Research Scientist

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Position Overview
The Research Scientist will independently contribute to cutting‑edge research on
* Borrelia burgdorferi
* and vector‑borne mechanisms of phage‑mediated genetic exchange in the tick–mouse model of Lyme disease. The role requires exceptional interdisciplinary expertise across microbial genomics, bioinformatics, molecular microbiology, and animal‑associated infection biology.

Duties and Responsibilities Research Design, Execution, and Innovation

• Independently design and conduct hypothesis‑driven experiments relevant to phage induction, plasmid recombination, cp32 dynamics, antigenic variation, and
  * Borrelia* pathogenesis.
• Develop new methodological approaches—both experimental and computational—to investigate surface‑protein diversity, recombination events, and mobile genetic elements within the Lyme disease system.
• Lead multiple concurrent research efforts requiring the integration of genomics, wet‑lab experimentation, and animal‑model data.

Genomics, Bioinformatics, and Computational Systems

• Develop, deploy, and maintain high‑throughput computational pipelines (Python, Bash, Linux/Unix) for Illumina, Nanopore, and hybrid genome assembly workflows.
• Perform comparative genomics on plasmids, phages, and mobile genetic elements; identify CRISPR arrays, anti‑phage systems, recombination events, and patterns of genome plasticity.
• Build custom visualization tools (e.g., Plotly‑Dash dashboards) for data presentation and public‑facing analytics.
• Administer and maintain laboratory servers, software environments, containerized workflows, and data storage systems supporting large‑volume sequencing datasets.
• Develop and maintain relational data structures for sequencing metadata, phenotypic data, strain collections, and analytical outputs.

Molecular Microbiology And Wet‑Lab Capabilities

• Perform complex molecular biology workflows including recombinant DNA methods, cloning, PCR/qPCR, DNA/RNA extraction, sequencing library construction, and phage purification.
• Maintain and characterize diverse bacterial isolates, including plasmid‑bearing strains, mutants, and engineered lines.
• Develop protocols and SOPs for advanced laboratory techniques such as inducible phage purification, genomic library preparation, and molecular characterization of phage/host interactions.

Vector‑Borne and Animal Model Experiments

• Support tick–mouse model experiments, including tick feeding, infection establishment, tissue harvesting, recovery of spirochetes, and downstream genomic analyses.
• Conduct mouse infection procedures (e.g., inoculation, monitoring, tissue collection) under IACUC protocols with high precision and strong documentation.
• Integrate in vivo results with genomic and molecular datasets to analyze phage induction, recombination, immune evasion, and strain competitiveness.

Leadership, Mentoring, and Training

• Mentor and supervise undergraduate and graduate students in experimental design, molecular biology, microbiology, computational analysis, and data visualization.
• Develop and deliver training modules or short workshops to onboard new researchers in laboratory procedures and computational tools.
• Provide day‑to‑day guidance to junior personnel, fostering a collaborative, rigorous, and supportive research environment.

Scholarly Writing, Reporting, and Grant Support

• Contribute substantially to manuscripts as a lead or co‑author, including data analysis, figure preparation, and methods writing.
• Prepare reports for funded federal grants, including progress summaries, data figures, and computational workflows.
• Assist in the conception and writing of new grant proposals, generating preliminary data and novel computational methods where needed.
• Present research findings at internal meetings, national conferences, and collaborative project discussions.

Required Qualifications – Experience, Education, Knowledge & Skills

• Ph.D. in Microbiology, Molecular Biology, Bioinformatics, Computational Biology, or a closely related discipline.
• Demonstrated excellence in genomic data analysis, including short‑read and long‑read assembly,…