Job ID: 140546

Assistant/Associate Project Scientist Bioinformatician in Microbial Genomics - Department of Plant and Microbial Biology

University of California Berkeley

  • Mar. 23, 2020
  • Assistant/Associate Project Scientist Bioinformatician in Microbial Genomics - Department of Plant and Microbial Biology
  • University of California Berkeley
    Berkeley, CA
  • 4/24/2020
  • Available immediately
  • Research Scientist/Associate
  • Biology - Microbiology

Assistant/Associate Project Scientist Bioinformatician in Microbial Genomics - Department of Plant and Microbial Biology

Dr. Kim Seed in the Department of Plant and Microbial Biology at the University of California, Berkeley invites applications for an Assistant or Associate Project Scientist in the area of bioinformatic approaches to microbial genomics, at 100% time starting Spring of 2020.

The Seed Laboratory studies how predation by bacteriophages impacts the evolution of the bacterial pathogen Vibrio cholerae. Studies in the Seed Lab have identified novel molecular mechanisms of phage defense in epidemic V. cholerae and reciprocal adaptations in phages that permit their long-term persistence in cholera endemic areas.

The candidate will provide significant support to the Seed Lab by leading research focusing on the analysis of next-generation sequencing (NGS) data sets (primarily whole genome sequencing). This project will include comparative genomics of bacteria and phages to formulate hypotheses underlying how bacteria and phage co-evolve.

Responsibilities in the Seed Lab will include;
  • Conceive of, design and execute research projects employing bioinformatics analyses of NGS data sets to advance the lab's overall research goals
  • Provide bioinformatic support to other researchers in the lab including NGS analysis and the development of custom scripts
  • Prepare papers for publication as both lead author and in supporting roles
  • Provide technical guidance and oversight to graduate and undergraduate students

Basic Qualifications (At the time of application):
  • Ph.D. or equivalent international degree, or enrollment in Ph.D. program or equivalent international program

Additional Qualifications (By start date):
  • Ph.D. or equivalent international degree

Preferred Qualifications (By start date):
  • A broad understanding of key bioinformatics concepts and algorithms, e.g., BLAST, sequence alignment, phylogenetic reconstructions, sequence assembly, read mapping, etc
  • Demonstrated experience with conception, design and execution of custom pipelines for NGS sequencing data analysis workflows
  • Fluency in Python, R or similar and ability to implement standard statistical analyses
  • Database management, basic IT infrastructure maintenance, familiarity with HPC environments
  • Exceptional organizational skills to manage many large overlapping data sets
  • Demonstrated ability to critically evaluate the primary literature. Strong analysis and problem-solving skills with ability to multi-task
  • Knowledge of core microbiology concepts (including phage biology) and wet-lab techniques a strong plus
  • Familiarity with external databases and tools such as NCBI Entrez, SRA and ENA PhD in microbiology, computational biology, molecular biology, bioinformatics or a related field with 2+ years of work experience
  • Record of publication in peer-reviewed journals

This position reports to Professor Kim Seed. The initial appointment will be at 100% time for one year with the possibility of extension based on performance and availability of funding.

Salary and Benefits:
This position provides full benefits.
Salary will be commensurate with qualifications and experience and based on UC Berkeley Project Scientist series salary scale.

To Apply:

Please direct questions to Professor Kim Seed,
For inquiries of an administrative nature, contact Zoe Stone at

This recruitment will remain open until filled.

Berkeley seeks to advance diversity, equity, and inclusion.
The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see:
The department is interested in candidates who will contribute to diversity and equal opportunity in higher education through their work.

Please reference in your cover letter when
applying for or inquiring about this job announcement.

Contact Information

  • N/A
    University of California Berkeley

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