DESCRIPTION

The Department of Medicine is responsible for fulfilling the teaching, research, and clinical missions of the University of California, San Diego and employs 500+ full-time salaried faculty members and 150+ academic appointees. Staff personnel include 800+ staff in 9 bargaining units, students, and volunteers. There are over 250 clinical faculties practicing at multiple sites and hospitals.

The Gymrek Lab http://gymreklab.com/ is performing genomics research to understand the contribution of complex genetic variation to a variety of traits and diseases in humans and model organisms.

Under supervision, acquires skills and knowledge of professional concepts in research data analysis. Works on small projects or segments of projects with limited scope and complexity. The main responsibility is building computational pipelines to perform sequence analysis and genotyping of humans and model organisms. This includes pipelines based on the established computational workflow, using Bash scripting and software such as PLINK, GATK, HipSTR, and BEAGLE; performing routine quality control for data inputs and analysis outputs, assisting with data organization and backup. Additional responsibility will include developing new pipelines, which require, under supervision, selecting software and testing different computational approaches.The successful applicant will have exceptional written and verbal communication, will carefully document their work and annotate their code. Excellent organization skills are required in order to work as part of a team.

Works on research data reporting assignments that are of moderate diversity in scope. Exercises judgment within generally defined practices and policies in selecting methods and techniques for obtaining solutions.

MINIMUM QUALIFICATIONS

• Six (6) years of related experience, education/training, OR a Bachelor's degree in related area and two (2) years of relevant experience/training.

• Thorough working knowledge of research function.

• Working skills in statistical analysis, systems programming, database design and data security measures.

• Demonstrated working skills in analysis and consultation.

• Strong skills to communicate complex information in a clear and concise manner both verbally and in writing.

• Knowledge of bioinformatics software related to sequencing and genotyping, ability to stay abreast of the recent developments in the field.

• Proven ability to plan and conduct studies related to genotyping and genotyping quality control, optimize parameters in the bioinformatics computational pipelines.

• Knowledge of Linux-based workflow development, including Bash scripting.

• Extensive experience in developing multistep analysis pipelines/workflows using scripting languages.

• Demonstrated experience in handling big data sets, experience in programming languages, including R, Python.

• Knowledge of Linux, High-Performance Computing, cloud technologies such as Amazon EC2.

• Excellent communication skills.

• Working knowledge of sequencing and genotyping-related software such as Bcftools, Bedtools, FastQC, Plink, Vcftools.

• Proven ability to carefully document the work and annotate the code.

• Experience in using software revision control systems (e.g. GIT).

PREFERRED QUALIFICATIONS

• Academic courses in statistical analysis, computational biology, molecular biology, genetics.

SPECIAL CONDITIONS

• Employment is subject to a criminal background check.