Bioinformatician II - Windreich Department of AI & Human Health

Job Description We 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 bachelor’s 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). 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 $65,885 - $100,000 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. #J-18808-Ljbffr Mount Sinai Morningside