Job Description

Overview:

The Bioinformatics Pipeline Engineer will work as part of the New York Center for Rare Diseases (NYCRD) at Montefiore-Einstein.  They will work closely with the Variant Interpretation Scientist to develop, implement, maintain and upgrade the software needed to analyse genomic data, using computationally efficient and secure pipelines within a local high-performance computing or remote cloud architecture.  While current short-read sequencing technology will be part of their responsibility, they will focus innovation on long-read sequencing data, and on the incorporation of Human Phenotype Ontology (HPO) terms in the diagnostic process.  Towards the latter goal, they will maintain and further develop our GenomeDiver software and interface, and work with the team from the Center for Health Data Innovations (CHDI) at Montefiore-Einstein on the ingestion of HPO terms mined using Natural Language Processing from patient notes in the electronic health record system.  The goal will be to discover the genetic cause of the patient’s rare disease, working in an innovation environment with internal and external colleagues committed to improving rare disease diagnostics and promoting equity in diagnostics in individuals of all genetic ancestries.  The position requires being on-site but with flexibility to build a hybrid model once the NYCRD infrastructure is developed. 

Requirements

• Bachelor's degree required (advanced degree such as an Master's Degree or a doctoral MD or PhD degree strongly advantageous)
• At least 3 years of relevant experience required
• Python or R basic competency
• SQL basic competency
• Scala/Java experience advantageous
• Javascript and Web Development experience a positive
• Experience in building, maintaining, and troubleshooting analytical workflows for massively-parallel sequencing data in high-performance computing and cloud environments.

Department: Pediatrics Bargaining Unit:  Non Union Campus:  CHAM Employment Status:  Regular Full-Time Address: 1300 Morris Park Avenue, Bronx
Shift:  Day Scheduled Hours: 8:30 AM-5 PM Req ID: 222002 Salary Range/Pay Rate: $93,750.00- $125,000.00   

For positions that have only a rate listed, the displayed rate is the hiring rate but could be subject to change based on shift differential, experience, education or other relevant factors.

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Diversity, equity and inclusion are core values of Montefiore. We are committed to recruiting and creating an environment in which associates feel empowered to thrive and be their authentic selves through our inclusive culture. We welcome your interest and invite you to join us.

Montefiore is an equal employment opportunity employer. Montefiore will recruit, hire, train, transfer, promote, layoff and discharge associates in all job classifications without regard to their race, color, religion, creed, national origin, alienage or citizenship status, age, gender, actual or presumed disability, history of disability, sexual orientation, gender identity, gender expression, genetic predisposition or carrier status, pregnancy, military status, marital status, or partnership status, or any other characteristic protected by law. 

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