Improving tools that read microbes' DNA in infections and the microbiome
Computational Methods for Microbial and Microbiome Sequence Analysis
['FUNDING_OTHER'] · JOHNS HOPKINS UNIVERSITY · NIH-11321139
This project develops faster, more accurate computer tools to read and clean up microbial and microbiome DNA so doctors and researchers can more reliably identify infections and microbes linked to health problems like cancer.
Quick facts
| Phase | ['FUNDING_OTHER'] |
|---|---|
| Study type | Nih_funding |
| Sex | All |
| Sponsor | JOHNS HOPKINS UNIVERSITY (nih funded) |
| Locations | 1 site (BALTIMORE, UNITED STATES) |
| Trial ID | NIH-11321139 on ClinicalTrials.gov |
What this research studies
If you have an infection or a condition linked to the microbiome, this project builds new computer programs that study DNA from microbes to find out which microbes are present and whether data are contaminated. The team creates algorithms for classifying microbes, assembling microbial genomes, and screening out contaminants that can produce false findings. They use machine learning tools such as Balrog and improve public genome databases to make results more accurate across many bacterial and archaeal species. Most of the work is done on computers and public sequence data but aims to improve tests and research that rely on patient samples.
Who could benefit from this research
Good fit: People with infections, suspected microbiome-related disorders, or cancer patients whose care involves microbial DNA testing would be most relevant to follow or contribute to this work.
Not a fit: Patients whose conditions have no link to microbes or microbiome data are unlikely to see direct benefit from this project.
Why it matters
Potential benefit: Could lead to clearer, more accurate microbial and microbiome test results, reducing misdiagnoses and helping doctors choose better treatments.
How similar studies have performed: Related computational tools from this group and others are already widely used and have shown improved accuracy, although contamination in public genome databases remains a problem.
Where this research is happening
BALTIMORE, UNITED STATES
- JOHNS HOPKINS UNIVERSITY — BALTIMORE, UNITED STATES (ACTIVE)
Researchers
- Principal investigator: SALZBERG, STEVEN L. — JOHNS HOPKINS UNIVERSITY
- Study coordinator: SALZBERG, STEVEN L.
About this research
- This is an active NIH-funded research project — typically early-stage science, not a clinical trial accepting patient enrollment.
- Some NIH-funded labs run parallel clinical studies or seek volunteers for related work. To check, contact the principal investigator or institution listed above.
- For full project details, budget, and progress reports, visit the official NIH RePORTER page below.
Conditions: Cancers