Associate Scientist II/ Scientist I, Bioinformatics Engineer
AbbVie’s mission is to discover and deliver innovative medicines that solve serious health issues today and address the medical challenges of tomorrow. We strive to have a remarkable impact on people’s lives across several key therapeutic areas: immunology, oncology, neuroscience, eye care, virology, women’s health and gastroenterology, in addition to products and services across its Allergan Aesthetics portfolio. For more information about AbbVie, please visit us at www.abbvie.com. Follow @abbvie on Twitter, Facebook, Instagram, YouTube and LinkedIn.
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 opened an exciting opportunity for a Bioinformatics Engineer (Genomics Data), embedded in AbbVie’s Cambridge Research Center in Cambridge, Massachusetts to provide support to our Immunology and Neuroscience bioinformatics groups. The successful candidate will work closely with bioinformaticians and engineers at sites in Cambridge, Ludwigshafen Germany, as well as the Bioinformatics Engineering team members located in Lake County Illinois, and South San Francisco. Physical location will be in Cambridge, Massachusetts.
- Engineer, maintain, and improve upon pipeline code base for bioinformatics processing and analysis of various *omics data types.
- Enable code reuse across different Linux environments / computing architecture deployed across multiple AbbVie research sites.
- Facilitate internal and external data availability to bioinformaticians.
- Develop and maintain structured data repositories for semi-automated computational reassessment and record keeping.
- Develop and support web-based applications (e.g. R Shiny) to enable data query, visualization and custom web-interfaces of data analytics pipelines.
- Interface with research-serving IT specialists to assure availability of appropriate HPC resources (compute, storage, networking).
- Engage in effective communications with stakeholders and other team members via asynchronous collaboration tools (e.g. Microsoft Teams).
Position will be hired based on level of education & experience.
- BS, MS in Computer Science, Bioinformatics, Software Engineering, Computer and Electrical Engineering, or related field, with 3-5+ years of relevant experience with Bachelor’s Degree and 0-2+ years of relevant experience with Master’s Degree.
- Fluency in 2 or more or relevant programming languages, such as R, Python, Perl, Java, or C++.
- Demonstrated experience with structured data storage technologies (relational or no-sql).
- Demonstrated proficiency in both traditional HPC and cloud-based Linux environments.
- Demonstrated experience working with Illumina NGS data generation and primary data processing.
- Demonstrated proficiency using version control systems (git).
- Experienced with large datasets wrangling, transfer, organization, and redundancy.
- Enjoy working in a fast paced and highly collaborative dynamic environment with a diverse team to tackle complex problems.
Additional desired skills include:
- Contemporary interactive data visualization methods like R Shiny, D 3, or Spotfire.
- Experience interfacing with LIMS.
- 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.
- Familiarity with annotation complexities (gene and features) from the various public annotation sources.
- Pipeline building tools like CWL or snakemake.
Significant Work Activities
Job Level Code
Equal Employment Opportunity
At AbbVie, we value bringing together individuals from diverse backgrounds to develop new and innovative solutions for patients. As an equal opportunity employer we do not discriminate on the basis 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, protected veteran status, or any other legally protected characteristic.