Bioinformatician II

University of Massachusetts Medical School
Job Location
Worcester, MA 01605
Yearly Salary
Job Description


Located in Worcester, the University of Massachusetts Medical School (UMMS) is one of the fastest-growing academic health centers in the country and is home to the School of Medicine, the Graduate School of Biomedical Sciences and the Graduate School of Nursing. During the past four decades UMMS researchers have made advances in a broad range of disease families, from HIV and infectious diseases to cancer, genetic disorders, diabetes and immune disease. UMMS faculty discovered the link between the immune system and type-1 diabetes, found the genetic cause underlying the third-most-common form of the muscular dystrophies, established the fundamental difference between HIV and other retroviruses and co-discovered RNA interference (a gene-silencing process which has become a tool in research focused on such areas as diabetes, HIV/AIDS and cancer).


Bioinformatics Core Facility uses sequence data to study the evolution of non-coding elements of the mammalian genome. In the last years sequencing has become the readout of choice for many assays ranging from transcriptional annotation and quantification (RNA-Seq), protein-nucleic acid interactions (ChIP and CLIP sequencing), genotyping through exome or whole genome sequencing. While allowing for unbiased, genome-wide data generation, the analysis of this data requires significant computational expertise and is often not carried out by those who generate it.

The Bioinformatics Core mission is two-fold:

  1. To evaluate, select, and implement when needed the best of breed computational solutions for the analysis of biological data.
  2. To allow those who generate the data to be able to analyze it using state of the art methods by reducing the computational expertise required to apply these methods.

Further, the Bioinformatics Core complements our software solutions by sponsoring a monthly seminar and by training sessions describing the theoretical and practical aspects of the solutions we host and by actively participating in the bioinformatics list serve where specific analysis questions are discussed.


Due to our continued growth, we are seeking an experienced Bioinformatician II who will be 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.


In this position, the candidate will participate in the design and implementation of a scalable, user-friendly online system that host complex and robust data analysis pipelines to be used by the university and by external partners. The successful candidate will participate in workshops designed to train PhD students, Postdoctoral candidates and staff members on the analysis tools we provide. The following essential responsibilities include:

  • 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


BS in computer science, or equivalent experience and 2 years of experience in relevant setting are required. Strong background in statistical methodology, software languages and computer systems (Perl, C or C++, R, MySQL, etc.) as well as experience in writing basic search algorithms and the ability to generate new algorithms and programs for custom data manipulation and analysis are essential.


The ideal candidate will have a strong background in computer science and a keen interest in biology. A key component of this position is teaching as well as having a strong interest in applying analytical methods to a science that has been transformed into a computational intensive discipline over the course of the last ten years is a must. Excellent communication skills, both oral and written, and interpersonal skills are necessary to interact with a wide range of individuals. Co-authorships on peer-reviewed publications are strongly preferred.



  • Java/Python/Perl/Awk application development languages
  • Extensive Linux knowledge
  • Web/Application servers: Apache, nginx
  • Web technologies: Javascript, JQuery, Ajax etc.
  • PHP5 or a web development knowledge with MySQL
  • Restful Web Service design and implementation
  • Amazon Web Services and Amazon
  • Docker
  • Pipeline, workflow design principles
  • PostgreSQL, Oracle and other open source database platforms
  • Familiarity with Sequencing Data analysis (RNA-Seq, ChIP-Seq, etc)
  • Familiarity with the Galaxy application
  • Understanding of Bowtie, BWA, Tophat, RSEM, STAR, third party analysis tools
  • Bioperl
  • Tomcat and other web servers


Additional Information:

Why Join UMass Medical School?

The University of Massachusetts Medical School (UMMS) offers a very competitive compensation and benefits package including four weeks paid vacation, free tuition at any Massachusetts state school, a robust and affordable variety of health and dental plans, participation in the state retirement plan, and a rewarding environment driven by distinctive work in progressive education and research.


If challenging and competitive work in a fast paced environment appeal to you, consider sharing your talents with one of the fastest growing academic health centers in the country.


Ranked 5th in primary-care education and 48th in research among the United States' 125 medical schools in the 2014 U.S. News & World Report annual guide, "America’s Best Graduate Schools,” UMMS is also a world recognized research center. Beyond its core mission of distinction in health sciences education, UMMS has exploded onto the national and international scene as a major center for research with UMMS researchers making pivotal advances in HIV, cancer, diabetes, genetic disorders, infectious disease and in understanding the molecular basis of disease.


UMass Medical School is committed to being an equal opportunity and affirmative action employer and recognizes the power of a diverse community. We encourage applications from protected veterans, individuals with disabilities and those with varied experiences, perspectives and backgrounds to consider UMass Medical School as their employer of choice.
Review of applications will begin immediately and the position will remain open until filled.

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