Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. However, microbial sRNAs have been primarily studied in model organisms and very little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. The goal of this project is to investigate the roles of regulatory sRNAs in the stress response of extremophile communities and their ability to cope with environmental changes.

In a top-down approach, we are using high-throughput multi-omics and a well-characterized microbial community inhabiting halite nodules (salt rock) as our model system (see Uritskiy et al., ISMEJ 2019). Enrichment cultures grown in the lab are also used to experimentally validate sense-and-respond mechanisms to perturbation revealed by molecular analyses of the natural communities. This work is in collaboration with scientists at NASA Ames and will require field work in the Atacama Desert, Chile. The position is for 2 years and is funded by NASA.

Qualified candidates will be enthusiastic, highly motivated, and will possess a demonstrable understanding of bioinformatics and computational biology with a background in molecular biology and/or microbial ecology. The candidate will have a doctoral degree in Genetics, Biology, Microbiology, Computer Science or a related field. Experience with whole metagenome assembly (not just 16S rDNA), functional annotation, and metatranscriptomics analysis is essential. Programming and statistical skills in languages such as Perl, Python, and R are also required.

How to Apply

Please send at

  • Letter of Interest, addressing the stated required skills for the position, research interests, and career goals
  • Detailed resume listing education and describing research experience
  • Names and contact information for three (3) professional references

For more information about our research, visit the lab website at

Application deadline:
Start date: ASAP
Location: Johns Hopkins University, Baltimore, MD, USA