University of Massachusetts Medical School

Bioinformatician II

5 months ago(7/21/2017 8:45 AM)
Requisition Number
# of Openings
Exempt/Non-Exempt Status





The laboratory of A.J. Marian Walhout, PhD is seeking outstanding candidates to join a multidisciplinary team of geneticists, bioengineers and bioinformaticians.


We are a highly interdisciplinary lab, combining experimental and computational efforts to study different types of biological networks, with a primary focus on gene regulation and metabolism and the connections between these two processes.


The Walhout Lab is one of the leading labs in the world in systems biology. Major contributions include the characterization of gene regulatory networks (Deplancke, Cell 2006; Martinez, Genes & Development 2008; Grove, Cell 2009; Fuxman Bass, Cell 2015), the reconstruction of metabolic networks (Yilmaz, Cell Systems 2015), and the discoveries of processes and mechanisms by which the microbiota affect host biology (MacNeil, Cell 2013; Watson, MacNeil, Cell 2013; Watson, Cell 2014; Watson, eLIFE 2016; Garcia-Gonzalez, Cell 2017).


Our research nimbly moves from experimentation to computation and vice versa. We seek a dynamic individual with an interest in large-scale data analysis (e.g., RNA-seq and metabolomics data), network biology and/or flux balance analysis.


Our laboratory is part of the Program in Systems Biology, which currently consists of five research groups, each with an extensive computational component. We are looking for enthusiastic bioinformaticians and computational biologists to become part of the team and collaborate with the computational community both in our lab and in our Program to facilitate their continuing excellence and growth.


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.


  • Co-authorships on peer-reviewed publications are preferred.
  • Experience using at least two of the following languages: Python, R, and Matlab.
  • Familiarity with RNAseq data and differential gene-expression analysis.
  • Experience using relation databases, mySQL and or structured data formats (e.g. HDF5).
  • Web experience (PHP, JavaScript, JSON, etc.) is a plus.
  • Normal visual acuity, hearing and manual dexterity.
  • Excellent communication skills.



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