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Bioinformatician Research Assistant/Associate - Plesa Lab

Apply now Job no: 527812
Work type: Faculty - Pro Tempore
Location: Eugene, OR
Categories: Research/Scientific/Grants, Engineering/Biomedical Engineering

Department: Knight Campus
Rank: Research Assistant
Annual Basis: 12 Month

Review of Applications Begins
August 5, 2021; position open until filled.

Special Instructions to Applicants
Along with your online application, please upload a CV and cover letter.

Department Summary
The Knight Campus for Accelerating Scientific Impact is a billion-dollar initiative designed to fast-track scientific discoveries and the process of turning those discoveries into innovations that improve the quality of life for people in Oregon, the nation and beyond. The Knight Campus will reshape the higher education landscape in Oregon by training the next generations of scientists, forging tighter ties with industry and entrepreneurs, and creating new educational opportunities for graduate and undergraduate students.

Position Summary
The Plesa research lab is seeking a research assistant/associate specializing in bioinformatics or computational biology to join the lab. This position will include:
• Analysis of NGS data from multiplex functional assays (developing, testing, and optimizing analytical pipelines)
• Analysis of large-scale datasets of protein function
• Improvement of design software for gene synthesis and oligo design
• Algorithm development for large-scale protein engineering
• Developing software for sequence optimization and new molecular biology methods
• Developing regression and classification models for high-dimensional data

This position will work closely with other lab researchers (students, postdocs, and technicians) and with Dr. Plesa. The position will be given a level of independence depending on the level of candidate experience.

The Plesa lab aims to accelerate the pace at which we understand and engineer biological systems, particularly proteins. We are interested in uncovering the rules for the engineering of novel protein function, particularly in the areas of sensing and interfacing with engineering. Towards this end, we develop new technologies for gene synthesis, multiplex functional assays, in-vivo mutagenesis, and genotype-phenotype linkages. These allow us to both access the huge sequence diversity present in natural systems as well as carry out testing of rationally designed hypotheses encoded onto DNA at much larger scales than previously possible. Using these approaches, we aim to quickly characterize and engineer entire protein families, rather than focusing on individual proteins. Our work is highly interdisciplinary and touches on aspects from many fields including bioengineering, protein engineering, biochemistry, synthetic biology, molecular biology, microbiology, structural biology, genetics, bioinformatics, and quantitative biology.

Minimum Requirements
Research Assistant:
• Bachelor's degree in Computer Science, Bioinformatics, Statistics, Mathematics, Bioengineering, Biochemistry, Biology, Biophysics, Physics, Chemistry, Chemical Engineering, or related disciplines
• Five years’ experience in computational biology / bioinformatics / software development

Research Associate:
• Terminal degree in Computer Science, Bioinformatics, Statistics, Mathematics, Bioengineering, Biochemistry, Biology, Biophysics, Physics, Chemistry, Chemical Engineering, or related disciplines

Professional Competencies
• High proficiency with Python and R scientific programming languages
• Familiarity with command-line Linux
• Strong understanding of modern scientific computing and data science tools, including high-performance computing environments.
• Expertise in the analysis of next-gen sequencing data
• Strong grasp of relevant biology, molecular biology, and statistics concepts
• Excellent organizational, written, and verbal communication skills
• Ability to work both independently, in a small group setting, and one-on-one with students, other staff, and collaborators in a positive and productive manner

Preferred Qualifications
• Experience in algorithm development, data mining, and statistical analysis of large datasets
• Familiarity of sequence-based analysis of proteins (phylogenetic tree generation, multiple sequence alignment, BLAST, pfam, etc.)
• Python software development


The University of Oregon is proud to offer a robust benefits package to eligible employees, including health insurance, retirement plans and paid time off. For more information about benefits, visit http://hr.uoregon.edu/careers/about-benefits.

The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status. The University is committed to providing reasonable accommodations to applicants and employees with disabilities. To request an accommodation in connection with the application process, please contact us at uocareers@uoregon.edu or 541-346-5112.

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Applications close:

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