Postdoctoral Scholar Research

Bioinformatics Position

Dr. P. Dreux Chappell at the University of South Florida College of Marine Science invites applications to fill a bioinformatics position investigating marine metagenomes and metatranscriptomes from samples collected in the Pacific Ocean in conjunction with US GEOTRACES Cruises GP15 and GP17-OCE. This project is collaborative with Dr. Sophie Clayton at the National Oceanography Centre (NOC) in the UK.

Project Overview:

The overarching goal of the project is to characterize phytoplankton realized niches and nutrient limitation status across the full latitudinal range of the Pacific Ocean using a combination of amplicon sequencing and metagenomic and metatranscriptomic analyses from samples collected concurrently with trace element and isotope (TEI) data on GEOTRACES cruises GP-15 and GP17-OCE (~1.25° resolution). We will use these field data to construct species distribution models (SDM) to infer the realized niches of oceanic phytoplankton, with a particular focus on micro-nutrients, e.g., dissolved iron (dFe).

We will develop and combine 'omics-derived nutrient limitation indices (NLIs) with environmental data to train supervised machine learning (ML) models to extrapolate basin-wide patterns of nutrient limitation status for phytoplankton functional types (PFTs). Our goal is to assess the feasibility of using routinely measured Essential Ocean Variables (EOVs) from existing databases and remote-sensing products to produce dynamic maps of PFT-specific NLI using ML models developed as part of this project.

Research Responsibilities:

The focus of the postdoctoral scholar's work will be to analyze metagenomic and metatranscriptomic samples to evaluate nutrient limitation of phytoplankton in the context of environmental data, including macro- and micronutrient concentrations and isotope values collected by other GEOTRACES researchers. Additionally, the postdoctoral scholar will use this information to develop the NLIs and work with the postdoctoral scholar at NOC to use the NLIs and environmental data in training the supervised ML models.

Salary and

Start Date:

This position is available as of September 1, but there is flexibility in start date. Applications will be reviewed until the position is filled. An annual salary of $60,000 plus benefits is budgeted. Initial appointment will be for one year, with re-appointment anticipated for a total of three years.

Career Development:

The successful candidate will be expected to present research results at national and international scientific meetings, lead the publication of scientific results in a peer-reviewed journal, and be encouraged to participate in the preparation of at least one NSF proposal. USF has an Office of Postdoctoral Affairs managed by USF Graduate Studies. The postdoctoral researcher will be encouraged to attend workshops/seminars on Developing Individual Development Plan (IDP) and preparing teaching/research statements.

Minimum Qualifications:

• Doctoral degree from an accredited institution in biology, microbiology, cell biology, computational biology, bioinformatics, genetics, molecular biology, oceanography, marine sciences, or related field at the time of appointment.
• Demonstrated research skills in genomics and/or transcriptomics
• Familiarity with high-performance computing (HPC) environments, Python scripting, and Git Hub for version control
• Demonstrated ability to write and publish papers

Preferred Qualifications:

• Experience analyzing transcriptome and genome data from non-model organisms with poorly annotated genomes.
• Experience working with marine microbe metagenomes/metatranscriptomes.
• Experience with high-performance computing systems.

Working at USF

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