Positions
The lab is currently accepting Ph.D. rotation students and undergraduate researchers, on both the wet-lab and the computational sides.
Graduate training
Rotation projects for Ph.D. students
Rotation projects are available in single-molecule accuracy measurement, targeted long-read sequencing of pharmacogenomic loci, and statistical characterization of sequencing error. The PI chairs the Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, and rotations are typically arranged through your program's rotation process.
Formal admission runs through the Rackham and departmental admissions portals. An email is welcome and useful for arranging a rotation, but it cannot substitute for a formal application.
Undergraduate research
Joining through UROP
The lab takes undergraduates through the University of Michigan Undergraduate Research Opportunity Program (UROP) and by direct arrangement. Projects are available on both the wet-lab and computational sides, and most students work on some of each: a project typically runs from library preparation at the bench through basecalling and analysis.
No prior research experience is required. Students are trained in the specific methods their project needs, and the mentors are the graduate students, postdocs, and staff who developed those methods.
Wet-lab projects
Bench projects are in nanopore library preparation, Cas9-guided targeted enrichment, and the construction of sequence-defined DNA standards by Golden Gate assembly. Recent undergraduate projects have measured nanopore ligation efficiency, compared staggered against blunt Cas9 cutting geometry, built CYP2D6 and CYP2D7 standards by full-gene synthesis, and developed bead-based immobilization and Cas9 elution for patient DNA.
Computational projects
Dry-lab projects score basecalls against known templates, build error metrics and demultiplexing pipelines, and evaluate or retrain nanopore basecallers. Python is the working language, with analyses run on Linux. Students have worked on empirical error-rate bounding and on the matrix formulation of the accuracy metrics.
Projects currently posted
Toward Single-Molecule Accuracy: Empirical Error Rate and Bias Measurement of Single Molecule DNA Sequencers (computational). Nanopore sequencers read DNA by measuring the electrical change as a molecule passes through a pore, and machine-learning basecallers convert that raw signal into bases. The accuracy of those basecallers has not been independently verified, which is an obstacle to using the technology in FDA-approved clinical assays. The student works with signal data from DNA standards the lab builds for this purpose: running analysis pipelines, deriving error-rate, methylation-associated error and sequence misclassification measures, and contributing to retraining the basecalling models. Python and Bash, with Epi2Me and GitHub; no prior machine-learning experience required. The project needs 5-hour blocks on weekdays. Mentors: Gregory A. Farnum and Brian D. Athey.
Improving Accuracy of Single Molecule Nanopore Sequencers by Fine-Tuning AI Basecallers using High Purity DNA Standards (computational). UROP project 35694. Mentor: Gregory A. Farnum.
Investigating Cas9-Cut DNA Overhang Structures to Improve Targeted Long Read Sequencing: From CYP2D6 Pharmacogenomics to Subtelomeric Telomere Enrichment (wet-lab and computational). UROP project 34601. Mentor: Brian D. Athey.
Building Agentic Infrastructure for Long-Read Genomics: Tool-Calling AI Agents that Run, Track, and Reproduce Sequencing Workflows across Lab Workstations and HPC (computational). UROP project 35698. Mentor: Haoran (Henry) Li.
Project titles and mentors are taken from the lab's UROP posting. The first entry carries the full description from its application; descriptions for the other three are added as their applications are finalized.
Presenting and publishing
Undergraduates present their own work. Four posters in the poster archive are first-authored by one of three undergraduates, presented at the UROP and DCMB meetings. Contributions to manuscripts are credited by name: the lab's current sequencing manuscript names thirteen people as having carried out the laboratory work. Students in the lab also pursue departmental honors theses.
Applying
Projects are posted through UROP. Summer proposals go up on a rolling basis, generally before the last week of April; the summer program is paid and full-time. Placement runs through the UROP portal.
Inquiries by email are welcome. Useful things to include: which side of the work interests you, your year and major, and when you could start. Reading one of the undergraduate posters first is worth the ten minutes, since they are the output of the kind of placement being advertised. Addresses are on the Contact page.