Mount Sinai Careers

SENIOR DATA ENGINEER - ICAHN INSTITUTE FOR GENOMICS & MULTI-SCALE BIOLOGY

New York, New York
Research


Job Description

Strength Through Diversity

Ground breaking science. Advancing medicine. Healing made personal.

 

Role and Responsibilities:

The Icahn Institute for Genomics & Multiscale Biology is looking for talented data engineers with the responsibilities and qualifications listed below. At the Icahn Institute, our vision is to transform biomedical research and healthcare delivery into a data-driven, evidence-based, patient-tailored discipline. The Icahn Institute was founded in 2011 to help advance precision medicine with cutting-edge technologies, novel partnerships between the public and private sectors, and world class computational and analytical resources. By maximally leveraging information from patients around the world, we deliver premier precision care optimized for each patient, while discovering breakthrough, next-generation treatments through insights derived from cutting-edge analytics applied to unprecedented amounts of patient-derived data. We promote a core set of values – designed to promote our future vision of team-oriented, data driven global biomedical research: 1) Do good for the patient, 2) Simplify, 3) Share openly, 4) Focus, 5) Synergize, 6) Contributions, not politics, and 7) Deliver.   

Some of the major responsibilities of Data Engineers are to collect, clean, transform, and structure messy data, and create robust, reproducible models that produce potentially valid scientific inferences.  Depending on expertise and interests, our data engineers spend their time either developing pipelines or wrangling datasets.

 

Pipeline development includes the creation and deployment of computational pipelines. Examples of currently used computational pipelines at the Institute are designed for:

  • Processing terabytes of sequence data (e.g. DNA FASTQ), read files to DNA variant cells, RNA FASTQ read files to transcript counts)
  • Converting free text in electronic medical records to feature vectors  using open-source natural language processing packages
  • Converting ICD-9 codes to ICD-10 codes for millions of electronic medical records
  • Transforming and loading MIMIC-III data into a PostgreSQL OHDSI Common Data Model Instance

Dataset wrangling includes collecting, indexing, and cleaning in-house and publicly-available datasets. Examples of current datasets in need of an expert data engineer include:

  • Mount Sinai electronic medical records
  • Publicly available data such as genome-phenome data, cancer genomics, population health and data from public cohort studies
Specific responsibilities include:
  • Collecting, cleaning, transforming and structuring disorganized data into analysis-ready datasets
  • Helping to design, build, run, monitor and maintain informatics pipelines
  • Integrating with services across computational platforms and programming languages
  • Architecting and maintaining databases, filesystems (local, remote and distributed) and custom file formats for storing/serializing clean, transformed data
  • Participating in preparation of manuscripts, grants and presentations
  • Fostering a data-centric culture using best practices for data provenance, structuring and access
 Requirements:
  • Bachelor’s, Master’s or Ph.D. in Bioinformatics, Computer Science, Statistics or a related quantitative discipline
  • Strong organizational and communications skills (verbal and written), with a demonstrated ability to work as a member of a team
  • Minimum 3 years’ experience in data engineering and/or software development
  • Proficiency with UNIX systems and several programming languages
  • Knowledge and experience with software engineering best practices, such as version control, code review, unit/regression testing, and continuous development/continuous integration 
Strength Through Diversity
 

The Mount Sinai Health System believes that diversity is a driver for excellence. We share a common devotion to delivering exceptional patient care. Yet we’re as diverse as the city we call home- culturally, ethically, in outlook and lifestyle. When you join us, you become a part of Mount Sinai’s unrivaled record of achievement, education and advancement as we revolutionize medicine together.

 

We work hard to acquire and retain the best people, and to create a welcoming, nurturing work environment where you can develop professionally. We share the belief that all employees, regardless of job title or expertise, can make an impact on quality patient care. 

 

Explore more about this opportunity and how you can help us write a new chapter in our story! 

 
Who We Are
 

Over 38,000 employees strong, the mission of the Mount Sinai Health System is to provide compassionate patient care with seamless coordination and to advance medicine through unrivaled education, research, and outreach in the many diverse communities we serve.

 

Formed in September 2013, The Mount Sinai Health System combines the excellence of the Icahn School of Medicine at Mount Sinai with seven premier hospital campuses, including Mount Sinai Beth Israel, Mount Sinai Beth Israel Brooklyn, The Mount Sinai Hospital, Mount Sinai Queens, Mount Sinai West (formerly Mount Sinai Roosevelt), Mount Sinai St. Luke’s, and New York Eye and Ear Infirmary of Mount Sinai.

 

The Mount Sinai Health System is an equal opportunity employer. We promote recognition and respect for individual and cultural differences, and we work to make our employees feel valued and appreciated, whatever their race, gender, background, or sexual orientation. 

 

EOE Minorities/Women/Disabled/Veterans

 

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