University of Massachusetts Medical School

  • Bioinformatician II

    Minimum Salary US-MA-Worcester
    Job Location 7 months ago(3/22/2018 10:56 AM)
    Requisition Number
    # of Openings
    Posted Date
  • Overview

    The University of Massachusetts Medical School (UMASS Medical) is a group of diverse businesses that make a significant contribution and impact in higher education, medical research, healthcare consulting/delivery and biotechnology throughout the commonwealth and the world. 


    We were recognized by US News & World Report Rankings as one of the best graduate schools for Primary Care Education and rank in the top 10 percent in the nation!  At UMass Medical School, Commonwealth Medicine and MassBiologics, our commitment to excellence, diversity, competitive salary & benefits.  Work-life integration will allow you to build a professionally rewarding career as we work together to positively impact the health of people around the globe. 




    In the Department of Molecular Cell & Cancer Biology of University of Massachusetts Medical School, we have developed a core team of accomplished computational biologists who work side-by-side with bench scientists to evaluate, select and develop algorithms and software pipelines to analyze, annotate, visualize and integrate various biological datasets, including those generated from high-throughput experiments such as ChIP-seq, ChIP-chip, RNA-seq, PAS-seq, iCLIP-seq, ATAC-Seq, miRNA-seq, exon sequencing, GUIDE-seq, single-cell sequencing, shRNA and gRNA screening, and CRISPR genome editing.  We are active contributors to the open-source open-development Bioconductor project. We have developed more than a dozen packages with various utilities, ranging from machine learning, peak calling, annotation, visualization, to gRNA design and evaluation.


    Under the direction of a member of the faculty, the Bioinformatician is responsible for the design, development, evaluation and iterative modification of a technical infrastructure to expedite the quantitative evaluation of data resulting from studies that are laboratory based.  The position will entail the establishment and maintenance of applicable in-house bioinformatics resources and interaction with individual lab members on customized research projects, as well independent projects that are solely computational. 




    • Establish general bioinformatics resources for day-to-day use by members of the laboratory.
    • In collaboration with a member of the faculty, generate customized programming solutions to improve user interaction with available bioinformatics resources
    • Implement and adapt programs for microarray analysis, high-throughput sequencing data analysis, cis regulatory motif identification, and multi-genome protein motif searches.
    • Independently develop, implement and maintain custom designed computational solutions relevant for ongoing lab-based projects.
    • Independently develop, implement and maintain computational methods for meta-analysis of data generated in the lab as well as publicly available data.
    • Independently execute a scientific computational project (e.g. a project that can result in a first author publication)
    • Supervise entry level bioinformaticians.
    • Local establishment and customization of model organism genomic databases and tools for batch sequence analysis utilizing these resources.
    • Interpret and present study results in support of laboratory members.
    • Provide tabular and written summaries of approaches and analyses in a form suitable for inclusion in manuscripts or grant applications, as well as media for presentation at scientific meetings
    • Develop and implement custom bioinformatics programming solutions in collaboration with lab as necessary
    • Coordinate and collaborate with other research computing expertise at the Medical School as necessary
    • Participate in conference calls and data management meetings as needed
    • Perform other duties as required



    • BS in computer science, or equivalent experience
    • 2 years of experience in relevant setting
    • Co-authorships on peer-reviewed publications are strongly suggested but not required
    • Strong background in statistical methodology, software languages and computer systems (Perl, C++, R, MySQL, etc.)
    • Experience in writing basic search algorithms and the ability to generate new algorithms and programs for custom data manipulation and analysis
    • Excellent communication skills, both oral and written, and interpersonal skills necessary to interact with a wide range of individuals.


    • Master's degree in Bioinformatics, Computer Science, Statistics or related computational disciplines
    • Minimum 1 year bioinformatics-related research experience
    • Proven research record such as co-authorship on peer-reviewed

    Additional Information

    Responsibilities include-

    • Develop novel algorithms and software tools for integrated data analysis and visualization of high-throughput dataset including next-generation sequencing data and proteomics data when existing software packages are not available or adequate
    • Enhance/Maintain Bioconductor packages developed in house
    • Collaborate closely with PIs and their lab members on research projects including evaluating, selecting, and implementing when needed the best of breed computational solutions for the analysis of biological data
    • Develop rapid prototypes and custom scripts for one-off type of analysis requests
    • Properly document the procedures used in computational analysis and provide summary report of results suitable for inclusion in manuscript and grant applications


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