Defining infection from multiple perspectives

Advisor:
Jennifer Geddes-McAlister (MCB)

The Geddes-McAlister lab uses cutting-edge mass spectrometry-based proteomics to explore the intricate relationships between host and pathogens during infection. We focus on microbial pathogens (e.g., fungi and bacteria) in a variety of host systems (e.g., mammalian and plant) and characterize changes in protein production within the cell, extracellular environment, and through post-translational modifications and interactions. We routinely use the publicly-available MaxQuant and Perseus platforms for our analyses and are seeking a BINF student to increase our knowledge and use of complementary platforms.

Specifically, the first objective of the project would design new data analysis tools in R and python to improve our analysis pipeline and generate new methods for data presentation (e.g., figures). A second objective would be the exploitation of readily-available software platforms (e.g., Cytoscape and STRING DB) to improve our understanding and ability to characterize protein-protein interactions, and the third objective would entail the design of a data analysis pipeline for the integration of multi-OMICs datasets (e.g., transcriptome, proteome, metabolome) to provide robust and novel insights at multiple molecular levels. Such a pipeline would provide ‘plug and play’ opportunities for application to diverse biological systems and questions. Notably, we have data from multiple projects available to support the Objectives listed above. Overall, we aim to define infection from multiple perspectives to uncover opportunities for new treatment strategies with impacts in the scientific, medical, and agricultural sectors.