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Bioinformatics Scientist
Job#: 02-19-12
Positions: 1
Posted: 03/26/2013
Job Type: Full Time
Location: Lexington, MA
Department: Genomic Applications
Category: Scientist
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Job Description


RainDance Technologies, Inc. of Lexington, Massachusetts is a privately held, life sciences company that is pioneering the use of high-throughput microdroplet-based analysis in human health and life science research. The company's core RainStorm™ technology generates millions of discrete droplets that can encapsulate a single molecule, single cell or reaction and be digitally analyzed and sorted one at a time. The power, precision and simplicity of microdroplets enable researchers to answer complex questions with unprecedented sensitivity and quantification.

We are expanding our research and development team by recruiting candidates interested in challenging opportunities for long-term professional growth and personal development. We offer the successful candidate the opportunity to be part of a dynamic team in a pioneering microfluidics company. Our facility provides a work environment outfitted with the latest research and development technology. RainDance Technologies’ employees have an opportunity to work with premier scientists, academic institutions and partner companies in the commercialization of our innovative microfluidics platforms.


  • A key function of the Bioinformatics Scientist role is the analysis of next generation sequencing data generated across the breadth of all sequencing platforms.  The data analysis will support RainDance’s commercialization activities including product development, marketing, and the support of outside customers.   Data analysis includes the development of algorithms and scripts to enhance and expand the capabilities of the current analysis software as well as evaluate existing Bioinformatics workflows and processes, and implement plans for optimization and automation, where applicable.
  • A second key function of the Bioinformatics Scientist role is the management, maintenance and improvement of the primer design pipeline utilized for the design of custom primer droplet libraries.  This includes the development and maintenance of databases for the storage and tracking of primers and sequencing data.  This role will also support the development of additional bioinformatics tools necessary to support internal projects and customer requirements. 


  • Analysis of sequencing data generated by the major next generation sequencing platforms.
  • Writing of reports and presentation of sequencing data analysis internally and to customers.
  • Working with customers to implement and optimize sequencing analysis pipelines at their site.
  • Maintaining and enhancing the RainDance primer design pipeline.
  • Designing primers for customer droplet libraries including trouble shooting and custom design requests.
  • Writing and validation of software and scripts for the analysis of sequencing data and the design of primers.
  • Evaluating commercially available software packages for the analysis of next generation sequencing data for recommendation to customers.
  • Developing and maintaining databases for sequencing data and analysis.
  • Supporting the development of additional bioinformatics capabilities as deemed necessary.
  • Assisting with collaborations and feasibility studies with academic institutions and industry partners



  • BS/MS in Bioinformatics, Computational Biology, Applied Math or Statistics.
  • 2-3 years of industry or academic experience (post graduation) analyzing next generation sequencing data in a bioinformatics environment.
  • Familiarity with software packages used in the analysis and visualization of next generation sequencing data such as GATK, SamTools, Picard, IGV, BWA, BLAT
  • Expertise in scripting languages (Python, Perl), mathematics software (R, Matlab), and object-orient programming (with Java/C++).
  • Experience with RDBMS (MySQL) and SQL
  • Experience working in a Linux environment.
  • Familiarity with Primer3 and other primer design software.
  • Knowledge and experience with public genomic databases such as UCSC Genome Browser, COSMIC, NCBI
  • Strong math background especially in the area of statistical analysis of large data sets.
  • Demonstrated ability to work in an interdisciplinary team setting
  • The ability to overcome technical challenges in a fast paced, commercial environment.
  • Excellent communication and organizational skills.
  • Self-starter who requires minimal supervision to be productive.


  • Background in molecular biology or biology related fields.
  • Familiarity with CLC Bio Genomics workbench
  • Experience in implementing cloud based approach to NGS data analysis
  • Experience developing web-based applications, preferably in .Net or similar technology
  • Machine learning and clustering approaches
  • Experience designing primers and probes for TaqMan qPCR assays.
  • Experience interacting one on one with customers.

 Interested candidates please submit resume with cover letter 

 RainDance is an Equal Opportunity Employer

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