for the metabolic transition from acidogenesis to solventogenesis in Clostridium acetobutylicum as part of the industrial-relevant acetone-butan...
-
Open Access This content is freely available online to anyone, anywhere at any time.
Article
Anti-inflammatory effects of reactive oxygen species – a multi-valued logical model validated by formal concept analysis
Recent findings suggest that in pancreatic acinar cells stimulated with bile acid, a pro-apoptotic effect of reactive oxygen species (ROS) dominates their effect on necrosis and spreading of inflammation. The ...
-
Open Access This content is freely available online to anyone, anywhere at any time.
Article
Enabling multiscale modeling in systems medicine
-
Article
The systems biology of mitochondrial fission and fusion and implications for disease and aging
Mitochondria organize themselves as dynamic populations within a cell, by undergoing continuous cycles of fission and fusion. The spatio-temporal distribution and abundance of mitochondria determines the cell’...
-
Article
A shift in the dominant phenotype governs the pH-induced metabolic switch of Clostridium acetobutylicumin phosphate-limited continuous cultures
In response to changing extracellular pH levels, phosphate-limited continuous cultures of Clostridium acetobutylicum reversibly switches its metabolism from the dominant formation of acids to the prevalent produc...
-
Article
Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes
A major challenge when attempting to model biochemical reaction networks within the cell is that the dimensionality can become huge, where a large number of molecular species can be involved even in relatively...
-
Open Access This content is freely available online to anyone, anywhere at any time.
Article
Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT
The stressosome is a bacterial signalling complex that responds to environmental changes by initiating a protein partner switching cascade, which leads to the release of the alternative sigma factor, σB. Stress p...
-
Book and Reference Work
-
Book
-
Chapter
Interdisciplinarity as both Necessity and Hurdle for Progress in the Life Sciences
The ability to sequence the genome of entire organisms has produced a fundamental change in the scientific practice of the life sciences. With the Omics revolution, biologists working with cellular systems hav...
-
Chapter
Modelling Molecular Processes by Individual-Based Simulations Applied to Actin Polymerisation
Used in ecology, economics and social science, agent-based modelling is also increasingly used in the life science. We use this technique to model and simulate the processing of actin filaments. These filament...
-
Chapter
Web Resources for microRNA Research
Over the last decade thousands of microRNAs (miRNAs) have been discovered in all kinds of taxa. The ever growing number of identified miRNA genes required ordered cataloging and annotation. This has led to the...
