IT Pro 3-Data Engineering

This Bioinformatics Engineer position is integral to the UMGC's operations, directly supporting the unit's work by managing the informatics infrastructure that processes data generated by sequencers and other lab instrumentation. The role involves close collaboration with other members of the informatics team, laboratory staff, and customers to enhance data handling processes and infrastructure. A primary objective is to implement analysis workflows for new services, ensuring seamless delivery of high-quality data to customers and supporting the overall research objectives of the University and its partners.

Workflow development (60%)
* Design, implement, and maintain automated pipelines for processing NGS data (e.g., WGS, RNA-seq, single-cell, ChIP-seq).
* Develop production-ready, version-controlled, well-documented software and command-line tools in Python, Perl, R, or similar languages.
* Collaborate with wet lab personnel to integrate sequencing instrumentation output into streamlined data workflows.
* Maintain and document a codebase in Git, and follow best practices for software development and reproducibility.
* Monitor workflow performance and proactively troubleshoot pipeline failures or anomalies in data quality.
Infrastructure development (30%)
* Support the development and maintenance of internal web applications, dashboards, or APIs for data reporting and user access.
* Automate routine processes including QC reporting, data transfers, and notification systems.
Customer support (10%)
* Provide consultation and support to Genomics Center staff and customers on bioinformatics tools, data formats, and analysis interpretation.

Mostly Remote Time spent working remotely is consistently 50% time or more. Collaborative or shared on campus work space to be provided while on campus.

Required Qualifications:
* Bachelor's degree in Computer Science, Computational Biology, Bioinformatics, or a related field plus at least four years of experience, or master's degree plus at least two years of experience.
* 2+ years of experience developing software in a Unix/Linux environment, with strong skills in Python or Perl, R, and Bash.
* 2+ years of experience developing and running computing workflows in a Linux/Unix high-performance computing environment
* Strong understanding of software development practices, including version control (Git), modular code, documentation, and testing.
* Strong proficiency with Linux, including file systems, command-line tools, scripting, and job scheduling.
* Familiarity with bioinformatics tools and file formats (e.g. FASTQ, BAM, VCF, BWA, STAR, samtools, bedtools).
* Familiarity with biological concepts relevant to genomics and molecular biology.
Preferred Qualifications:
* Master's or Doctorate degree in Computer Science, Computational Biology, Bioinformatics, or a related field.
* Experience developing and maintaining analysis pipelines for NGS data.
* Experience with workflow management systems (e.g., Snakemake, Nextflow, Cromwell).
* Experience with containerization (Docker, Singularity) and deployment tools.
* Experience with data visualization libraries.
* Web development experience.
* Experience working in an academic research environment.

Must be able to lift 25 pounds.

The University of Minnesota Genomics Center (UMGC) provides genomic technologies and services to researchers and clinicians at the University of Minnesota, and to external academic and industry scientists throughout the United States and internationally. Our mission is to advance the use of genomics and achieve this by acquiring state-of-the-art instrumentation and offering an array of services, including next-generation sequencing, long-read sequencing, expression analysis, genotyping, epigenomics, single-cell and spatial genomics, metagenomics, as well as related support services such as nucleic acid extraction and quality control. We strive to keep pace with the ever-broadening world of "omics" technologies and to expand our role at the University and the wider biotech community.

Pay Range: $98,300 - $117,000; depending on education/qualifications/experience

Time Appointment Category: 75%-100% Appointment (If job description above does not specify appointment or expected weekly hours, assume a 100% appointment.)

Position Type: Faculty and P&A Staff

Please visit the Office of Human Resources website for more information regarding benefit eligibility.

The University offers a comprehensive benefits package that includes:

• Competitive wages, paid holidays, and generous time off
• Continuous learning opportunities through professional training and degree-seeking programs supported by the Regents Tuition Benefit Program
• Low-cost medical, dental, and pharmacy plans
• Healthcare and dependent care flexible spending accounts
• University HSA contributions
• Disability and employer-paid life insurance
• Employee wellbeing program
• Excellent retirement plans with employer contribution
• Public Service Loan Forgiveness (PSLF) opportunity
• Financial counseling services
• Employee Assistance Program with eight sessions of counseling at no cost
• Employee Transit Pass with free or reduced rates in the Twin Cities metro area

Applications must be submitted online. To be considered for this position, please click the Apply button and follow the instructions. You will be given the opportunity to complete an online application for the position and attach a cover letter and resume.

Additional documents may be attached after application by accessing your "My Job Applications" page and uploading documents in the "My Cover Letters and Attachments" section.

To request an accommodation during the application process, please e-mail employ@umn.edu or call (612) 624-8647.

The University recognizes and values the importance of diversity and inclusion in enriching the employment experience of its employees and in supporting the academic mission. The University is committed to attracting and retaining employees with varying identities and backgrounds.

The University of Minnesota provides equal access to and opportunity in its programs, facilities, and employment without regard to race, color, creed, religion, national origin, gender, age, marital status, disability, public assistance status, veteran status, sexual orientation, gender identity, or gender expression. To learn more about diversity at the U: http://diversity.umn.edu

Any offer of employment is contingent upon the successful completion of a background check. Our presumption is that prospective employees are eligible to work here. Criminal convictions do not automatically disqualify finalists from employment.

The University of Minnesota, Twin Cities (UMTC)

The University of Minnesota, Twin Cities (UMTC), is among the largest public research universities in the country, offering undergraduate, graduate, and professional students a multitude of opportunities for study and research. Located at the heart of one of the nation's most vibrant, diverse metropolitan communities, students on the campuses in Minneapolis and St. Paul benefit from extensive partnerships with world-renowned health centers, international corporations, government agencies, and arts, nonprofit, and public service organizations.

At the University of Minnesota, we are proud to be recognized by the Star Tribune as a Top Workplace for 2021, as well as by Forbes as Best Employers for Women and one of America's Best Employers (2015, 2018, 2019, 2023), Best Employer for Diversity (2019, 2020), Best Employer for New Grads (2018, 2019), and Best Employer by State (2019, 2022).