Job Description

The Prensner laboratory ( at Chad Carr - Pediatric Brain Tumor Center in the Department of Pediatric Oncology and Department of Biological Chemistry is looking for an exceptional candidate for a unique Research Lab Specialist position focused on computational biology and bioinformatics.

This position affords the exciting opportunity to conduct research with cutting-edge sequencing-based data for childhood cancer.  Current interests for the lab include transcriptome assembly, RNA modifications / epitranscriptomics, and protein sequencing in the context of childhood cancer.

Prior work in the lab has focused on the dark genome in cancer (Prensner et al., Nature Biotechnology 2021), gene discovery in pediatric brain cancer (Hofman et al., Molecular Cell, 2024), and small open reading frames (Prensner et al., Molecular & Cellular Proteomics 2023; Mudge, Ruiz-Orera, Prensner et al, Nature Biotechnology 2022).  We have conducted high-depth proteomics analyses of cancer and non-cancer (Deutsch, 2024).  We have employed transformer models for small open reading frames in machine learning studies (Clauwaert et al, 2024).

The successful candidate will play a key role in the Prensner laboratory to develop an analytical pipeline for multi-omics datasets in cancer.  This candidate will drive forward research projects utilizing the following sequencing-based data types: ribosome profiling, RNA-sequencing, long read Oxford Nanopore Technology direct RNA sequencing, single cell RNA-seq. The Prensner lab has in-house Illumina and Oxford Nanopore sequencers to generate data rapidly.

In addition, this candidate will be critical to developing a novel bioinformatics approach for single-molecule protein sequencing.  The Prensner Lab is the only location at the University of Michigan and one of ~12 labs nationally that has an in-house protein sequencer for small open reading frame discovery.

This candidate will be expected to contribute to ongoing lab projects in a collaborative nature as well as drive independent research with the goal of publication.  He/she/they will receive commensurate academic credit for these efforts.

PRINCIPAL DUTIES AND RESPONSIBILITIES

• Develops bioinformatics pipelines for RNA sequencing-based data types (RNAseq, ribosome profiling, scRNAseq)
• Creates analytical frameworks for epitranscriptomics from long-read RNA sequencing
• Analyzes single peptide protein sequencing data using machine learning tools
• Contributes to maintenance and updating of existing computational pipelines in conjunction with the supervising bioinformatician
• Documents, compiles, and analyzes lab operations. Reports data to supervisor in oral and written reports.
• Attends team meetings.
• Other related tasks as required.

Education

• Bachelor or master's degree in computational biology, bioinformatics, the life sciences, engineering, or a related discipline.

Experience

• 1-3 years of experience

Skills and abilities

• Fluency with R, Python and/or Bash.  Unix/Linux experience is also helpful
• Prior experience with writing code in a variety of project settings
• Prior experience with nucleotide sequencing data is highly desired
• Familiarity with Docker containers and/or Snakemake workflows is helpful
• Exceptional organization and attention to detail are essential
• Excellent communication skills and the ability to interact with all levels of staff and with external contacts are needed.
• Ability and eagerness to learn in a self-motivating environment.

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.

Job openings are posted for a minimum of seven calendar days.  The review and selection process may begin as early as the eighth day after posting. This opening may be removed from posting boards and filled anytime after the minimum posting period has ended.

The University of Michigan is an equal opportunity/affirmative action employer.

About University of Michigan - Ann Arbor

A great university is made so by its faculty and staff, and Michigan is recognized as one of the best universities to work for in the country. The Michigan culture is known for engaging faculty and staff in all facets of the university to create a workplace that is vibrant and stimulating.For two consecutive years, the Chronicle of Higher Education has placed U-M in its "Great Colleges to Work For" survey. In particular, the university earns high marks for strong relations between faculty and administrators, a collaborative system of governance, strong pay and benefits, and a healthy work/life balance.

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