Postdoctoral Fellow-MSH-30001-337

Job Title: Postdoctoral Fellow – Spatial and Single-Cell Multi-Omics

Introduction:
We are seeking a highly motivated Postdoctoral Fellow to join our team and play a key role in developing, optimizing, and applying spatial and single-cell multi-omic technologies. The successful candidate will contribute to experimental method development, sequencing-based assay optimization, and associated computational analyses to study gene regulation, chromatin organization, and epigenomic mechanisms in complex biological systems.

This position is ideal for a candidate with strong interests in technology development, single-cell/spatial genomics, epigenomics, and integrative analysis. The fellow will work closely with experimental and computational scientists in a highly collaborative environment and will have opportunities to lead independent projects, publish high-impact studies, and develop new tools for the broader research community.

Key Responsibilities:

Spatial and Single-Cell Method Development:
Develop, optimize, and benchmark new spatial and single-cell multi-omic assays, including approaches that integrate transcriptomic, epigenomic, chromatin accessibility, DNA methylation, chromatin conformation, and/or protein-level measurements.

Experimental Optimization and Troubleshooting:
Design and perform experiments to improve assay sensitivity, throughput, robustness, and compatibility with primary tissues, low-input samples, and clinically relevant specimens. Optimize sample preparation, nuclei/cell isolation, library construction, sequencing strategies, and quality-control steps.

Multi-Omic Data Generation and Analysis:
Generate and analyze spatial and single-cell datasets, including single-cell RNA-seq, single-cell epigenomic assays, spatial transcriptomics, and other multi-omic platforms. Perform quality control, normalization, clustering, annotation, differential analysis, trajectory analysis, and regulatory feature identification.

Data Integration:
Integrate transcriptomic, epigenomic, spatial, and other omics datasets to investigate gene regulatory programs, cell-state transitions, tissue organization, and disease-associated molecular mechanisms.

Pipeline and Tool Development:
Develop, customize, and maintain computational pipelines for processing, analyzing, visualizing, and interpreting large-scale single-cell and spatial multi-omic datasets. Ensure that workflows are reproducible, scalable, and well documented.

Validation and Benchmarking:
Benchmark new methods against existing technologies using both experimental and computational metrics. Validate key biological findings through orthogonal genomic, molecular, imaging, or functional approaches.

Collaboration and Communication:
Work closely with lab members, collaborators, and core facilities to design experiments, analyze data, interpret results, and prepare manuscripts, grant applications, and presentations.

Documentation and Dissemination:
Maintain clear experimental records, analysis notebooks, protocols, and code documentation. Contribute to protocol sharing, software release, manuscript preparation, and presentation of research findings at scientific meetings.

Qualifications:

• Ph.D. in Genomics, Molecular Biology, Epigenomics, Computational Biology, Bioinformatics, Biomedical Engineering, Computer Science, or a related field.

• Strong interest in developing and applying spatial and single-cell multi-omic technologies.

• Experience with single-cell or spatial genomic methods, such as scRNA-seq, scATAC-seq, CUT&Tag/CUT&RUN, DNA methylation profiling, Hi-C/chromatin conformation assays, spatial transcriptomics, or related platforms.

• Experience with next-generation sequencing library preparation, assay optimization, or molecular biology techniques is highly desirable.

• Proficiency in computational analysis using R, Python, or related programming languages.

• Familiarity with common single-cell analysis frameworks and tools, such as Seurat, Scanpy, ArchR, Signac, Cell Ranger, Snakemake, Nextflow, or related platforms, is preferred.

• Strong problem-solving skills and ability to troubleshoot both experimental and computational workflows.

• Ability to work independently while also contributing effectively to collaborative projects.

• Excellent written and verbal communication skills.

• A strong publication record or demonstrated potential for independent scientific productivity.

Preferred Qualifications:

• Experience developing or optimizing new sequencing-based technologies.

• Experience working with primary tissues, low-input samples, embryos, organoids, tumors, or clinically derived specimens.

• Experience integrating multi-omic datasets, including transcriptomic, epigenomic, spatial, chromatin accessibility, DNA methylation, or chromatin conformation data.

• Familiarity with machine learning, statistical modeling, regulatory genomics, or gene regulatory network analysis.

• Experience with high-performance computing environments and reproducible workflow management.

Position Summary:
The Postdoctoral Fellow will contribute to the development of innovative spatial and single-cell multi-omic technologies and apply these approaches to address important questions in gene regulation, epigenomics, development, and disease. The position offers an excellent opportunity to gain expertise at the interface of experimental technology development, computational genomics, and biological discovery.

, 816 - Genetics/Genomic Sci - ISM, Icahn School of Medicine

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.

Compensation

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 $72500 - $80000 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.