Bioinfo-Comput Biologist Inter

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How to Apply

Please submit a CV, a link to a code portfolio, a brief cover letter, and contact information for three references. In your cover letter, tell us about a system you deployed that other people use, and what broke. Review of applications will begin immediately and continue until the position is filled.

Who We Are

• The Parker generates mechanistic knowledge about how disease susceptibility is encoded in the non-coding genome, with a focus on metabolic traits. We combine statistical genetics, single-cell and single-nucleus multi-omics, and computational genomics to translate GWAS signals into biology. Our work spans method development, data generation (snRNA-seq, snATAC-seq, MPRA, spatial omics), and integrative analysis at scale. Dr. Parker also directs the Epigenomic Metabolic Medicine Center at the University of Michigan.
• We are a group of roughly 20 scientists and we take lab culture seriously. We value openness, scientific rigor, direct and collegial communication, and good humor. We invest in each other through regular mentorship, quarterly wellness meetings, and an annual lab retreat.
• For more information, see http://theparkerlab.org.

Mission Statement

Michigan Medicine improves the health of patients, populations and communities through excellence in education, patient care, community service, research and technology development, and through leadership activities in Michigan, nationally and internationally. Our mission is guided by our Strategic Principles and has three critical components; patient care, education and research that together enhance our contribution to society.

Job Summary

The Parker Lab at the University of Michigan (http://theparkerlab.org) is hiring a Bioinformatician Intermediate to stand up and operate the Apache Texera platform at Michigan as part of BRIDGE, a new NSF-funded national center. Texera is an open-source, browser-based system that lets scientists build and run data analysis workflows without writing code. Our team leads the metabolic traits domain of the center.

The core of the job is deployment and operations: getting Texera running reliably on Michigan?s high-performance computing infrastructure, extending it to AWS as demand grows, and keeping it working for the metabolic trait researchers who use it. You will also port our single-cell and single-nucleus multi-omic pipelines onto the platform as reusable workflows, and answer questions from users when they run into trouble.

This is a hands-on, build-it role. Dr. Steve Parker sets scientific direction and Dr. Ha Vu provides day-to-day supervision. You will work directly with the Apache Texera engineering team at UC Irvine, who have a working reference deployment, and with Michigan?s research computing staff.

Responsibilities*

• Deploy and operate Texera on Michigan HPC infrastructure, integrating its architecture with a Slurm-managed cluster.
• Extend the deployment to AWS to provide elastic compute as user demand grows.
• Maintain the deployment: monitoring, upgrades, storage, authentication, troubleshooting, and cost management.
• Implement our single-cell and single-nucleus multi-omic pipelines (snRNA-seq, snATAC-seq, multiome) as containerized, reusable Texera workflows, and scale them to atlas-level and population-scale datasets.
• Provide technical support to platform users and triage issues, escalating upstream to the Texera team where appropriate.
• Contribute fixes and operators upstream to Apache Texera, and document the Michigan configuration so it is reproducible.

Required Qualifications*

• Master's or PhD in computational biology, bioinformatics, computer science, or a closely related field. Equivalent research software engineering experience will be considered.
• Demonstrated experience deploying and maintaining containerized services, including Docker or Singularity.
• Strong Linux systems skills and substantial hands-on experience in an HPC environment, particularly Slurm.
• Strong programming skills in Python and/or R, with version control, testing, and documentation as habits.
• Experience building reproducible analysis pipelines, for example with Nextflow, Snakemake, or WDL.
• Working knowledge of sequencing data analysis, sufficient to build and debug genomics workflows and answer user questions about them.
• Evidence of independent delivery: a track record of taking a loosely specified goal to a working, documented, running result with limited supervision.
• Ability to explain technical problems clearly to scientists without computational training.
• English language proficiency.

Desired Qualifications*

• AWS experience, including EKS, EFS, and cost-aware resource provisioning.
• Kubernetes networking and configuration management, for example Helm, VXLAN overlays, Ansible, or Terraform.
• Depth in single-cell or single-nucleus data analysis. We prioritize methodological understanding over familiarity with specific tools.
• Experience with workflow platforms such as Texera or Galaxy.
• Java or Scala, which would let you contribute native operators to the Texera codebase.
• Prior open-source contribution in a public repository.
• Prior work on metabolic, endocrine, or cardiometabolic disease.

We do not expect all of this in one person. Tell us whether you are coming from research computing and want more genomics, or from computational genomics and want to build infrastructure that many people use.

Modes of Work

Positions that are eligible for hybrid or mobile/remote work mode are at the discretion of the hiring department. Work agreements are reviewed annually at a minimum and are subject to change at any time, and for any reason, throughout the course of employment. Learn more about the work modes.

Additional Information

Full time, based in Ann Arbor, Michigan, with possible hybrid flexibility. University of Michigan classification: Bioinformatics Scientist Intermediate, salary commensurate with experience. Grant-funded, with initial appointment through [end date] and renewal contingent on continued funding.

Background Screening

Michigan Medicine conducts background screening and pre-employment drug testing on job candidates upon acceptance of a contingent job offer and may use a third party administrator to conduct background screenings. Background screenings are performed in compliance with the Fair Credit Report Act. Pre-employment drug testing applies to all selected candidates, including new or additional faculty and staff appointments, as well as transfers from other U-M campuses.

U-M EEO Statement

The University of Michigan is an Equal Opportunity Employer. We are committed to providing an environment of mutual respect where equal employment opportunities are available to all applicants, including protected veterans and individuals with disabilities.