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 world class 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. The scale and complexity of these projects present unique engineering challenges.  To attend to these challenges, we have an exciting opportunity for a Senior Engineer, Bioinformatics, embedded within the GRC’s Computational Oncology group in a hybrid arrangement at AbbVie’s new South San Francisco location.  The candidate will manage engineers, work closely with computational biologists and research project teams to develop analytical pipelines, databases, and scientific applications for the GRC.  

Key Responsibilities

• Supervise team of 3 engineers, perform annual evaluations and support professional development.  Perform balancing and prioritization of engineering project work for regional GRC divisions.
• Interface with Computational Oncology Bioinformaticians and Analysts to optimize existing pipelines, workflows, and systems, as well as engineer new pipelines, workflows, and systems
• Translate and implement algorithms and protocols for on-prem or cloud-based high performance computing environments
• Develop and maintain structured data repositories in for computational reassessment and record keeping with accompanying API or web-based front-end access
• Provide sub-team personnel leadership through task and project prioritization and support
• Interface with research-serving IT teams to assure sufficient HPC resource availability to support bioinformatic data processing and analysis

• Sr.Scientist II -  BS, MS, or Ph.D in Bioinformatics, Software Engineering, Computer Science, Computer and Electrical Engineering, or related field, with at least 12+ (BS), 10+ (MS), or 4+ (Ph.D) years of relevant experience
• Principal Scientist I -  BS, MS, or Ph.D in Bioinformatics, Software Engineering, Computer Science, Computer and Electrical Engineering, or related field, with at least 14+ (BS), 12+ (MS), or 6+ (Ph.D) years of relevant experience
• Demonstrated experience in a supervisory role - Leadership capabilities, managing work assignments, employee development, etc.
• Fluency in 2 or more or relevant programming languages (e.g., Python, Perl, R)
• Experience with database management technologies (e.g., Postgres, MariaDB, SQLite, NoSQL)
• Git versioning systems
• Containerization technologies (Docker, Singularity)
• Familiarity with workflow languages and tools (e.g., CWL, Nextflow)
• Demonstrated expertise in Linux environments, distributed computing, and HPC in local and cloud computing environments
• Familiarity with standard tools and data formats related to NGS resequencing projects processing and analysis (e.g., QC, alignment, variant detection, feature counts)
• Strong communication skills in a collaborative environment

Additional desired skills include:

• Web application frameworks (e.g., Dash, Flask, Django)
• Contemporary data visualization methods like D3, R Shiny, or Spotfire;