Single Cell Spatial Transcriptomics Jobs in New York

Job Description
The Laboratory of Tissue Immunity and Regeneration at the Icahn School of Medicine at Mount Sinai is seeking a highly qualified and motivated Bioinformatician II to support computational and analytical research efforts across a diverse portfolio of sequencing- and omics-based studies.
The laboratory uses state-of-the-art genomic technologies, including bulk RNA sequencing, bulk ATAC sequencing, single-cell RNA sequencing, single-cell Multiome, and Spatial Transcriptomics/Visium HD, to investigate fundamental and translational questions in tissue immunity, inflammatory memory, regeneration, and inflammatory diseases of the skin and gut.
The Bioinformatician II will serve as an integral member of the research team and a key computational partner to experimental investigators. This individual will be responsible for the design, execution, and interpretation of bioinformatic analyses across multiple projects, and will contribute to the development of reproducible analytical workflows and publication-quality scientific outputs. The position requires a high level of technical expertise, strong organizational skills, and the ability to work effectively in a collaborative, fast-paced academic research environment.
Responsibilities

• Conduct end-to-end computational analyses for bulk RNA-seq, bulk ATAC-seq, single-cell RNA-seq, single-cell Multiome, and Spatial Transcriptomics/Visium HD datasets.
• Process, quality control, analyze, visualize, and interpret high-dimensional sequencing and omics datasets.
• Develop, optimize, maintain, and document reproducible computational pipelines and workflows to support scalable analysis across multiple research projects.
• Partner closely with laboratory scientists and collaborators to translate biological questions into rigorous computational strategies and analytical plans.
• Generate high-quality figures, summaries, and data outputs for internal research meetings, grant applications, manuscripts, and scientific presentations.
• Manage computational analyses in a high-performance computing environment and ensure effective organization of data and analytical workflows.
• Support ongoing and new research initiatives through timely, accurate, and scientifically rigorous analysis.
• Contribute to manuscript preparation and other scholarly outputs arising from the laboratory's research program.

Qualifications

• M.S. in Bioinformatics, Biomedical Informatics, Computational Biology, or Genomics. Alternately, M.S. in a discipline requiring strong computational and analytical skills supplemented with some biology exposure. Ph.D in a related field preferred. Those with a Bachelors degree and additional post-graduate experience are considered.
• 2+ years post-graduate experience in a research environment, including the manipulation of large biological datasets.
• Advanced knowledge of genetics and/or statistical analysis software and online resources. Experience in programming environments such as MatLab, R statistical package, BioConductor, Perl and C++.

Preferred Skills

• Prior experience analyzing bulk RNA-seq, bulk ATAC-seq, scRNA-seq, single-cell Multiome, and Spatial Transcriptomics/Visium HD data.
• Familiarity with single-cell analysis frameworks and data structures, including Seurat and AnnData.
• Experience developing and maintaining bioinformatics pipelines for sequencing-based workflows.
• Demonstrated ability to independently perform analyses from raw data processing through downstream interpretation.
• Experience working in a highly collaborative laboratory or translational research environment.
• Strong written and verbal scientific communication skills, including experience preparing publication-quality figures and analyses.
• Interest in inflammatory disease biology, tissue immunology, regeneration, and translational team science.

Compensation Statement
The Mount Sinai Health System (MSHS) provides salary ranges that comply with the New York City Law on Salary Transparency in Job Advertisements. The salary range for the role is $65,885.00 - $100,000.00 Annually. Actual salaries depend on a variety of factors, including experience, education, and operational need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits.
About Us
Strength through Unity and Inclusion
The Mount Sinai Health System is committed to fostering an environment where everyone can contribute to excellence. We share a common dedication to delivering outstanding patient care. When you join us, you become part of Mount Sinai's unparalleled legacy of achievement, education, and innovation as we work together to transform healthcare. We encourage all team members to actively participate in creating a culture that ensures fair access to opportunities, promotes inclusive practices, and supports the success of every individual.
At Mount Sinai, our leaders are committed to fostering a workplace where all employees feel valued, respected, and empowered to grow. We strive to create an environment where collaboration, fairness, and continuous learning drive positive change, improving the well-being of our staff, patients, and organization. Our leaders are expected to challenge outdated practices, promote a culture of respect, and work toward meaningful improvements that enhance patient care and workplace experiences. We are dedicated to building a supportive and welcoming environment where everyone has the opportunity to thrive and advance professionally. Explore this opportunity and be part of the next chapter in our history.
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.
Equal Opportunity Employer
The Mount Sinai Health System is an equal opportunity employer, complying with all applicable federal civil rights laws. We do not discriminate, exclude, or treat individuals differently based on race, color, national origin, age, religion, disability, sex, sexual orientation, gender, veteran status, or any other characteristic protected by law. We are deeply committed to fostering an environment where all faculty, staff, students, trainees, patients, visitors, and the communities we serve feel respected and supported. Our goal is to create a healthcare and learning institution that actively works to remove barriers, address challenges, and promote fairness in all aspects of our organization.