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Computer Programmer @ The University of Massachusetts Boston

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Position details:

The Computer Programmer/Software Engineer will participate in the fields of computational and systems biology, bioinformatics, and cancer genomics within the Biology Department.  The incumbent will assist the laboratory Principal Investigator (PI) in new and ongoing research projects in the laboratory; and will participate in and assist with the organization of the laboratory’s software development efforts.  Current projects include developing software to analyze protein-DNA binding specificity and to find genetic markers for cancer phenotypes. Future projects include developing software for determining protein-RNA binding specificity and epigenetic markers for cancer phenotypes.  The incumbent will use and develop machine learning methods combined with biophysical models to explain gene regulatory phenomena.
  • This position provides an excellent opportunity to participate in cutting-edge research in genomics and computational biology. The position offers a stimulating academic environment with opportunities to learn new programming skills, collaborate in a team setting, gain valuable written/oral communication skills, and possibly co-author publications.

Duties:

  • Work in the fields of computational and systems biology and cancer genomics;
  • Analyze high-throughput experimental genomics data in R, Perl, Python, or Java;
  • Participate in the laboratory’s software development efforts;
  • Develop new algorithms to analyze biological data;
  • Program efficient code in Java, R, Perl, and possibly other languages;
  • Program Java Swing and Java Web Start (JWS) applications;
  • Program profile hidden Markov models in Java;
  • Perform other duties as assigned. 

Requirements:

Bachelor’s Degree in Computer Science, Computational Biology, Bioinformatics, or related field is required; Master’s degree preferred. Minimum of one-three years of work experience in computational biology, bioinformatics and Java programming is required. Experience in the software engineering lifecycle: data modeling, process modeling, prototyping, testing, release, change management, and version control (Git) is required.  Experience in R and working with mammalian genomic sequences is preferred. Experience in GUI (Swing) programming, dynamic programming, machine learning, and hidden Markov model is preferred.

  • Proficiency in Linux/Unix, Java, Perl, bash scripting, and DNA sequence analysis;
  • Proficiency in object-oriented programming;
  • Proficiency with Microsoft Office Suite and other administrative software;
  • Ability to follow oral and written instructions;
  • Ability to work well with others;
  • Strong quantitative, statistical, and programming skills;
  • Strong oral and written communication skills;
  • Strong attention to detail;
  • Strong record-keeping skills;
  • Strong commitment to customer service. 

Application Instructions:

Please apply online with your resume, cover letter, and list of three professional work references.

  • Professional Union. Benefited.
  • Full-Time. Grade 29.
  • Normal Hiring Range: $38,785-$42,179
  • Unrestricted funding.
Review of candidates will begin following the application closing date.
Closing date for applications: August 18, 2014

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Current projects include developing software to analyze protein-DNA binding specificity and to find genetic markers for cancer phenotypes. Future projects include developing software for determining protein-RNA binding specificity and epigenetic markers for cancer phenotypes. The incumbent will use and develop machine learning methods combined with biophysical models to explain gene regulatory phenomena.