Scientist, Informatics Jobs

The Genomics Research Center (GRC) is a center of excellence for genetics and genomics that supports both Discovery and Development. The GRC plays an integral role towards our goal of developing extraordinary genetics and genomics research, focusing on finding the right targets and helping us better understand not only human disease biology but also the behavior of and response to our drugs in clinical trials. Within the GRC, the Department of Bioinformatics is responsible for data analysis and provides analytical insight for both internal and external data. This involves the identification and characterization of underlying genetic, epigenetic, or genomic factors that are associated with disease diagnosis, prognosis, and response (efficacy and safety) to drug treatment, identification of new targets, and interpretation of the impact of genetic and genomic evidence from population-based studies. To attend to these challenges, we have an exciting opportunity for a Bioinformatics Engineer, embedded within the GRC’s Computational Oncology bioinformatics group in a hybrid arrangement at AbbVie’s South San Francisco, CA location. The candidate will work closely with computational biologists and research project teams to develop analytical pipelines, databases, and scientific applications for the GRC.
Responsibilities

• Demonstrated experience with software devops and CI/CD processes.
• Build the infrastructure required for optimal extraction, transformation, and loading of data from a wide variety of data sources using SQL and AWS ‘big data’ technologies.
• Strong communication skills in a collaborative environment.
• Demonstrated experience working with the Arvados genomic data management and processing platform.
• Demonstrated AWS Data Platform experience: S3, EC2, Dynamo, RDS
• Identify, design, and implement internal process improvements: automating manual processes, optimizing data delivery, re-designing infrastructure for greater scalability, etc.
• Develop and support NGS pipelines using scientific workflow language via best practices, including unit testing, CI/CD, containerization, and code reviews.
• Demonstrated NGS bioinformatics pipeline development experience with the CWL (Common Workflow Language).
• Demonstrated experience across multiple tiers of an application, including a database, network, operating system, and containers.
• Design, develop and maintain Application Programming Interfaces (APIs), microservices, and asynchronous queuing systems.
• Bachelor’s or Master’s in computer Science, data scientist/engineering, bioinformatics, or related field. With at least 2-5 (BS) or 2+(MS) years of relevant experience.
• Familiarity with standard tools and data formats related to genomics resequencing projects processing and analysis.
• Work with bioinformatic scientists as the stakeholders to assist with data-related technical issues and support their data infrastructure needs.

Preferred:

• Fluency in 1 or more relevant programming languages (e.g., Python, R)
• Experience developing somatic variant detection and QC pipelines.
• Additional scientific workflow language experiences such as Nextflow, or Snakemake

AbbVie is an equal opportunity employer including disability/vets. It is AbbVie’s policy to employ qualified persons of the greatest ability without discrimination against any employee or applicant for employment because of race, color, religion, national origin, age, sex (including pregnancy), physical or mental disability, medical condition, genetic information, gender identity or expression, sexual orientation, marital status, status as a disabled veteran, recently separated veteran, Armed Forces service medal veteran or active duty wartime or campaign badge veteran or a person’s relationship or association with a protected veteran, including spouses and other family members, or any other protected group status. We will take affirmative action to employ and advance in employment qualified minorities, women, individuals with a disability, disabled veterans, recently separated veterans, Armed Forces service medal veterans or active-duty wartime or campaign badge veterans. The Affirmative Action Plan is available for viewing in the Human Resources office during regular business hours.