A5067929604- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Protein Structure and Dynamics
- Photosynthetic Processes and Mechanisms
- Algal biology and biofuel production
- Metabolomics and Mass Spectrometry Studies
- Microbial Community Ecology and Physiology
- Biofuel production and bioconversion
- Cell Image Analysis Techniques
- Bioinformatics and Genomic Networks
- Machine Learning in Materials Science
- Scientific Computing and Data Management
- Slime Mold and Myxomycetes Research
Pacific Northwest National Laboratory
2023-2025
University of Warwick
2021-2022
Abstract Background Spatial organization plays an important role in the function of many biological systems, from cell fate specification animal development to multistep metabolic conversions microbial communities. The study such systems benefits use spatially explicit computational models that combine a discrete description cells with continuum one or more chemicals diffusing within surrounding bulk medium. These allow silico testing and refinement mechanistic hypotheses. However, most...
High performance computing has a great potential to provide range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies bacteria cells. The aim understand cell generated substantial interest they can have strong economic and societal impacts through their roles in industrial bioreactors complex community structures, called biofilms, found clinical settings. Investigating...
We develop a systems approach based on an energy-landscape concept to differentiate interactions involving redox activities and conformational changes of proteins nucleic acids in multi-layered protein-DNA regulatory networks under light disturbance. Our is data-driven modeling workflow using physics-informed machine learning algorithm train non-linear mathematical model for interpreting gene expression dynamics lead discovery protein regulators proteome analysis. distinguish...
Bacteriophage auxiliary metabolic genes (AMGs) alter host metabolism by hijacking reactions. Previous studies used functional annotations to infer AMG impacts, but how these propagate and interact affect global phage production remains understudied. We demonstrate the first integration of AMGs assembly into a genome-scale model, using P-HM2 infection Prochloroccocus marinus MED4 as test system. Our model predicts that 17 directly hijacked reactions substantially impact over 30% metabolism,...
Abstract Motivation Spatial organisation plays an important role in the function of many biological systems, from cell fate specification animal development to multi-step metabolic conversions microbial communities. The study such systems benefits use spatially explicit computational models that combine a discrete description cells with continuum one or more chemicals diffusing within surrounding bulk medium. These allow silico testing and refinement mechanistic hypotheses. However, most...