Senior Engineer, Genomics Data

Employer
AbbVie
Location
Cambridge, MA, US
Posted
Sep 08, 2019
Ref
1904867
Discipline
Science/R&D, Genomics
Required Education
Bachelors Degree
Position Type
Full time
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. We have an exciting opportunity for a Senior Engineer, Bioinformatics, based in Cambridge Massachusetts. The candidate will work closely with computational biologists and research project teams in Immunology discovery to develop immunology focused databases, analytical pipelines and scientific applications for the GRC.

Key Responsibilities
  • Optimize existing pipelines, workflows, and systems, as well as engineer new pipelines, workflows, and systems.
  • Translate and implement algorithms and protocols in a local or cloud high performance computing environments.
  • Ingest external immunological genetic & genomics datasets and generate analysis-specific data frames / databases for rapid manipulation and analyses.
  • Develop and maintain data repositories in a structured manner for semi-automated computational reassessment and record keeping.
  • Identify and understand immunology analytical needs and translate that into solution designs and develop custom visual query and analytical applications.


Level and compensation will be commensurate with experience.

Basic:

  • BS, MS (preferred), or Ph.D in Bioinformatics, Software Engineering, Computer Science, Computer and Electrical Engineering, or related field, with at least 10+ (BS), 8+ (MS), or 0+ (Ph.D) years of relevant experience.
  • Fluency in 2 or more or relevant programming languages, such as Python, Perl, R, Java, or C++; contemporary data visualization methods like D3, R Shiny, or Spotfire; as well as experience database management in SQL, SQLite, or MongoDB.
  • Demonstrated expertise in Linux environments, distributed computing, and HPC in local and cloud computing environments.
  • Familiarity with standard tools and data formats related to gene expression, enrichment analysis, genetic, genomic, or epigenetic data, e.g., encountered when analyzing high-throughput transcriptomic, whole exome, whole genome, whole methylome, GWAS, or targeted resequencing data.
  • Strong communication skills in a collaborative environment.

Additional desired skills include:

  • Experience analyzing and interpreting gene expression data for understanding disease mechanisms and model organism prioritization
  • Experience handling, visualizing, recording, and managing data with SQL or other enterprise solutions
  • Fluency with consortium disease specific (like the Accelerating Medicines Partnership - RA/SLE, the Crohn and Colitis Foundation) or genomic databases (such as those relating to genome annotation, genetic variants, public data repositories).
  • Experience interpreting biological data related to diseases associated with cancer, neurodegenerative disease, immunological, or metabolic disorders