Computation Scientist

Required Qualifications: (as evidenced by an attached resume)
Advanced Degree in Bioinformatics, Computational Biology, Computer Science, or a closely related discipline. Five (5) years of full time research experience in computational science. Experience in developing and implementing bioinformatics pipelines. Experience with programming languages and scripting (e.g., Python, R, Bash). Experience working with Linux systems. Experience working with HPC cluster environments, job scheduling systems (e.g., Slurm, PBS, Torque), as well as high-performance data processing frameworks such as Spark and Hadoop. Experience with HIPAA and PHI. Experience implementing and/or applying AI methods in biomedical data analysis. Experience working with containerization technologies (e.g., Docker, Singularity). Experience with genomic data analysis and associated bioinformatics tools (e.g., GATK, BWA, SAMtools).

Preferred Qualifications:
Ph.D. in Bioinformatics, Computational Biology, Computer Science, or a closely related discipline. Experience with workflow management systems (e.g., Nextflow, Snakemake, CWL). Experience with machine learning and AI models. Experience with compiled programming languages (e.g., C, C++, Rust) Laboratory or healthcare experience. Experience working with version control systems (e.g., Git) and collaborative development workflows. Experience in training and mentoring users in computational tools and methodologies.

Brief Description of Duties:
The Computational Scientist is part of the Division of Information Technology's (DoIT) Research Computing team, reporting to the Chief Research Information Officer. This position is a pivotal role in supporting both research and clinical laboratories by developing, optimizing, and porting biomedical data analysis pipelines, including those that employ artificial intelligence (AI) methods, to HIPAA-compliant and standard High-Performance Computing (HPC) clusters. This role involves significant data preparation, quality control, and analysis, and application of AI methods. It offers a unique opportunity to contribute to cutting-edge biomedical research and clinical applications within a collaborative and dynamic environment. The Computational Scientist is expected to have excellent problem-solving skills and written and verbal communication skills.

Biomedical Data Analysis:
Perform comprehensive data analyses on biomedical data including multi-modal data analysis with genomics, imaging and clinical data and other high throughput biological data. Adapt and apply state-of-the-art AI methods for feature extraction, classification, and predictive analytics. Interpret and visualize complex biological data to support research and clinical decision-making. Collaborate with researchers to design experiments and analyze results using statistical and computational methods.

Pipeline Development and Optimization:
Develop, implement, and maintain statistical, machine learning, and AI pipelines and other informatics pipelines for biomedical data analysis. Optimize existing pipelines for performance, scalability, and reliability on HPC clusters.

Porting and Deployment:
Port existing pipelines to HIPAA-compliant HPC environments, ensuring adherence to all regulatory and institutional data security policies. Deploy and manage pipelines on standard HPC clusters, adapting workflows as necessary to different computational environments.

Collaboration and Support:
Work closely with researchers, clinicians, and laboratory staff to understand computational needs and provide effective solutions. Provide training, documentation, and technical support to end-users on pipeline usage and best practices.

Data Security and Compliance:
Ensure all computational activities comply with HIPAA regulations and institutional policies regarding protected health information (PHI). Work with IT to Implement and monitor data security measures to maintain the integrity and confidentiality of sensitive data.

Research and Development:
Stay current with emerging technologies, tools, and methodologies in AI methods, data analysis and quality control, bioinformatics, computational biology, and HPC. Participate in interdisciplinary research projects, contributing computational expertise to advance scientific objectives.

Systems Integration and Maintenance:
Collaborate with IT and HPC administrators to integrate biomedical data analysis tools and pipelines into existing computational infrastructure. Assist in the installation, configuration, and troubleshooting of software on HPC systems.

Documentation and Reporting:
Maintain comprehensive documentation of pipelines, workflows, and computational procedures. Contribute to scientific publications, presentations, and grant proposals as appropriate.

Special Notes:
The Research Foundation of SUNY is a private educational corporation. Employment is subject to the Research Foundation policies and procedures, sponsor guidelines and the availability of funding. FLSA Exempt position, not eligible for the overtime provisions of the FLSA. Minimum salary threshold must be met to maintain FLSA exemption.

For this position, we are unable to sponsor candidates for work visas.

Resume/CV and cover letter should be included with the online application.

SUNY implemented a hybrid telecommuting pilot program. This position has been approved to participate in the pilot, which allows for up to 5 remote days per pay period.

This position will remain posted until filled or for a maximum of 30 days. An initial review of all applicants will occur two weeks from the posting date. For full consideration, applications must be received before the initial review date. If within the initial review no candidate was selected to fill the position posted, additional applications will be considered for the posted position; however, the posting will close once a finalist is identified, and at minimal, two weeks after the initial posting date.

Stony Brook University is committed to excellence in diversity and the creation of an inclusive learning, and working environment. All qualified applicants will receive consideration for employment without regard to race, color, national origin, religion, sex, pregnancy, familial status, sexual orientation, gender identity or expression, age, disability, genetic information, veteran status and all other protected classes under federal or state laws.

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