A5066544731- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Cell Image Analysis Techniques
- Cardiac Ischemia and Reperfusion
- Protein Kinase Regulation and GTPase Signaling
- Scientific Computing and Data Management
- Ion channel regulation and function
- Cellular transport and secretion
- Receptor Mechanisms and Signaling
- Neuroscience and Neuropharmacology Research
- Protein Structure and Dynamics
- Advanced Fluorescence Microscopy Techniques
- Cardiac Fibrosis and Remodeling
- Surface and Thin Film Phenomena
- Cardiac electrophysiology and arrhythmias
- Simulation Techniques and Applications
- Heat shock proteins research
- Genetics, Bioinformatics, and Biomedical Research
- Photoreceptor and optogenetics research
- Mitochondrial Function and Pathology
- Model-Driven Software Engineering Techniques
- Cardiomyopathy and Myosin Studies
- Single-cell and spatial transcriptomics
- Cardiac Imaging and Diagnostics
UConn Health
2013-2025
University of Bucharest
1986-2023
University of Connecticut
1994-2022
Michigan State University
2000
University of Georgia
2000
Yale University
1999
University of Washington
1999
Carol Davila University of Medicine and Pharmacy
1994
Baystate Medical Center
1994
The increasing use of computational simulation experiments to inform modern biological research creates new challenges annotate, archive, share and reproduce such experiments. recently published Minimum Information About a Simulation Experiment (MIASE) proposes minimal set information that should be provided allow the reproduction among users software tools.In this article, we present Description Markup Language (SED-ML). SED-ML encodes in computer-readable exchange format required by MIASE...
The Virtual Cell (VCell; http://vcell.org/) is a problem solving environment, built on central database, for analysis, modelling and simulation of cell biological processes. VCell integrates growing range molecular mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral diffusion electrophysiology, can associate these with geometries derived from experimental microscope images. It has been developed deployed as web-based, distributed, client–server system, more...
Cellular organisms respond at the cellular and molecular level when confronted with sudden changes in environment, adaptation represents ability of cells to acclimate themselves their new environment. In this study we examined response bovine vascular endothelial (VEC) oxidative stress by exposing cultured two different concentrations H2O2, 0.04 or 0.08 mM, for 18-24 h. H2O2-exposed VEC displayed good viability (85-90% mM H2O2; 75-80% H2O2) exhibited normal morphology. H2O2 treatment was...
Reproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved helpful means enabling reuse existing work in modern biology. The Required the Annotation Models (MIRIAM) promote exchange and biochemical computational models. However, information about model alone not sufficient to enable its efficient setting. Advanced numerical algorithms complex modeling workflows used biology make reproduction simulations difficult. It therefore essential...
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging reproduce reuse simulations, in part, because the numerous formats methods for simulating various subsystems scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find use simulation tools, we developed BioSimulators (https://biosimulators.org), central registry of capabilities...
The BioModels Repository contains over 1000 manually curated mechanistic models drawn from published literature, most of which are encoded in the Systems Biology Markup Language (SBML). This community-based standard formally specifies each model, but does not describe computational experimental conditions to run a simulation. Therefore, it can be challenging reproduce any given figure or result publication with an SBML model alone. Simulation Experiment Description (SED-ML) provides...
Summary Constructing a model in hierarchical fashion is natural approach to managing complexity, and offers additional opportunities such as the potential re-use components. The SBML Level 3 Version 1 Core specification does not directly provide mechanism for defining models, but it packages extend add syntactical constructs. Hierarchical Model Composition package adds necessary features support modeling. enables modeler include submodels within an enclosing model, delete unneeded or...
Most of the fascinating phenomena studied in cell biology emerge from interactions among highly organized multimolecular structures embedded into complex and frequently dynamic cellular morphologies. For exploration such systems, computer simulation has proved to be an invaluable tool, many researchers this field have developed sophisticated computational models for application specific biological questions. However, it is often difficult reconcile conflicting results that use different...
Cytosolic calcium acts as both a coagonist and an inhibitor of the type 1 inositol 1,4,5-trisphosphate (InsP3)–gated Ca channel, resulting in bell-shaped dependence channel activity (Bezprozvanny, I., J. Watras, B.E. Ehrlich. 1991. Nature. 351:751–754; Finch, E.A., T.J. Turner, S.M. Goldin. Science. 252: 443–446; Iino, M. 1990. Gen. Physiol. 95:1103–1122). The ability to inhibit activity, however, varies dramatically depending on InsP3 concentration (Combettes, L., Z. Hannaert-Merah, J.F....
Rule-based modeling is invaluable when the number of possible species and reactions in a model become too large to allow convenient manual specification. The popular rule-based software tools BioNetGen NFSim provide powerful simulation capabilities at cost learning complex scripting language which used specify these models. Here, we introduce tool that combines new graphical specification with existing engines seamless way within familiar Virtual Cell (VCell) environment. A mathematical can...