Research Scientist

Ideal Candidate

You thrive on discovery through computation, enjoy teaching others, and have:

• Strong bioinformatics skills: comfort with BLAST/HMMER searches, multiple‑sequence alignment, and scripting.
• Competency in Unix and Python (additional languages welcome).
• An eye for detail, strong organizational and communication skills, and a desire to learn new techniques.
• Self-motivation with an ability to perform complex tasks effectively and independently with general instruction, while embracing teamwork and mentorship.

There is potential for long-term professional growth, including increased responsibility, leadership roles, authorship on manuscripts, and career advancement within the lab.

Key Responsibilities

• Under the direction of the Principal Investigator, design and execute protein bioinformatics projects. Duties include mining public databases for homologs via BLAST/HMMER; performing sequence alignment and phylogenetic tree construction with software such as IQ‑TREE, PAML, or FastML. Most necessary training will be provided.
• Work closely with experimental colleagues to guide downstream wet‑lab validation. 
• Write clean, well‑documented Python/Bash scripts and manage them with Git.
• Optimize jobs on HPC clusters (e.g., SLURM) and oversee data backup/archiving.
• Create concise training manuals and teach students and staff on BLAST, sequence alignments, phylogenetics, and Unix/Python fundamentals.
• Keep meticulous Jupyter notebooks, stay current with literature, analyze results, and contribute to manuscripts, figures, and grant proposals.
• Participate in weekly meetings, help plan future projects, and foster an inclusive, supportive environment.

Minimum Qualifications

• Bachelor’s degree in bioinformatics, computational biology, computer science, molecular biology, or a related field

Preferred Qualifications

• Master’s, PhD, or extensive research experience emphasizing bioinformatics, phylogenetics, or machine learning.
• Hands‑on experience with BLAST (or HMMER), sequence alignment tools (e.g., MAFFT, Clustal Omega, MUSCLE), and basic Unix command‑line usage.
• Proficiency in Python for data processing and visualization.
• Practical experience with phylogenetic software (IQ‑TREE, RAxML, PhyML) and downstream analyses.
• Familiarity with HPC environments, workflow managers (Snakemake/Nextflow), and containerization (Docker/Singularity).
• Working knowledge of protein biochemistry or structural biology concepts.
• Demonstrated teaching or mentoring experience and strong presentation skills.
• Excellent organizational, record‑keeping, and time‑management abilities.

This position may be subject to a Level 1 or Level 2 criminal background check 

Applicants for USF employment are entitled to request reasonable accommodation(s) in the application process. A request is to be made at least five (5) working days prior to the time the accommodation(s) is needed. Contact the USF ADA Lead (hr-ADA-Request@usf.edu) to coordinate your accommodation request.

The University of South Florida is a high-impact global research university dedicated to student success. Over the past 10 years, no other public university in the country has risen faster in U.S. News and World Report's national university rankings than USF. Serving more than 50,000 students on campuses in Tampa, St. Petersburg and Sarasota-Manatee, USF is designated as a Preeminent State Research University by the Florida Board of Governors, placing it in the most elite category among the state's 12 public universities. USF is a member of the American Athletic Conference.

Working at USF 

With more than 16,000 employees at USF, the University of South Florida is one of the largest employers in the Tampa Bay region.  At USF you will find opportunities to excel in a rich academic environment that fosters the development and advancement of our employees.  We believe in creating a talented, engaged and driven workforce through on-going development and career opportunities. We also offer a first class benefit package that includes medical, dental and life insurance plans, retirement plan options, tuition program and generous leave programs and more.

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