Lenore Pipes
University of Hawaii at Manoa, HI·Computer Science·Early-career
Water, soil and sediment hold traces of DNA shed by the organisms that live there. This environmental DNA can reveal which species are present, from microbes to marine life, without ever seeing them.
- Fields
Computer Science
Ecology & Evolution
Genetics
- Topics
metagenomics
metabarcoding
environmental DNA
- Grants
- 2 known grants, through Dec 2028
What they work on
- Replace arbitrary species-assignment cut-offs in the tronko phylogenetic placement software with local thresholds based on Bayesian estimates of effective population size across the tree.
- Build a pipeline and web portal that use tronko to detect SARS-CoV-2 in wastewater samples and an expectation-maximization algorithm to estimate the proportions of viral strains.
- Develop a reference database builder that finishes within a day, using in silico primer amplification and k-mer matching against local or networked nucleotide databases.
- Develop a damage-aware phylogenetic placement algorithm that models position-dependent chemical damage to identify degraded sedimentary ancient DNA from Pacific sediment cores without complete reference genomes.
- Forecast shifts in marine communities under projected environmental scenarios using Bayesian joint species distribution models based on historical sedimentary ancient DNA records.
More about the research
Reading it requires software that can match millions of short, often damaged DNA fragments to the right species. The lab develops statistical and computational methods for this task. It applies them to modern samples, such as wastewater tracking of SARS-CoV-2, the virus that causes COVID-19, and to ancient DNA preserved in ocean sediments.
Why it matters
Faster and more accurate environmental DNA analysis could help public health agencies track which SARS-CoV-2 strains are spreading through wastewater, giving early warning of outbreaks. It could also improve biodiversity monitoring and pathogen detection. Reconstructing past ocean communities from ancient DNA could support forecasts of how marine ecosystems will shift, bringing ocean forecasting capability to Hawai'i.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Closest labs
Stephen Keller
University of Vermont, VT·Ecology & Evolution
Reconstruct about 13,000 years of alpine plant community history at the species level using ancient DNA from lake sediment cores in the Adirondacks, Green and White Mountains, and Katahdin.
Daniel Gruner
University of Maryland, MD·Ecology & Evolution
Measure the spread and extent of non-native plant invasions in Hawaiian forests using satellite, helicopter, drone and ground-based imaging and lidar, across islands ranging from 0 to 5 million years old.
Dorota Porazinska
University of Florida, FL·Ecology & Evolution
Describe new species of freshwater nematodes in the families Tobrilidae, Plectidae and Monhysteridae from Nebraska Sandhills aquatic habitats, using body-shape (morphological) analysis and DNA barcoding of individual specimens.
The school
University of Hawaii at Manoa: 23 labs on PI Pages, $376M a year on research, 182 research doctorates a year.
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