As a member of the MSSM Scientific Computing Group, the Associate Computational Scientist works with scientists and researchers to effectively use MSSM HPC (high performance computing) clusters; assists in the research and deployment of codes on new technologies, and works with research groups to identify, implement and improve their computational and data workflow.

The Department of Immunology and Immunotherapy (Icahn School of Medicine at Mount Sinai) is looking for a highly motivated, detail-oriented individual to join our sequencing and imaging analysis team. The bioinformatics analyst is responsible for maintaining and contributing to our RNA sequencing (single cell and bulk RNA sequencing) and multiplex image data and code repositories.

Responsibilities

• Contribute to setup, management and maintenance of sequencing and imaging data analysis pipelines.
• Manage sequencing and imaging data storage infrastructure.
• Adapt and optimize established internal and external coding workflows to process laboratory data.
• Curate, integrate and analyze internal and external sequencing and imaging data.
• Integrate with computational and biological team members to address needs of laboratory research.
• Work with the software engineering team to ensure pipeline upgrades and new pipelines are properly implemented in laboratory workflow.
• Assist collaborators with data access, analysis, and interpretation.
• Stay current on innovations in RNA sequencing and imaging analysis.

Qualifications

• Masters degree or equivalent in a domain science; Ph.D. in a scientific domain preferred.
• Beginner level, with some experience in a scientific/academic computing environment or equivalent preferred.

Preferred Skills

• Masters degree or equivalent in a domain science; Ph.D. in a scientific domain preferred and in computational biology, bioinformatics, computer science, or similar.

• Strong scientific programming skills in R, Python, bash.

• Experience with pipeline development and management.

• Experience maintaining sequencing and imaging data and code infrastructure.

• Experience in batch HPC cluster environment with a parallel file system.

• Experience working in a Linux environment and scientific workflows.

• Attention to detail, documentation, organizational, and problem-solving skills

• Experience in an academic or research community environment. 

• Team-oriented with excellent written and verbal communication skills.

• Experience benchmarking various analysis tools.

• Experience working with large datasets.

• Background in genomics and statistics.

• Experience analyzing single-cell RNA sequencing data and whole-slide histopathology images is a plus.

   

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About the Mount Sinai Health System:

Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with more than 48,000 employees working across eight hospitals, more than 400 outpatient practices, more than 300 labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time — discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it. Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes more than 9,000 primary and specialty care physicians; 13 joint-venture outpatient surgery centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report's Best Hospitals, receiving high "Honor Roll" status, and are highly ranked: No. 1 in Geriatrics, top 5 in Cardiology/Heart Surgery, and top 20 in Diabetes/Endocrinology, Gastroenterology/GI Surgery, Neurology/Neurosurgery, Orthopedics, Pulmonology/Lung Surgery, Rehabilitation, and Urology. New York Eye and Ear Infirmary of Mount Sinai is ranked No. 12 in Ophthalmology. U.S. News & World Report’s “Best Children’s Hospitals” ranks Mount Sinai Kravis Children's Hospital among the country’s best in several pediatric specialties. The Icahn School of Medicine at Mount Sinai is ranked No. 11 nationwide in National Institutes of Health funding and in the 99th percentile in research dollars per investigator according to the Association of American Medical Colleges. Newsweek’s “The World’s Best Smart Hospitals” ranks The Mount Sinai Hospital as No. 1 in New York and in the top five globally, and Mount Sinai Morningside in the top 20 globally.

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