Postdoctoral position:
Position 1: Learning the shape of the protein universe
Proteins play a central role in all parts of biology from immune recognition to brain activity. A key challenge is to predict how protein sequence and structure determines function, such as the protein’s binding affinity to ligands or its enzymatic activity. With the growth of molecular data, machine learning has become a powerful tool in protein science. However, these techniques often generate black-box models, which are powerful but hard to interpret. In this project, we aim to characterize a structure-function map for proteins by developing equivariant neural networks that take protein structures as input and through transformations that respect the physical symmetries in the data, learn interpretable models of protein structures that could reflect the underlying biophysical function. The resulted biophysically grounded models will be used to develop generative models to design proteins with desired function.
This project will involve development of novel AI techniques suitable for large scale analysis of protein 3D structures.
Position 2: Statistical physics of immune system
The adaptive immune system incorporates all aspects of life, from molecular signaling to cellular evolution. The result is an information processing molecular organization with many interacting components, which can reliably sense and adaptively respond to diverse and evolving pathogens. The vast differences in immune repertoires between individuals suggest the existence of many molecular solutions to statistically similar pathogenic environments. In this project, we aim to understand the organization and encoding in the adaptive immune system, using high-throughput molecular data and statistical modeling.
Duration: The initial 12-month appointments are renewable for up to 5 total years.
Skillset: Successful applicants will have strong quantitative and computational skillset. They will have a PhD in a relevant field (e.g. Theoretical Physics, Applied Math, Computer Science, Computational biology) or will be on track to obtain one before joining the lab. Previous work in biology is not necessary but the applicant should be committed to work in a multidisciplinary team. They must have strong written and oral communication skills and commitment to working as part of a constructive, productive team.
Application: To apply for these postdoctoral positions, please email a research statement, CV, contact information for at least three references, and relevant publications/preprints to armita@uw.edu. In your statement please describe your research interests and why you are a suitable candidate to lead any of the above projects.
Members of the underrepresented groups are strongly encouraged to apply.
Review of candidates will begin immediately and continue until the position is filled.
General Openings:
We are always looking for enthusiastic Bachelor/Master/PhD students and Postdocs to join our group at the University of Washington.
Graduate students must enroll via one of the graduate programs (physics, MCB,…) at UW.
To inquire about potential positions, please submit your CV and a short research statement, describing your interests and why you want to join our group.