Contact Name: Sam Danziger
Contact Email: sam.danziger[at]seattlebiomed.org
Department: Seattle Biomed
Description:
We have completed a pilot study using protein arrays with children in Papua New Guinea to study mixed infection of P. Falciparum and P. Vivax malaria causing parasites. These experiments have allowed us to identify combinations of antigens that correlate with resistance to malaria fever. We hope the follow-up studies will ultimately lead to a malaria vaccine, especially one that works in areas with multiple parasites.
10-week Project #1: The data involves 224 children in Papua New Guinea who were each tested for serum response to 4441 antigen polypeptides. Each of these children was either suffering from malaria fever, or had developed a malaria resistance. For this project, the student would expand a deep learning module written in [R] to detect relevant antigen combinations encoded in the hidden layer(s) and improve the classifier. There would be plenty of opportunity to compare results with known (dynamic) malaria surface adhesion molecules.
10-week Project #2: Seven other centers around the globe have used the same array for similar studies. This project would involve retrieving and curating the data from published studies (as well as through contacts with the company that prints/analyzes the arrays) and formulating research questions to explore with the combined data set. There would be plenty of opportunity to apply / develop / expand machine learning and analysis techniques developed in the original study.
Requirements:
Familiarity with [R] statistical programming language or similar programming language.