Senior Bioinformatics Scientist

Department
 

BSD DFI - Translational Informatics

About the Department
 

The Duchossois Family Institute 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
 

The Senior Bioinformatics Scientist conducts bioinformatics research and has deep specialized knowledge for developing methods and software tools to analyze and interpret data for genomic and microbiome studies.

This role is responsible for all aspects of research data management for clinical data, microbiome sequence data and results of analysis within the translational informatics. Plans and conducts clinical and non-clinical research. Manages engineering and technical support activities to develop and maintain tools and computational methods needed to gather and analyze data. 

Implements SOPs and data models for all the biomedical data generated within DFI from the various cores (MMF, HMMF). Works on external collaborations on bioinformatics projects that aligned with DFI’s mandate when required. Lead development of solutions that involve multi-omic data including clinical data within the transitional informatics team at DFI and also help in training and mentoring junior team members and interns. Solves complex problems; takes a Leads implementation or broad perspective to identify innovative solutions. Works independently, with guidance in only the most complex situations.

Responsibilities

• Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data. 

• Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform.

• Functional analysis of the metagenome data by managing the KEGG database and integrating it within translational applications.

• Facilitate the development of analytical pipelines for 16s and shotgun metagenome data.

• Collaborate with CRI to facilitate access to and integration of clinical data for various clinical projects within DFI and also external collaborations such as PreSET. 

• Leads implementation or modification of existing web-based bioinformatics tools.

• Provides expertise to biomedical informatics related concepts, applications, and tools.

• Improves development of training, tools, and process documentation.

• Performs other related work as needed.

Minimum Qualifications
 

Education:

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

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Work Experience:

Minimum requirements include knowledge and skills developed through 7+ years of work experience in a related job discipline.

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Certifications:

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Preferred Qualifications
 

Education:

• Master’s degree in Bioinformatics, Public Health, Industrial Engineering or a related field.

Experience:

• Extensive knowledge of microbial metabolic pathways. 

• Expertise with Machine Learning and Shiny Fundamentals.

• Participation in workshops focusing on the analysis of next-generation sequencing data.

Technical Skills or Knowledge:

• Expertise with programming languages R-script, Python, SQL, JavaScript, and metagenomic pipelines (dada2, prokka, kneaddata, spades, kraken2, metaphlan, bowtie2, blastn).

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

• Experience with RNA-Seq analysis.

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. 

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

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
 

Research

Role Impact
 

Individual Contributor

FLSA Status
 

Exempt<