Job: Bioinformatician - The Ragon Institute of MGH, MIT and Harvard

Direct Supervisor:     Shiv Pillai, M.D. Ph.D. (

Email Contact:          Vinay Mahajan M.D. Ph.D. (


Employing Hospital and Department:       

Ragon Institute of MGH, MIT, and Harvard


Minimum degree and field of knowledge:  Ph.D. in bioinformatics, computational biology, or a related field, and experience with the analysis of next-generation sequencing data in a high-performance computing environment. An exception can be made for outstanding candidates with a Master’s/Bachelor’s degree with relevant experience.


Years experience required:  2 (including relevant work as a part of a graduate thesis)



A position is open for a full-time bioinformatician in the Pillai laboratory at the Ragon Institute of MGH, Harvard and MIT. The Pillai laboratory studies genetic and epigenetic mechanisms underlying chronic inflammatory diseases in humans and in mouse models, making extensive use of next-generation sequencing technologies. The laboratory is the site of an NIH-designated Autoimmunity Center for Excellence, and  applies Next Generation sequencing based analyses to a variety of clinical samples from immunological disorders.

The candidate will be expected to perform computational analyses related to a broad range of projects aimed at obtaining an improved understanding of the mechanisms underlying immunological disorders. This position also offers a stimulating and multi-disciplinary environment with numerous opportunities for interaction with our collaborators at other institutions including Nir Yosef (UC Berkeley), Ramnik Xavier (MGH), and Alex Shalek (MIT). The selected candidate will be co-mentored by Dr. Nir Yosef who will communicate regularly on a weekly basis by Skype and occasionally in person.


Job Duties:

The candidate will develop and implement analytical pipelines for the analysis of next-generation sequencing data including RNA-Seq, single-cell RNA-Seq, CHIP-Seq, ATAC-Seq, whole-genome bisulfite sequencing, exome sequencing, whole-genome sequencing, and variant analysis. In addition to interfacing with laboratory colleagues to prepare, analyze, and interpret next-generation sequencing data, the candidate will be expected to contribute to manuscript preparation, and build a strong publication based track-record for herself or himself.


Specific responsibilities include the following:

  • Communicate with colleagues to understand and develop requirements and specifications for the analysis of next-generation sequencing experiments.
  • Write new code as needed to enhance the rapidly evolving set of analysis methods for high throughput sequencing datasets
  • Develop reproducible pipelines for the analysis of NGS data on high-performance computing clusters (including RNA-Seq, ATAC-Seq, CHIP-Seq, and  single-cell RNA-Seq)
  • Integrate multiple data types using systems approaches for generating novel biological insights
  • Write detailed reports to be used to disseminate results to collaborators and prepare manuscripts




   Minimum Qualifications

  • Proficiency in R, Bash scripting and at least one other programming language (e.g. Python, Perl)
  • Familiarity with high performance computing environments


   Preferred Qualifications

  • Two or more years of prior experience with running next-generation sequencing pipelines for the analysis of RNA-seq, SNP analysis, CHIP-Seq etc. is strongly preferred
  • Knowledge of statistical models and practical machine learning
  • Solid understanding of statistical issues with the analysis of genomic data
  • Familiarity with R Bioconductor tools
  • Experience with distributed version control tools, and reproducible analysis.
  • Knowledge of immunology and/or genetics will be a plus.



  • Ability to work independently and display initiative within a team environment
  • Demonstrate integrity, excellence, accountability, and teamwork in all interactions
  • Good oral and written communication skills
  • Ability to maintain organized, detailed, and up-to-date documentation
  • Strong interest in immunology and biomedical research



Application Information:
The position is open immediately, although the start date is flexible. Please submit a cover letter, CV, and references to Shiv Pillai ( Unfortunately, due to the number of applications we receive, we may not be able to reply individually to all inquiries. All applicants must be available to come to Cambridge, MA USA for an interview.

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