I am a research scientist with a background in electrical engineering and computer science. The main focus of my research is a network approach to computational and systems biology and bioinformatics, particularly protein-protein interaction data sets and host-pathogen interactions. I have experience working on interdisciplinary projects in the computational and life science fields.
My interests include:
- Data mining: identifying patterns and relationship among the data, e.g., between genes/proteins, their biological function, disease, aging, and evolution.
- Data integration: developing computational methods for integration of heterogeneous data, e.g., protein interactions, gene expression, domain annotation, and transcriptional information to obtain condition-specific protein-protein interactions.
- Network alignment: identifying common network wiring patterns, e.g., comparison of biological networks to identify evolutionarily conserved subnetworks.
- Mathematical modeling: determining the appropriate mathematical representation of the system, e.g., predicting molecular interactions, identifying best-fitting models for molecular systems, and simulating biological system models.
- Data visualization: representing the data and results in a comprehensible way to highlight meaningful patterns in the system, e.g. distinguishing genes/proteins involved in a disease.
Software/applications I have contributed to:
- sysBio - R package for systems biology modeling - (Independent) package/functions design, implementation (R), and evaluation. Source available at: https://github.com/Vessy/sysBio.
- HPIA - Host-pathogen interaction alignment algorithm - (@BHSAI, PMID: 25738731) algorithm design, implementation (C++), and evaluation. Executable available at: http://bhsai.org/downloads/hpia/.
- DBSecSys - Database of bacterial secretion systems - (@BHSAI,
PMID: 25030112) technical expertise and participation
in design (database schema design and visualization) and evaluation. Available at:
- PADDS - Parameter dependent domain-domain interaction selection algorithm - (@BHSAI, PMID: 23651452) algorithm design, implementation (C++), and evaluation. Executable available at: http://bhsai.org/downloads/padds/PADDS.htm.
- dMerger - Protein-domain annotation merger algorithm - (@BHSAI, PMID: 23651452) algorithm design, implementation (C++), and evaluation. Executable available at: http://bhsai.org/downloads/padds/dMerger.htm.
- C-GRAAL - Common-neighbors-based global graph alignment algorithm - (@UCI, PMID: 22234340) algorithm design, implementation (C++), and evaluation. Executable available at: http://bio-nets.doc.ic.ac.uk/C-GRAAL/.