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Job description
Position Summary
We have an exciting opportunity to join our team as a Sr. Bioinformatics Programmer working in a Molecular Diagnostics environment.
This position is an onsite role for a minimum of 6 months with the potential for hybrid role after that based on performance. Ability to be onsite 3 to 5 days a week a must (possibility of full remote work is currently not available).
NYU Langone Health, a world‑class, patient‑centered, integrated, academic medical center, and one of the nation’s premier centers for excellence in clinical care, biomedical research and medical education, is seeking a highly motivated, enthusiastic individual to join the Department of Molecular Pathology working in the field of Clinical Genomics and Precision Medicine.
The Molecular Pathology Lab at NYU Langone Health with the Applied Bioinformatics Laboratories (ABL) is seeking a highly motivated, enthusiastic and creative individual to become a member of our clinical bioinformatics team. The successful candidate will be primarily responsible for the development and maintenance of computational pipelines and work closely with clinicians to develop bioinformatic tools for clinical Next Generation Sequencing (NGS) based diagnostics. In addition, bioinformatics analysis of various types of patient genomic, epigenomic and transcriptomic data is required.
This is a great opportunity to be involved in an innovative environment utilizing and mastering bioinformatics programming skills, develop new analysis tools/pipelines, analyze challenging datasets, and be involved in cutting edge NGS based cancer diagnostics, clinical genomics and hands on precision medicine for the benefit of patients.
Job Responsibilities
Enhance or develop new automated workflows/pipelines within a nextflow environment for bioinformatic tools utilizing next generation sequencing data in clinical diagnostic assays
Use existing bioinformatics pipelines to analyze the molecular patient data generated in the clinical lab
Oversee systems support for existing bioinformatics pipelines and develop new pipelines to support new molecular assays
Support the team in its common clinical genomics and precision medicine goals
Perform quality control of the generated sequencing data and develop solutions to enhance future performance
Perform different types of data analysis relating to the genomics-based approaches utilized by the lab, in an independent fashion.
Develop new methods for multi‑omics data analysis and integration
Work with bioinformatics scientists and clinical pathologists to analyze and interpret patient NGS results for better potential treatment options
Work with lab users to analyze biomedical data and address clinical needs using bioinformatics techniques and tools
Work with MCIIT and HPC team to provide current and future solutions for server, storage and other requirements.
Preferred Qualifications
Expert in creating customized sequencing analysis pipelines, in applications for data analysis, and executing standard bioinformatics pipelines (relevant examples in a GitHub repository)
Basic knowledge and understanding of software engineering concepts
Knowledge of algorithms, data structures, machine learning
Prior experience working in CLIA environment is a plus
Experience in variant calling benchmarking and clinical validation analysis (e.g. concordance, limit of detection, assay reproducibility)
Experience with running workflows on public cloud (GCP / AWS)
Experience with developing and querying databases using SQL queries
Experience with web-development (HTML, CSS, JavaScript, TypeScript and related)
Minimum Qualifications
To qualify you must have a M.Sc. plus a minimum of 3 years’ experience in Bioinformatics, Computer Science, Programming, Software Development, or related field
Previous experience with NGS data and associated bioinformatics tools
Experience in Unix/Linux systems including high-performance computing environments
Strong programming skills in Python, R, shell scripting
Proficiency in Nextflow, Django, Docker and Singularity containers
Work experience and algorithm understanding of standard software tools used to generate and manipulate FASTQ, BAM, VCF files including but not limited to BWA, GATK, Picard, samtools, bcftools
Knowledge in the analysis of SNV, Indel, CNV and structural variants for both somatic and germline disease, additional understanding of variant annotation
Familiarity with various NGS QC principles
Knowledge of biology, cancer genomics or an understanding of key and complex biological concepts
Detail-oriented, well organized and an interest in clinical sequencing and disease related or cancer genomics
Ability to work independently (e.g., recommend new software or bioinformatic tools, find papers relevant to the subject, assess methods, implement methods, and apply them to datasets to reproduce results)
Team oriented with excellent written and verbal communication skills
Ability to function in a multidisciplinary team including MD’s and PhD’s
Qualified candidates must be able to effectively communicate with all levels of the organization.
Benefits and Wellness
NYU Grossman School of Medicine provides its staff with far more than just a place to work. Rather, we are an institution you can be proud of, an institution where you'll feel good about devoting your time and your talents. At NYU Langone Health, we are committed to supporting our workforce and their loved ones with a comprehensive benefits and wellness package. Our offerings provide a robust support system for any stage of life, whether it's developing your career, starting a family, or saving for retirement. The support employees receive goes beyond a standard benefit offering, where employees have access to financial security benefits, a generous time‑off program and employee resources groups for peer support. Additionally, all employees have access to our holistic employee wellness program, which focuses on seven key areas of well‑being: physical, mental, nutritional, sleep, social, financial, and preventive care. The benefits and wellness package is designed to allow you to focus on what truly matters. Join us and experience the extensive resources and services designed to enhance your overall quality of life for you and your family.
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 $84,577.92 - $105,039.78 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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Worksite address
new york, NY, 10261, US
Who can apply
Review the original listing for work authorization, qualifications and employer requirements.