Bioinformatics Research Scientist, Division of Infectious Diseases and International Health

The Division of Infectious Diseases and International Health is seeking a talented and passionate Bioinformatics Research Scientist to support ongoing bioinformatics analysis needs. The individual will integrate their knowledge and experience into current research and clinical efforts undertaken by two investigators, especially in analyzing large-scale genomic data with a focus on its applications in the field of microbiology. There will be an expectation for research and development in public health emerging pathogen genomics with applications in metagenomics, comparative microbial genomic and mobile genetic elements. There will also be a need to maintain and develop, document, and validate comparative genomic analysis for speciation as well as strain comparison. The candidate will need to collaborate closely with the wet lab technologists and be comfortable handling appropriate private health information required with the clinical work. Overseeing the training of another bioinformatics scientists in running and maintaining the computing pipelines will be expected.

Development in the area of pathogen genomics would be welcome and encouraged. This can include long read plasmid analysis and comparison to understand mobile resistance, metagenomics, antimicrobial resistance evaluation, data sharing, and development in computing efficiencies/pipeline development. There would also be opportunities for collaboration with public health, biocomplexity institutes, and hospital epidemiology.

The candidate will have the opportunity to collaborate with additional faculty and public health leaders through the CDC Pathogen Genomic Center of Excellence on multiple distinct projects including microbiome, microbe strain relatedness, and developing and designing queries for virulence and resistance genes. The candidate is expected to work on the university-shared high-performance computing infrastructure that is tailor designed to address the substantial processing, networking, and data moving challenges arising from genomic science. The candidate will also be responsible for writing manuscripts describing their work and presenting at national/international conferences.

Essential Duties and Responsibilities:

• Collaborate extensively with Investigators and Faculty on all aspects of their research projects, from experimental design to data processing/analysis/visualization/exploration, as well as downstream statistical analysis for biological insights
• Develop and implement automated NGS analysis workflows for genomic/metagenomics datasets
• Ability to adapt to the highly dynamic nature of the bioinformatics field and contribute to the evaluation, testing, and implementation of new software packages and algorithms
• Act as a liaison to various data science sections across the University of Virginia, including the health system data warehouse teams and the academic research computing teams
• Provide bioinformatics consulting and data analysis/visualization support to various faculty. Train/mentor/supervise junior researchers who are interested in learning the recent developments in bioinformatics tools
• In addition to the above job responsibilities, other duties may be assigned.

Required Knowledge & Skills:

• Understanding of next generation sequencing technologies and their applications, including Illumina, Nanopore, and PacBio platforms, is a must
• Strong knowledge of working in a Linux environment; experience working on a high-performance computing cluster is desirable
• Advanced proficiency in Python, Perl, or another scripting language
• Advanced proficiency in R/Python (or other), for data management, data visualization and statistical analysis
• Experience in using common open-source bioinformatics tools for analyzing next-generation sequence datasets
• Prior experience working with prokaryotic whole genome sequencing data is desirable
• Prior experience working with metagenomics/metatranscriptomics datasets for microbiome research is desirable
• Familiarity with both structured (SQL) and/or unstructured (no-SQL) databases is desirable; not required
• Prior experience using a workflow management system like Nextflow/Snakemake/WDL-Cromwell to setup, execute and monitor complex bioinformatics pipelines is desirable
• Familiarity using version control tools like Git/Github
• Motivated, independent and highly organized
• Excellent written and oral communication skills

Qualified candidates must have a Ph.D in computational biology, microbial genetics, bioinformatics, computer science, or a related field. A minimum of 2 years of related experience is preferred.

This position is located in Charlottesville, VA.

This is a restricted position; continuation is dependent on funding and satisfactory performance.

This position will remain open until filled. The University will perform background checks on all new hires prior to employment. A completed pre-employment health screen is required for this position prior to employment.

To Apply:

Please apply through Workday , and search for R0042263. Complete an application online with the following documents:

• CV
• Cover letter
• Contact information for 3 references

Upload all materials into the resume submission field, multiple documents can be submitted into this one field. Alternatively, merge all documents into one PDF for submission. Internal applicants must apply through their UVA Workday profile by searching 'Find Jobs'.

For questions about the application process, please contact Jessica Russo, Recruiter, at sxv9zv@virginia.edu .

For more information about UVA and the Charlottesville community please see http://www.virginia.edu/life/charlottesville and https://embarkcva.com/ .

COVID Vaccination Requirement and Guidelines

Please visitthe UVA COVID-19 Job Requirements and Guidelines webpageprior to applying for current information regarding vaccination requirementsandguidelines for employment at UVA.

The University of Virginia, i ncluding the UVA Health System which represents the UVA Medical Center, Schools of Medicine and Nursing, UVA Physician’s Group and the Claude Moore Health Sciences Library, are fundamentally committed to the diversity of our faculty and staff. We believe diversity is excellence expressing itself through every person's perspectives and lived experiences. We are equal opportunity and affirmative action employers. All qualified applicants will receive consideration for employment without regard to age, color, disability, gender identity or expression, marital status, national or ethnic origin, political affiliation, race, religion, sex (including pregnancy), sexual orientation, veteran status, and family medical or genetic information.