Bioinformatician III

Organization
Icahn School of Medicine at Mount Sinai New York
Job Location
New York, NY 10029
Job Description
  • Build and maintain comprehensive variant databases from a wide variety of public repositories.
  • Build and maintain a comprehensive variant store from over 100,000 exomes.
  • Manage software and scripts in the Clinical Genome Informatics group.

Assist bioinformatics scientists to integrate different types of genetic, functional, and clinical data to discover causal variants and genes for cardiovascular diseases, Alzheimer’s disease, cancer, and other genetic diseases.

Requirements

Requirements:

  • Strong coding proficiency in Python, R, and Perl programming languages in a Linux environment.
  • Extensive experience with RDBMS, SQL programming (especially schema design), and ETL processes.
  • Hands-on experience building biomedical databases from public repositories, such as Uniprot, dbSNP, Medline, GTEx, 1000 Genomes, UK10K, Clinvar, COSMIC.
  • Domain knowledge in genetics and genomics, especially data representation and conventions for exchanging information about genetic variants.
  • Hands-on experience working with NGS and genotyping tools and data/file formats, especially VCF.
  • 2 years post-graduate experience in above categories.

 

Desirable experience:

  • Experience with Hadoop (Impala/Parquet, Spark/Shark) and programming in Java/Scala.
  • Experience with clinical genetic test is a plus.
  • Developing codebases using distributed version control tools (especially Git or Mercurial) and software issue tracking systems (especially JIRA).
  • Deploying jobs/pipelines on a high-performance Linux computing cluster.
  • Working in a production or clinical environment.
How to Apply

If interested, please submit a letter of interest and resume to Xiang Zhou at [email protected](http://rongchenlab.org).

About Our Organization

The Icahn Institute for Genomics and Multiscale Biology at Mount Sinai is seeking talented, self-motivated individuals to participate in leading edge research in translational bioinformatics as members of the Clinical Genome Informatics group. Successful applicants will be part of an interdisciplinary team that develops computational databases and methods to annotate and interpret large-scale human genome and exome sequencing data to better understand cancer mutations and the genetics of Mendelian and complex diseases.  Successful applicants will also play a role in developing systems for integrating novel informatics and genomic tools and methodologies into clinical practice.

The vision of the Icahn Institute at Mount Sinai is to integrate the digital universe of information to better diagnose and treat human disease. While other institutions focus primarily on genomics, systems biology, or data analytics, we’re uniquely dedicated to an integrated and holistic view of biology as the path to dramatic improvements in healthcare and disease prevention.  We harness the power of “Big Data” and sophisticated analytics to build predictive biological network models that offer novel insights on disease.  We seek to apply these models in a clinical setting to improve diagnosis and treatment for our patients. 

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