Bioinformatician II - Windreich Department of AI & Human Health

DescriptionWe are seeking a highly motivated genetic epidemiologist/statistical geneticist to join our growing computational genomics team as Bioinformatician II. The candidate will be working under the supervision of Drs. Ruth Loos and Nathalie Chami. The ideal candidate will bring strong proficiency in R, Python, and Unix/Linux shell scripting, with hands-on experience developing reproducible and scalable analysis pipelines for genomic and multi-omics data.This role will support multiple high-impact research programs involving biobank-scale datasets, EHR-linked analyses, and multi-omics integration, and will actively contribute to collaborative projects across national and international consortia. Experience with AI/ML approaches is a strong plus.

Responsibilities - Perform large-scale genetic analyses, including QC pipelines, GWAS, rare variant association analyses, PRS construction, fine-mapping, proteomics, and integrative genomics.

• Strong experience with genetic analyses tools including PLINK, SAIGE, Regenie, BOLT-LMM, GCTA, LDSC, KING, bcftools, samtools, vcftools.

• Conduct proteomic and multi-omics analyses, including pQTL mapping, protein–trait associations, and pathway-level interpretation.

• Support investigators by designing, executing, and maintaining reproducible analytical workflows using RStudio, Python, and shell scripting.

• Develop and maintain computational pipelines in JupyterLab or similar tools for scalable analyses.

• Manage, explore, and analyze EHR-linked clinical data, integrating phenotype curation with genomic and proteomic data.

• Apply and support machine learning approaches for prediction, clustering, and risk modeling; experience with LLMs is a plus.

• Collaborate with multi-institutional consortia and contribute to shared deliverables, data harmonization efforts, and consortium-driven analyses.

• Prepare high-quality visualizations, summaries, and reports for manuscripts, grant applications, and presentations.

• Maintain rigorous documentation, version control (Git/GitHub), and reproducibility standards.

• Working knowledge of cloud computing environments (e.g. AWS, DNAnexus) and HPC clusters.

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. 4+ years of experience preferred.
• 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

· Proficiency in R, Python, and shell scripting

· Strong experience with statistical genetics analysis workflows.

· Hands-on experience analyzing large-scale genomic datasets (e.g., WES/WGS, UK Biobank, All of Us, etc.).

· Familiarity with proteomics datasets (e.g., Olink, SomaScan) and associated analysis frameworks.

· Working knowledge of cloud computing environments (e.g. AWS, DNAnexus) and HPC clusters.

· Experience with APIs, data ingestion/ETL pipelines, and workflow automation (e.g.WDL, Nextflow).

· Proficiency with generating and maintaining reproducible pipelines (Git/GitHub).

Employer DescriptionStrength 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 $65885 - $100000 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.