Bioinformatician, Sr. Analyst - Duchossois Family Institute

University of Chicago

University of Chicago

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Chicago, IL, USA
Posted on Monday, February 5, 2024


BSD DFI - Bioinformatics

About the Department

The Duchossois Family Institute (DFI) focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact human health. Bioinformaticians in the DFI perform genomic analyses including genome assembly and annotation and working with computation software programs to analyze microbial genome sequences and characterizing their metabolite utilization and secretion.

Job Summary

At the DFI, we rely on a dynamic team of bioinformaticians, data scientists, and programmers to handle our rapidly growing biomedical data and its analysis. The Bioinformatician, Sr. Analyst will work as part of the translational informatics team improving existing 16S rRNA, whole genome sequencing and Shotgun metagenomics/transcriptome pipelines, analyzing genomics and developing Web applications. The ideal candidate will work closely with clinical and laboratory investigators to analyze 16S rRNA and shotgun metagenomic sequences and use a range of statistical tests to compare microbiota and microbiome compositions in longitudinal and cross-sectional studies. In addition, the ideal candidate will also work closely with investigators to customize and perfect analytical Web applications being developed at the DFI.


  • Develop and maintain existing Web application to facilitate genomics data accessing and sharing.

  • Plans own resources to implement or modify existing web-based bioinformatics tools.

  • Participate in agile software development including design, implementation, and deployment.

  • Works with the sequencing core at the DFI to understand the protocols and handle analysis of sequence data.

  • Participate in the design and implementation process through sequencing data analysis and taxonomy classification.

  • Data analysis of high throughput genomics, transcriptomics and genetic data.

  • Implement and integrate existing suitable bioinformatics tools to current pipeline.

  • Transfer abstract workflows into production level software by automating them using workflow orchestration tools such as Nextflow.

  • Use existing HPC resources to run the analytical workflows at scaleSupport all phases of bioinformatics activities by helping devise or modify procedures to solve complex problems.

  • Develop Python and JavaScript libraries for the visualization of microbiome/metagenome, metabolome and other biomedical datatypes generated at the DFI.

  • Assist with the executions, tests and actively seeks project specific solutions.

  • Work in collaboration with others working to complete projects in a timely and efficient manner.

  • Assist in creating data algorithms and specialized computer software to identify and classify components of a biological system (e.g. DNA and protein sequences).

  • Support the development of data models, databases or software applications.

  • Produce, present and discuss high quality data analysis reports.

  • Participate in the communication of results through scientific publications.

  • Participates in creating data algorithms and specialized computer software to identify and classify components of a biological system (i.e. DNA and protein sequences).

  • Applies basic application of computational tools and information technology to gather, analyze and visualize data in biology and biomedical research.

  • Interprets data analysis of high throughput genomics, proteomics and genetic data.

  • Plans own resources to implement or modify existing web-based bioinformatics tools.

  • Performs other related work as needed.

Minimum Qualifications


Minimum requirements include a college or university degree in related field.

Work Experience:

Minimum requirements include knowledge and skills developed through 2-5 years of work experience in a related job discipline.



Preferred Qualifications


  • Degree in Biomedical Informatics, Bioinformatics, or Computational Biology.

  • Master’s degree.


  • Experience working on the analysis of the microbiota and microbiome associated data sets with a range of different experimental and clinical samples.

  • Extensive experience with bioinformatics tools/packages such as Mothur, QIIME, DADA2, Phyloseq, MEGAHIT, metaSPAdes, Metaphlan2, MG-RAST, HUMAaN2, Kraken, Bracken, and others that are used in the analysis of metagenomic sequence data.

  • Experience with sequencing technologies used for metagenome sequencing and familiarity with metabolomics concepts.

  • Experience with microbial genomics and familiarity with microbial metabolic pathways.

Technical Skills or Knowledge:

  • Fluency with multiple programming languages with Python, R-script, SQL, JavaScript strongly preferred.

  • Experience with design and development of relational databases and RDBMS such as PostgreSQL, MySQL.

  • Experience working on Linux and/or Unix systems, bash scripting.

  • Experience with website development and administration is strongly preferred.

  • Working knowledge of container technologies/platforms such as Docker and Singularity.

  • Experience using HPC resources and technologies such as Slurm, PBS, Condor, etc., for high-throughput analysis of sequence data.

  • Experience with workflow technologies such as Nextflow, CWL, Galaxy and running pipelines at scale.

  • Knowledge of Cloud computing using AWS, Azure or Google Cloud a plus.

  • Proficiency with Git/Github.

Preferred Competencies

  • Must work closely with students, postdoctoral fellows, and faculty members.

  • Must pay great attention to detail and help investigators design studies that will provide useful and ultimately publishable data.

  • Must have flexibility in order to provide analyses that, in some circumstances, are required for grant or presentation deadlines.

Working Conditions

  • Office environment.

Application Documents

  • Resume (required)

  • Cover Letter (preferred)

When applying, the document(s) MUST be uploaded via the My Experience page, in the section titled Application Documents of the application.

Job Family


Role Impact

Individual Contributor

FLSA Status


Pay Frequency


Scheduled Weekly Hours


Benefits Eligible


Drug Test Required


Health Screen Required


Motor Vehicle Record Inquiry Required


Posting Statement

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Staff Job seekers in need of a reasonable accommodation to complete the application process should call 773-702-5800 or submit a request via Applicant Inquiry Form.

We seek a diverse pool of applicants who wish to join an academic community that places the highest value on rigorous inquiry and encourages a diversity of perspectives, experiences, groups of individuals, and ideas to inform and stimulate intellectual challenge, engagement, and exchange.

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