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
Appointment: 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.
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: http://policy.ucop.edu/doc/4000376/NondiscrimAffirmAct. The department is interested in candidates who will contribute to diversity and equal opportunity in higher education through their work.
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