A5063233199- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Protein Structure and Dynamics
- Metabolomics and Mass Spectrometry Studies
- Biofuel production and bioconversion
- Advanced Control Systems Optimization
- Evolution and Genetic Dynamics
- Malaria Research and Control
- Fungal and yeast genetics research
- Computational Drug Discovery Methods
- Enzyme Catalysis and Immobilization
- Fault Detection and Control Systems
- thermodynamics and calorimetric analyses
- Statistical Distribution Estimation and Applications
- Receptor Mechanisms and Signaling
- Mosquito-borne diseases and control
- Sphingolipid Metabolism and Signaling
- Cystic Fibrosis Research Advances
- Photosynthetic Processes and Mechanisms
- Neurotransmitter Receptor Influence on Behavior
- Forest ecology and management
- Mathematical and Theoretical Epidemiology and Ecology Models
- Neuroscience and Neuropharmacology Research
Georgia Institute of Technology
2015-2025
The Wallace H. Coulter Department of Biomedical Engineering
2014-2025
The University of Texas at Dallas
2025
Emory University
2013-2023
Oak Ridge National Laboratory
2015-2018
University of Idaho
2018
University of Georgia
2018
Division of Parasitic Diseases and Malaria
2017
AID Atlanta
2015-2017
Medical University of South Carolina
1997-2016
Abstract Rationale: Modern molecular biology is generating data of unprecedented quantity and quality. Particularly exciting for biochemical pathway modeling proteomics are comprehensive, time-dense profiles metabolites or proteins that measurable, instance, with mass spectrometry, nuclear magnetic resonance protein kinase phosphorylation. These contain a wealth information about the structure dynamics network from which were obtained. The retrieval this requires combination computational...
This year we celebrate the 150th anniversary of law mass action. is often assumed to have been "there" forever, but it has its own history, background, and a definite starting point. The had an impact on chemistry, biochemistry, biomathematics, systems biology that difficult overestimate. It easily recognized direct basis for computational enzyme kinetics, ecological models, models spread diseases. article reviews explicit implicit role action in reveals how original, more general...
Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole be further integrated with ecosystem, weather, climate to predict how various interactions respond environmental perturbations. These have the potential fill in missing mechanistic details generate new hypotheses prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, increase...
High levels of polychlorinated biphenyls (PCBs) have been reported in the tissues some species marine mammals. The high concentrations are concern because a growing body experimental evidence links PCBs to deleterious effects on reproduction, endocrine homeostasis, and immune system function. Much recent research has focused determining exposure mammal populations PCBs, but very little effort devoted actual risk assessments that needed determine expected impacts documented exposures. We...
Abstract Background The estimation of parameter values continues to be the bottleneck computational analysis biological systems. It is therefore necessary develop improved methods that are effective, fast, and scalable. Results We show here alternating regression (AR), applied S-system models combined with for decoupling systems differential equations, provides a fast new tool identifying from time series data. key feature AR it dissects nonlinear inverse problem estimating into iterative...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAccuracy of alternative representations for integrated biochemical systemsEberhard O. Voit and Michael A. SavageauCite this: Biochemistry 1987, 26, 21, 6869–6880Publication Date (Print):October 1, 1987Publication History Published online1 May 2002Published inissue 1 October 1987https://pubs.acs.org/doi/10.1021/bi00395a042https://doi.org/10.1021/bi00395a042research-articleACS PublicationsRequest reuse permissionsArticle...
The inverse problem of identifying the topology biological networks from their time series responses is a cornerstone challenge in systems biology. We tackle this here through parameterization S-system models. It was previously shown that parameter identification can be performed as an optimization based on decoupling differential equations, which results set algebraic equations. A novel solution proposed for models when no information about network known. method eigenvector matrix formed...
Like many other environments, Lake Mendota, WI, USA, is populated by thousand microbial species. Only about 1,000 of these constitute between 80 and 99% the total community, depending on season, whereas remaining species are rare. The functioning resilience lake ecosystem depend microorganisms, it therefore important to understand their dynamics throughout year. We propose a two-layered set dynamic mathematical models that capture interpret yearly abundance patterns within metapopulation....
Modern methods of genomics have produced an unprecedented amount raw data. The interpretation and explanation these data constitute a major, well-recognized challenge.Biochemical Systems Theory (BST) is the mathematical basis well-established methodological framework for analyzing networks biochemical reactions. An existing BST model yeast glycolysis used here to explain interpret glycolytic gene expression pattern heat shocked yeast. Our analysis demonstrates that observed profile satisfies...
The combination of high-throughput methods molecular biology with advanced mathematical and computational techniques has propelled the emergent field systems into a position prominence. Unthinkable decade ago, it become possible to screen analyze expression entire genomes, simultaneously assess large numbers proteins their prevalence, characterize in detail metabolic state cell population. Although very important, focus on comprehensive networks biological components is only one side...
Abstract Motivation: At the center of computational systems biology are mathematical models that capture dynamics biological and offer novel insights. The bottleneck in construction these is presently identification model parameters make consistent with observed data. Dynamic flux estimation (DFE) a methodological framework for estimating metabolic from time-series DFE consists two distinct phases, an entirely model-free assumption-free data analysis model-based characterization process...
Abstract Background The problem of estimating the parameters dynamic models complex biological systems from time series data is becoming increasingly important. Methods and results Particular consideration given to metabolic that are formulated as Generalized Mass Action (GMA) models. estimation posed a global optimization task, for which novel techniques can be applied determine best set parameter values measured responses system. challenge this task nonconvex. Nonetheless, deterministic...