What are the responsibilities and job description for the Bioinformatics Scientist / Engineer position at Southern Research?
Bioinformatics Scientist/Engineer (REMOTE or BIRMINGHAM, AL)
General Summary
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.
Essential Duties & Responsibilities
- 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
- Performs 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
Requirements/Minimum Qualifications
- 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
Preferred Qualifications
- 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
Core Values
Cultivating human connection – putting people first. We know that every individual makes a difference and that no one can do it alone. We believe the world’s most powerful resource is human potential. We are an inclusive and courageous team where innovation and diversity of though go hand in hand. We understand that relationships move at the speed of trust.
Operating with precise execution – measuring what matters and owning results as a team. We leverage data to drive decisions that advance science. We recognize the importance of a stable foundation coupled with an agile mindset. We hold ourselves accountable and take pride in our work. We give and receive candid feedback as a gift that keeps us growing.
Harnessing relentless curiosity – our unstoppable, innovative force. We are driven to ask sharp questions and push the boundaries of knowledge. We use creativity and critical thinking as catalysts for finding solutions that change lives. We learn by doing, consistently striving to improve our relationships, training, methodologies, questions and results.
Stewarding a healthy community – implementing sustainable operations for a safe, engaging environment. We don’t compromise on safety and health for our employees, customers or community. We believe a healthy community begins with inclusive economic opportunities. We respect the dignity of the patients we ultimately serve. We are motivated to serve communities that are underserved and markets that are overlooked.
Job Specific Behaviors
Strategic Decisionmaker – Obtains information and identifies key issues relevant to achieving a long-range goal; commits to a course of action after developing alternatives based on logical assumptions, facts, constraints, and resources.
Strategic Relationship Builder – Uses appropriate interpersonal styles to work effectively with others to meet mutual goals and objectives; understands the role & interrelationships of each organizational function; possesses skill in managing across functional and organizational lines.
Mission and Community Driven – Has an authentic desire to help steward Southern Research’s culture, guard of our values, and champion our mission of innovation-driven economic development through translation of excellent scientific research.
Impactful Communicator - Expresses thoughts and ideas effectively in individual and group situations; adjusts language to the needs of the audience.
Results Oriented – Establishes stretch goals and manages to focus outcomes; demands excellence and demonstrates a strong commitment to organizational success; works to do what is best for all stakeholders.
Coaches / Develops Others – Uses appropriate interpersonal style to guide direct reports to action, create a sense of ownership, and encourage individuals to stretch beyond their own capabilities.
Inclusive – Holds a strong conviction that inclusion and innovation go together.
Highly collaborative – Cares less about who did it than how it got done; takes pride in shared outcomes and believes the whole is greater than the sum of the parts when it comes to team efforts.
Deeply curious – Recognizes that “innovation requires not knowing long enough to learn new things” and that “being actively open-minded involves searching for reasons why we might be wrong—not for reasons why we must be right—and revising our views based on what we learn.”
Action oriented – Translates goals and objectives into actionable, metrics focused priorities and work streams for the team to execute.
Process Refiner – Observes details to continuously improve processes, looks for opportunities to create regular feedback loops to refine, and loves measuring what matters; strongly believes that “getting it right is more important than being right.”
Physical Demands
- Ability to work in an office setting using a computer for extended periods
- Some travel may be required (up to 4 times per year)
Certifications, Licenses & Registrations
None required