Senior Bioinformatics Programmer

NYU Langone Medical Center•New York, NY

41d

About The Position

The Center for Human Genetics and Genomics is seeking an experienced bioinformatics programmer to join the deciphEHR team, pioneering genomic medicine at NYU Grossman School of Medicine. This role is a key part of a dynamic and rapidly growing project. The candidate will write software to optimize and integrate large-scale whole genome sequencing (WGS) processing and electronic health records (her) data. Specifically, the individual will develop the data infrastructure for processing and querying large genomic datasets by our end users, as well as be involved in cutting edge genomic medicine research. We seek an individual experienced in writing production grade bioinformatics pipelines with experience in database/ data warehouse integration in a research or clinical setting.

Requirements

Master's degree in computer science/data science/bioinformatics/Statistics/Information Science or related technical disciplines.
Proven programming skills in Python, Bash/UNIX, R. Proficient in Git for version control.
At least one year experience with a big data technology such as Spark, Hadoop, etc.
At least 3 years of experience with a workflow language (WDL, Snake-make), Docker/Singularity, and HPC.
At least 4 years of experience with standard genomics bioinformatics tools (PLINK, GATK, etc).
Must be able to work in a demanding and dynamic team environment and work independently.
Knowledge of algorithms and data-structures.
Experience with Web-based application development languages such as HTML/JavaScript.
Must demonstrate excellent communication skills, both oral and written, within the team and end users.

Nice To Haves

Ph.D. in Computer Science / Data Science / Bioinformatics/ Statistics/Information Science or related technical disciplines.
Candidates with a Master's degree in the above fields will be considered if they possess significant relevant experience.
Familiarity with Databricks for big data analytics and managing large-scale genomic datasets
Qualified candidates must be able to effectively communicate with all levels of the organization.

Responsibilities

Develop production genomic workflows on HPC as well as cloud environments
Develop a genomic data warehouse for efficient querying of large data using Glow
Perform data processing and QC for genomic and clinical datasets
Participate in data and software maintenance work for our team
Document all required software, code, and experiments
Extract and manage multidimensional descriptive, numeric and digital data from the EPIC EHR database for phenotype analysis

Benefits

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.

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