Senior Bioinformatics Programmer

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Position Summary:

The Petljak Lab is seeking a highly motivated and creative Senior Bioinformatics Programmer to join our multidisciplinary team within the newly established Cancer Genomics & Genetics Program at NYU Grossman School of Medicine. This is a highly collaborative, fast-paced, and scientifically engaged position suited to someone who thrives in an ambitious research environment, takes strong ownership of their work, and is motivated to drive projects forward. The position offers exposure to leading experts and collaborations across cancer biology, genomics, computational biology, and related disciplines.
The Petljak Labs research sits at the intersection of computational and experimental biology, cancer genomics, mutagenesis, and tumor evolution, with the goal of understanding how mutational processes arise and shape cancer development and therapeutic responseand using these insights to identify new opportunities for cancer prevention and treatment. Our work builds on recent studies deconvoluting mutational signatures from cancer genomes and using them as molecular readouts to identify the sources, mechanisms, and functional consequences of individual mutational processes (Cell, 2019; Nature, 2023; Nature Genetics, 2023; Cell Trends In Cancer, 2026).

The successful candidate will become a lead computational scientist within the lab, working closely with experimental scientists and clinical collaborators across multiple cancer genomics projects involving both patient specimens and experimental model systems. The core of the position is bioinformatics and computational analysis across the laboratorys research projects, primarily conducted within a high-performance computing (HPC) environment, with two main areas of focus: 1) analysis and interpretation of next-generation sequencing and large-scale genomic datasets, together with the development, execution, and maintenance of robust, reproducible analytical pipelines and workflows for these data types, including but not limited to whole-genome sequencing, whole-exome sequencing, RNA sequencing, and single-molecule/duplex DNA sequencing; and 2) development and implementation of creative computational approaches for specialized analyses across diverse datasets generated by cutting-edge experimental platforms and multimodal studies. Examples include custom genomic analyses, quantitative analysis of live-cell imaging data, and integration of genomic readouts with patient clinical features, environmental exposures, and other molecular and phenotypic data. Interest in thoughtfully evaluating and applying emerging AI-enabled tools to improve the efficiency, usability, and reproducibility of bioinformatics workflows and research operations is welcomed.

Supporting these core analytical responsibilities, the candidate will take ownership of developing and maintaining the laboratorys computational infrastructure, managing laboratory-generated and externally accessed datasets, and ensuring reproducibility and version control. The candidate will also coordinate with institutional HPC and IT teams, external vendors, and other service providers to troubleshoot and resolve needs related to computation and its supporting infrastructure as they arise.

The candidate will work with substantial independence while being deeply integrated into our research team based in the state-of-the-art CURE building at 345 Park Avenue South. Regular interactions with the Principal Investigator and lab members will provide opportunities to shape analytical strategy, contribute intellectually across multiple projects, mentor and supervise junior researchers and students, and help drive studies from experimental design through biological interpretation and publication.

Job Responsibilities:

Bioinformatics Pipelines: Develop, execute, optimize, standardize, and maintain robust and reproducible bioinformatics pipelines for quality control and processing of next-generation sequencing datasets, establishing consistent analytical workflows and best practices across the laboratory's research projects.

Computational Analyses: Develop and implement custom computational approaches and software for downstream analysis, integration, visualization, and interpretation of sequencing and other specialized datasets generated across the labs research projects, including cutting-edge experimental platforms and multimodal studies.

HPC Computing & Troubleshooting: Ensure efficient and reliable execution of analytical workflows within the available HPC infrastructure, including troubleshooting and coordinating with the institutional HPC team as needed.

Reproducibility, Standardization & Version Control: Establish and maintain standardized computational workflows, analytical conventions, and best practices across the laboratory to ensure consistency and reproducibility of analyses. Maintain appropriate documentation and version control using Git/GitHub and workflow management systems such as Snakemake or Nextflow.

Computational Infrastructure & Data Management: Develop and maintain effective systems for the storage, organization, curation, processing, access, and sharing of the laboratory's genomic and other research data, as well as large-scale external datasets used by the lab. This includes managing appropriate computational resources and technologies such as internal servers and SLURM-based compute clusters, MariaDB, Docker/Singularity, Git/GitHub, Google Cloud, and Google Drive, and coordinating access, approvals, and ongoing management of controlled-access datasets as required.

Computational Operations Management: Oversee the laboratory's day-to-day computational and software needs, proactively addressing issues and coordinating with institutional HPC and IT teams, software vendors, and other service providers as needed.

Data Interpretation & Communication: Interpret data in close collaboration with experimental scientists and clinical collaborators; present and summarize findings to the research team and clearly communicate analytical approaches, results, limitations, and biological implications. Support the team in its research goals.

Professional Development: Remain current with advances in cancer genomics, bioinformatics, and computational biology, and independently identify, learn, and implement new computational methods, software, and programming approaches required by evolving research needs.

Additional Responsibilities: Perform other responsibilities related to the laboratory's evolving computational, bioinformatic, and analytical needs as required.

Minimum Qualifications:

To qualify you must have a Ph.D. or M.Sc. in Bioinformatics, Systems Biology, Computer Science or related field is required for consideration for this position. Knowledge of cancer biology and understanding of key concepts in cancer genomics. 3+ years of experience with next-generation DNA sequencing data, with significant experience in building computational pipelines for analyses of sequencing data. Experience in effectively managing multiple concurrent projects. Demonstrated advanced proficiency in Unix/Linux systems including HPC environments and containerization. Demonstrated advanced proficiency in developing customized, reproducible bioinformatics pipelines using Snakemake, Nextflow, or similar workflow management system. Demonstrated advanced proficiency in using version control systems such as Git/GitHub. Strong understanding of statistical principles and demonstrated ability to select and apply appropriate statistical methods for the analysis and interpretation of genomic and other biological datasets. Scripting languages: R and Python. Ability to work independently while collaborating effectively with team members and contributing to shared research goals. Excellent communication skills and proficiency in written and oral English.

Preferred Qualifications:

Ph.D. preferred

Qualified candidates must be able to effectively communicate with all levels of the organization.

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NYU Grossman School of Medicine is an equal opportunity employer and committed to inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration. We require applications to be completed online.

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NYU Langone Health provides a salary range to comply with the New York state Law on Salary Transparency in Job Advertisements. The salary range for the role is $90,000.00 - $115,000.00 Annually. Actual salaries depend on a variety of factors, including experience, specialty, education, and hospital need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits.

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