Michael Gruenstaeudl
Fort Hays State University, KS·Genetics
Researchers routinely download genome sequences from public databases and reuse them in new studies. Mitochondria (the cell's energy compartments) and plastids (plant compartments such as chloroplasts) each carry their own small genome, and tens of thousands of these are stored in GenBank, a public DNA sequence database.
- Fields
Genetics
Computer Science
Biology
- Topics
organelle genomes
mitochondrial genome
mtDNA
- Grants
- 1 known grant, through Aug 2027
What they work on
- Build a tool that automatically links organelle genome records on GenBank to their original short-read sequencing data in the Sequence Read Archive (SRA), making the raw evidence behind each genome available for checking.
- Develop a tool that scores genome quality from sequencing coverage, the number of reads supporting each position, and sequencing evenness, how uniformly that support is distributed across the genome.
- Create a tool that re-assembles each archived genome from scratch using modern assemblers and flags positions where the archived sequence disagrees with the fresh assembly.
- Develop a tool that evaluates gene annotations by contrasting a record's gene labels against those of closely related individuals or species, and test all four tools on datasets including thousands of human mitochondrial genomes.
More about the research
They feed into work on human genetics, microbiology, environmental health, toxicology and forensics. A considerable share of these records, however, show signs of trouble: sequences pieced together incorrectly from sequencing reads, or genes that are missing or mislabeled. Such problems appear even in records flagged as reference genomes, so studies that reuse them can inherit the mistakes.
Why it matters
Many biomedical studies depend on mitochondrial and plastid genomes pulled from GenBank, including work in human genetics, toxicology, environmental health and forensics. The proposed tools would let researchers measure the accuracy and completeness of each record, so they can assemble curated sets of trustworthy genomes and avoid propagating assembly or annotation errors into new analyses.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Closest labs
Daniel Sloan
Colorado State University-Fort Collins, CO·Genetics
Test whether plant MSH1, a repair protein likely acquired from giant viruses, drives a new form of mismatch repair that cuts both DNA strands and then repairs the break by copying a template, keeping plant mitochondrial mutation rates exceptionally low.
Emily Beck
University of Kansas, KS·Genetics
Identify how the nuclear genome compensates for fast-evolving, highly divergent mitochondrial genomes in admixed threespine stickleback populations, using publicly available sequencing data.
Bryan Greenhouse
University of California-San Francisco, CA·Microbiology & Immunology·Early-career
Determine how a person's existing anti-PfEMP1 antibodies and the var genes a parasite first switches on together shape the outcome of new Plasmodium falciparum infections, using plasma, RNA sequencing and clinical records from a Ugandan cohort.
The school
Fort Hays State University: 1 labs on PI Pages.
Reach out
A start for your email. Fill in the brackets.