Research Data Analyst 2- Hybrid - 141446

University of California - San Diego Medical Centers; San Diego (CA); On-site; USD 90,000 - 120,000; Full time

Job summary

University of California - San Diego Medical Centers seeks a bioinformatics specialist to build and optimize computational pipelines for sequencing and genotyping in HPC and cloud environments. You will document workflows, ensure data quality, and contribute to data reporting across research projects.

The role requires strong scripting in Bash, Linux expertise, and experience with tools like PLINK, GATK, HipSTR and BEAGLE, plus programming in Python and R.

Qualifications

• Six years of related experience, education/training, OR a Bachelor's degree in related area plus two years of related experience/training.
• Working knowledge of research function.
• Working skills in statistical analysis, systems programming, database design and data security measures.
• Working skills in analysis and consultation.
• Skills to communicate complex information clearly in writing and speech.
• Knowledge of bioinformatics software related to sequencing and genotyping, with staying current in the field.
• Experience planning and conducting studies related to genotyping and genotyping QC, optimizing pipeline parameters.
• Knowledge of Linux-based workflow development, including Bash scripting.
• Experience developing multistep analysis pipelines/workflows using scripting languages including WDL.
• Experience handling big data sets; programming in R and Python.
• Knowledge of Linux, HPC, cloud technologies such as Amazon EC2, and the All of Us Research Workbench.
• Ability to manage time and complete assigned parts on deadline.
• Excellent communication skills.
• Working knowledge of sequencing and genotyping software such as Bcftools, Bedtools, FastQC, Plink, Vcftools.
• Documentation and code annotation proficiency; experience with Git.
• Experience performing genome-wide analysis of tandem repeats in human populations.

Responsibilities

• Build computational pipelines to perform sequence analysis and genotyping in HPC and cloud compute environments.
• Develop new pipelines under supervision, selecting software and testing different computational approaches.
• Document work and annotate code; organize and backup data.
• Handle research data reporting tasks of moderate diversity in scope and provide results under supervision.

Skills

Bash scripting

Linux

Bioinformatics pipelines

Genotyping analysis

GATK

PLINK

HIPSTR

BEAGLE

Python

R

Data security

Big data handling

Education

Bachelor's degree in related area

Tools

GIT

HPC

Cloud computing platforms

Amazon EC2

Job description

DESCRIPTION

Department of Pediatrics is one of the largest departments within the UCSD School of Medicine with comprehensive clinical programs, extensive basic science and clinical research, and diverse educational opportunities for students, residents and fellows. The internationally renowned faculty play a major role in medical and graduate student training, providing educational and programmatic offerings that span several disciplines and provide diversity to meet the interests of a broad spectrum of students and scholars. More than one hundred trainees at the graduate student and postdoctoral level, as well as more than 300 professional, research and administrative staff who along with the department administrators interact closely with the faculty. The diverse mix of ages, backgrounds, and talents creates a robust work environment with challenging career opportunities and a commitment to continued growth potential. We constantly seek to recruit highly motivated, technologically advanced and interested individuals to become a part of our dynamic cutting-edge research, clinical, and educational environment.

Under supervision, uses skills and knowledge of professional concepts in research data analysis. The main responsibility is building computational pipelines to perform sequence analysis and genotyping of humans and model organisms in HPC and cloud compute environments. 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. Performs other duties as assigned.

MINIMUM QUALIFICATIONS

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

• Working knowledge of research function.

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

• Working skills in analysis and consultation.

• 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 including WDL.

• 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, and the All of Us Research workbench.

• Proven ability to effectively manage time and see assigned parts of projects through to completion on deadline.

• 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).

• Experience performing genome-wide analysis of tandem repeat variation in human populations.

SPECIAL CONDITIONS

• Employment is subject to a criminal background check.

Pay Transparency Act

Annual Full Pay Range: Unclassified - No data available (will be prorated if the appointment percentage is less than 100%)

Hourly Equivalent: Unclassified - No data available

Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable).