Southern Research Institute-posted 11 months ago
Birmingham, AL
Professional, Scientific, and Technical Services

Southern Research (SR) is at a pivotal moment in its 84-year history. At the start of 2022, SR launched a new strategic plan focused on translational research in the life sciences. SR intends to invest over $150 million in this new strategy, including development of new facilities, platforms, and programs. We believe in the power of SR and our partners to unlock the immense potential of Alabama's biotech ecosystem to spur economic development, create jobs, and draw investment. Downtown Birmingham sees over $700M in extramural biomedical research every year, including over $300M from the NIH, in large part due to the contributions of Southern Research and the University of Alabama at Birmingham. We are on a mission to translate our R&D volume into investment, high-performance companies, and quality jobs in Alabama and in the Southeast United States. The Bioinformatics Engineer will report to the Director Bioinformatics. In this role, you will be responsible for overseeing the development, implementation, and maintenance of bioinformatics software and infrastructure to support cutting-edge research. You will work with external biobanks, clinical sequencing laboratories and clinical data health ecosystems to aggregate and assimilate molecular datasets and analysis pipelines in the cloud to support a bioinformatic research community.

  • Develop a standardized data infrastructure for genomic and clinical datasets
  • Integrate clinical and molecular dataset and ensure all data reaches high quality standards
  • Develop and implement quality control measures to ensure the accuracy and completeness of clinical, genomic and health data
  • Perform analytics on connected data sets within cloud-based computational resources
  • Develop and maintain cloud applications and workflows for the management and analysis of data
  • Design and develop new web services and APIs to drive communication across systems
  • Developing and adopting standards for user authentication
  • Create and maintain databases, data repositories, and analytical platforms to facilitate data integration, sharing, and access for internal and external stakeholders
  • Collaborate with data analysts and researchers to provide access to clean, standardized data for research and analytics projects
  • Collaborate with IT team to optimize database systems to support bioinformatics data storage, analysis, and visualization
  • Perform other duties as requested
  • Bachelors or Master's in Bioinformatics, Computational Biology, Biological Computational Sciences, or a related field
  • 5+ years of experience in Bioinformatics programming
  • Experience working with one or more programming languages such as Python, JAVA and Perl
  • Strong understanding of data modelling, data structures, databases and ETL processes
  • Experience in designing, building, and using APIs
  • Extensive experience with AWS cloud computing infrastructure for bioinformatics primary, secondary, and tertiary analysis
  • Familiarity with NGS pipelines such as GATK pipeline, Dragon pipeline and running NGS pipelines on cloud
  • Experience with high-throughput data analysis (e.g., next-generation sequencing) and familiarity with relevant bioinformatics databases and resources
  • Demonstrated expertise in the design and implementation of computational pipelines for data analysis, integration, and visualization
  • Desire to continuously learn new technologies and bring innovative ideas into the team
  • Experience with SQL and no-SQL databases
  • Experience in SOAP and REST-based web service development
  • Proficiency in healthcare data standards (e.g., HL7, FHIR, OMOP CDM, GA4GH standards like Beacon)
  • Familiarity with EMR systems and healthcare information exchange protocols
  • Familiarity with AWS health related services such as AWS HealthOmics, AWS HealthLake and OHDSIonAWS
  • Familiarity with OHDSI tools and FHIR to OMOP CDM ETL process
  • Knowledge of healthcare privacy and security regulations (e.g., HIPAA)
  • Extensive knowledge of bioinformatics methodologies, algorithms, and tools commonly used in the analysis of biological data sets
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