Job: Bioinformatics Programmer, Genetic Services Laboratory, University of Chicago, Chicago USA
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2.1 years ago by
hp0 wrote:

Genetic Services Laboratory within the Department of Human Genetics, University of Chicago is looking for a Bioinformatics Programmer.

Job Description:

The incumbent will work largely on the support and maintenance of analysis pipelines for automated processing of data from next generation sequencing projects in the DNA diagnostic laboratory in the Department of Human Genetics. The candidate will be expected to maintain and upgrade our in-house developed LAMP stack based NGS data review system. The candidate will also work to help with the expansion of array-CGH technology in the diagnostic lab with regards to data organization, analysis and array design. The candidate will be expected to work with laboratory personnel to design, develop, test and execute custom applications for laboratory automation including interfaces to/from scientific instruments and the Laboratory Information System (LIS).

Responsibilities include:

  • Supporting and maintaining automated analytic pipelines for next generation sequencing data analysis.
  • Maintaining and upgrading our in-house NGS data analysis and review system
  • Documenting scripts and updates in a systematic and detailed manner
  • Maintaining accurate records of all activities carried out in conjunction with different projects
  • Attending lab meetings/exome meetings and reading current journal articles pertaining to relevant projects


  • Master's degree in bioinformatics or a related field required.
  • Minimum of 2 years of work experience related to the analysis of high-throughput sequencing preferred
  • Knowledge and demonstrated experience of the following languages is essential: Perl/Python, PHP5, MySQL, HTML, JavaScript, CSS, BASH
  • Experience in version control with git is essential
  • Strong ability to administer/navigate Linux/Unix and OSX environments required
  • Experience with creating and maintaining databases with MySQL is essential
  • Knowledge of various next generation sequencing data analysis tools such as BWA, GATK, SAMTOOLS, Picard, snpEff, Annovar etc
  • Experience with developing, deploying and managing NGS data analysis pipelines required
  • Experience with HPC job submission, monitoring and debugging required
  • Ability and willingness to pick up new programming languages as necessary required.
  • Ability to coordinate multiple projects in a demanding research and diagnostic environment required
  • Strong communication and organizational stills required
  • Background in genetics preferred
  • Experience with CAP/CLIA protocols/requirements is preferred

How to Apply:

Apply online at

The University of Chicago is an Affirmative Action/Equal Opportunity/Disabled/Veterans Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national or ethnic origin, age, status as an individual with a disability, protected veteran status, genetic information, or other protected classes under the law. For additional information please see the University's Notice of Nondiscrimination. Staff Job seekers in need of a reasonable accommodation to complete the application process should call 773-702-5800 or submit a request via Applicant Inquiry Form.

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