A5107139754- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- RNA Research and Splicing
- Biomedical Text Mining and Ontologies
- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Cell Image Analysis Techniques
- Monoclonal and Polyclonal Antibodies Research
- Single-cell and spatial transcriptomics
- Simulation Techniques and Applications
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Fungal and yeast genetics research
- Genetics, Bioinformatics, and Biomedical Research
- Renal Diseases and Glomerulopathies
- Gene expression and cancer classification
- DNA and Biological Computing
- RNA modifications and cancer
- Microtubule and mitosis dynamics
- Nutrition and Health in Aging
- Genomics and Chromatin Dynamics
- Chemical Synthesis and Analysis
- Mast cells and histamine
University of Connecticut
2016-2025
UConn Health
2015-2025
University of Toronto
2021
University of Pittsburgh
2009-2011
National Institute of Advanced Industrial Science and Technology
2010
Dankook University
2010
Los Alamos National Laboratory
2002-2006
Weizmann Institute of Science
1999-2002
Abstract Summary: BioNetGen allows a user to create computational model that characterizes the dynamics of signal transduction system, and accounts comprehensively precisely for specified enzymatic activities, potential post-translational modifications interactions domains signaling molecules. The output defines parameterizes network molecular species can arise during provides functions relate variables experimental readouts interest. Models be generated are relevant rational drug discovery,...
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...
Resilience, the ability to resist or recover from adverse effects of a stressor, is widespread interest in social, psychologic, biologic, and medical research particularly salient as capacity respond stressors becomes diminished with aging. To date, on human resilience responses factors influencing these has been limited.The National Institute Aging convened workshop August 2015 needs for improve measures predict assess Effects aging-related impairing homeostatic were developed examples...
Abstract Aggregation of FcεRI on mast cells and basophils leads to autophosphorylation increased activity the cytosolic protein tyrosine kinase Syk. We investigated roles Src Lyn, immunoreceptor tyrosine-based activation motifs (ITAMs) β γ subunits FcεRI, Syk itself in Our approach was build a detailed mathematical model reactions involving Syk, bivalent ligand that aggregates FcεRI. applied experiments which covalently cross-linked IgE dimers stimulate rat basophilic leukemia cells. The...
Abstract We present a method for generating biochemical reaction network from description of the interactions components biomolecules. The are specified in form rules, each which defines class associated with type interaction. Reactants within have shared properties, rule defining class. A also provides rate law, governs class, and template transforming reactants into products. set rules can be applied to seed chemical species and, subsequently, any new that found as products reactions...
Signaling complexes typically consist of highly dynamic molecular ensembles that are challenging to study and describe accurately. Conventional mechanical descriptions misrepresent this reality can be actively counterproductive by misdirecting us away from investigating critical issues.
Biomolecular condensates are formed by liquid-liquid phase separation (LLPS) of multivalent molecules. LLPS from a single ("homotypic") constituent is governed buffering: above threshold, free monomer concentration clamped, with all added molecules entering the condensed phase. However, both experiment and theory demonstrate that buffering fails for dependence multicomponent ("heterotypic") LLPS. Using network-free stochastic modeling, we can be described solubility product constant (Ksp):...
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 Proteolysis MAP (PMAP, http://www.proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP comprised of five databases, linked together one environment. foundation ProteaseDB SubstrateDB, are driven by an automated annotation pipeline that generates dynamic 'Molecule Pages', rich molecular information. also contains two annotated databases focused on function; CutDB has information more than 5000...
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held Heidelberg, Germany, July 2019. The annual event brings together researchers, biocurators and software engineers to present recent results discuss future work area standards for systems synthetic biology. COMBINE initiative coordinates development various community formats computational models life sciences. Over past 10 years, has brought standard communities have...
ABSTRACTLive poultry markets (LPMs) are regarded as hubs for avian influenza virus (AIV) transmission in and a major risk factor human AIV infections. We performed an surveillance study at wholesale LPM, where different species were sold separate stalls, nine retail LPMs, which received from the LPM but one stall, Guangdong province 2017 to 2019. A higher isolation rate was observed LPMs than LPM. H9N2 dominant subtype mainly present chickens quails. The genetic diversity of viruses greater...
The activities and interactions of proteins that govern the cellular response to a signal generate multitude protein phosphorylation states heterogeneous complexes. Here, using computational model accounts for 307 molecular species implied by specified four involved in signalling immunoreceptor FcɛRI, we determine relative importance can be generated during signalling, chemical transitions among these species, reaction paths lead activation tyrosine kinase (PTK) Syk. By all measures over...
Rule-based modeling provides a means to represent cell signaling systems in way that captures site-specific details of molecular interactions. For rule-based models be more widely understood and (re)used, conventions for model visualization annotation are needed. We have developed the concepts an extended contact map guide illustrating annotating models. An represents scope by providing illustration each molecule, component, direct physical interaction, post-translational modification,...