Computational biology postdoc: machine learning and Salmonella bacterial genomics

We will be filling this position as soon as possible. For full consideration please apply by June 15, 2022

Position description

This is a postdoc position to develop new Salmonella typing and phenotype prediction methods from genomes and metagenomes using population genomics and machine learning. The project is novel in a number of ways. We will be using graph representations to identify polymorphisms in 325,000 genomes then use that information to train graph neural networks for genotyping and the prediction of sanitizer and antimicrobial resistance. The same data will be used for active learning to train models for sanitizer and antibiotic resistance. Because of the genome size and the number of genomes, Salmonella is a great system to develop new non-linear polygenic scoring models that could have a major impact on other areas of genomics.

Salmonellosis is also a serious disease that sickens 1 million Americans a year and causes billions in economic losses. This work will be used to develop new methods for metagenomic Salmonella detection and characterization. It is also the first step in developing new rapid diagnostics that can genotype Salmonella on the farm or at the point-of-care without culturing.

Desired Skills

I anticipate that a successful applicant will have an interest or experience in:

  • Computer science, microbiology, machine learning, computational biology or bioinformatics
  • The applicant should have experience in statistics

I recognize that each person has a unique mix of experience and individual strengths and I encourage any applicant with a strong record of research productivity and relevant experience to apply, even if your mix of skills is different than what is listed above.

This is a non-permanent U.S. federal government position and compensation includes competitive postdoctoral pay starting at $66,214 for GS-11 Step 1, Medical, Dental, TSP (401K-like plan with 5% employer match), FERS Pension. The position is fully funded for up to 3 years.

Due to funding restrictions, the position is only open to US citizens.

The position is located in Gainesville, FL at the USDA Agricultural Research Service lab and the University of Florida Emerging Pathogens Institute. The position is eligible for 80% telework.

How to apply

Interested? Email me your CV today.

USDA/ARS is an equal opportunity provider and employer.