Single Cell Rna Sequencing Jobs (NOW HIRING)

Job Description
We are seeking a highly motivated, detail-oriented Senior Scientist with a PhD and/or a strong background in genomics and immunology to join our multidisciplinary team at the Tisch Cancer Institute. Our group investigates the molecular and cellular mechanisms regulating immune compartments in myeloproliferative neoplasms (MPNs) and acute myeloid leukemia (AML), using state-of-the-art single-cell NGS platforms.
The successful candidate will drive the day-to-day execution of genomics assays, including:
• Single-cell CITE-seq and other multi-omics assays
• Immune repertoire (TCR/BCR) sequencing
• Single-cell DNA and multi-omics assays
• Bulk sequencing (RNA-seq, WGS/WES) as needed
• RT-qPCR, molecular biology, and functional assay workflows
This position offers an opportunity to work at the interface of translational hematology, immunology, and computational genomics, in close collaboration with clinicians, bioinformaticians, and trainees.
The scientist will report directly to Dr. Md Babu Mia, lead of the Computational Biology and Machine Learning program within the MPN team.
Responsibilities
Genomics & Single-Cell Assays

• Plan, perform, and troubleshoot end-to-end NGS workflows, including:
  • Single-cell CITE-seq (RNA + protein) and other antibody-tagged assays
  • TCR/BCR repertoire library preparation
  • Single-cell DNA and Protein assays for clonal architecture analysis
  • Bulk RNA-seq and targeted sequencing panels
  • Validation of NGS outputs using molecular and functional assays
• Perform sample and library QC, including cell counts/viability, nucleic acid quality assessment (TapeStation, Qubit), library quantification, and thorough documentation of all metrics

Primary Human Samples & Hematology Focus

• Isolate, process, and bank primary human hematopoietic and immune cells
• Operate multicolor flow cytometry for immunophenotyping and cell sorting to support genomics experiments
• Adhere to institutional, IRB, and HIPAA guidelines for handling patient-derived samples, including accurate chain-of-custody and de-identification procedures

Collaboration, Data Handling & Basic Analysis

• Coordinate with genomics core facilities and external vendors for sequencing runs, including sample submission, run tracking, and communication of QC outcomes
• Organize and manage NGS data and metadata (FASTQs, count matrices, sample sheets) in collaboration with computational team members
• Perform basic data handling and QC, such as generating reports on read counts, mapping rates, and cell-level QC metrics using established pipelines
• Work closely with bioinformaticians and statisticians to ensure experimental design and metadata capture support robust downstream analyses

Laboratory Operations & Documentation

• Maintain detailed laboratory notebooks, SOPs, and digital records for all experiments, protocols, and sample inventories
• Contribute to optimization and standardization of protocols for single-cell and bulk assays, including pilot studies and method comparisons
• Assist in training and mentoring students and junior staff in genomics workflows and good laboratory practice

Scientific Contributions

• Contribute to write-ups for manuscripts, presentations, and grant applications
• Present progress at lab meetings, project meetings, and collaborative discussions
• Support preparation of manuscripts for high-impact journals and abstracts for national conferences

Qualifications

• Ph.D in in Molecular Biology, Hematology, Immunology, Cancer Biology, Genomics, or a closely related biomedical discipline.
• Minimum five years of experience with scientific investigation.
• Must have demonstrated outstanding achievement in a field of research
• Must have contributed to a number of peer-reviewed publications, inventions or the like, at least some of which have had a major impact on advancing the field or discipline.
• Prior experience successfully securing external grant funding is highly desirable.

Preferred Qualifications:

• Postdoctoral experience.
• Substantial hands-on laboratory experience in NGS-based assays, with proficiency in several of the following (and strong interest in learning the rest):
  • CITE-seq or related single-cell RNA + protein platforms
  • Bulk RNA-seq and/or DNA sequencing (WGS/WES, targeted panels)
  • RT-qPCR, standard molecular biology, and functional assay techniques
• Solid conceptual knowledge of hematology and immunology, ideally in the context of blood cancers or immune dysregulation
• Experience working with primary human cells, including isolation, cryopreservation, and basic culture
• Proficiency in multicolor flow cytometry, including instrument operation, compensation, panel design, and analysis.
• Comfort with basic biostatistics and computational biology concepts
• Strong organizational skills, meticulous attention to detail in sample tracking and metadata, and rigorous adherence to SOPs
• Demonstrated ability to work independently while functioning effectively in a collaborative, interdisciplinary environment
• Track record of contribution to peer-reviewed publications in genomics, immunology, or hematology
• Eagerness to learn new technologies and stay current with emerging genomics platforms

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 $58,661.00 - $125,008.22 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.