Machine learning/computational biology postdoc in bacterial genomics

We will be filling this position as soon as possible, for full consideration please apply by August 15, 2020

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 ~250,000 genomes then use that information to train disentangled variational autoencoders to create reduced representations of genome space and synthetic data for training neural networks for phenotype prediction and antimicrobial resistance. The same data will be used for active learning to train models for sanitizer 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. Improving methods of detection will help to reduce outbreaks.

Desired Skills

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

  • computer science, machine learning, applied math, computational biology or bioinformatics.
  • This position focuses on the development of applications for analysis of this data and the publication of software tools. A successful candidate will likely have some experience in version control, data structures, ML frameworks like Keras, Tensorflow, or PyTorch and proficiency in Python.
  • The applicant should have a good understanding of 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 federal government position and compensation includes competitive postdoctoral pay starting at $64,009 for GS-11 Step 1, Medical, Dental, TSP (401K-like plan with 5% employer match), FERS Pension. The position is fully funded for 4 years.

Due to funding restrictions, the position is only open to US citizens or permanent US residents seeking citizenship.

The position is located in Gainesville, FL at the USDA Agricultural Research Service lab and the University of Florida Emerging Pathogens Institute. While relocation may ultimately be required the position could be started remotely due to the COVID19 maximum telework policy.

Interested? Email me today.

USDA/ARS is an equal opportunity provider and employer.