Lisa Zeigler Allen, PhD

Adjunct Scientist

Dr. Lisa Zeigler Allen is an adjunct scientist in the Microbial and Environmental Genomics Department. Her research is directed towards understanding microbial and viral interactions through large-scale metagenomic, single cell/virion genomic and cultivation based approaches. She led the experimental design and implementation of the first single virion isolation and genomic characterization and is currently using these techniques to evaluate samples from the natural environment.  Through community level analyses of microbial and virioplankton consortia and culture-based virus/host dynamics, in particular eukaryotic phytoplankton host/virus, she is investigating the influence of viruses on host function, ecosystem performance, community-level diversity and the evolution of hosts.

Prior to becoming an Assistant Professor at JCVI, Lisa received her PhD in Oceanography from Scripps Institution of Oceanography where she studied marine natural products and microbial and viral ecology using genome-enabled approaches. She received her Bachelor of Science degree in Biological Sciences at Washington State University and conducted undergraduate research on plant genetics in the lab of Diter von Wettstein.


Nature communications. 2022-05-04; 13.1: 2448.
Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region
James CC, Barton AD, Allen LZ, Lampe RH, Rabines A, Schulberg A, Zheng H, Goericke R, Goodwin KD, Allen AE
PMID: 35508497
Microbiology resource announcements. 2021-08-26; 10.34: e0061521.
Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent
Skoog EJ, Huber JA, Serres MH, Levesque A, Zeigler Allen L
PMID: 34435861
Scientific reports. 2021-08-02; 11.1: 15592.
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom
Oliver A, Podell S, Pinowska A, Traller JC, Smith SR, McClure R, Beliaev A, Bohutskyi P, Hill EA, Rabines A, Zheng H, Allen LZ, Kuo A, Grigoriev IV, Allen AE, Hazlebeck D, Allen EE
PMID: 34341414
Journal of visualized experiments : JoVE. 2013-05-26; 75: e3899.
Isolation and genome analysis of single virions using 'single virus genomics'
Zeigler Allen L, Ishoey T, Novotny MA, McLean JS, Lasken RS, Williamson SJ
PMID: 23728084
Genome research. 2013-05-01; 23.5: 867-77.
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, Torriani F, Nealson KH, Pevzner PA, Friedman R, Venter JC, Lasken RS
PMID: 23564253
The ISME journal. 2012-07-01; 6.7: 1403-14.
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic
Zeigler Allen L, Allen EE, Badger JH, McCrow JP, Paulsen IT, Elbourne LD, Thiagarajan M, Rusch DB, Nealson KH, Williamson SJ, Venter JC, Allen AE
PMID: 22278668
PloS one. 2012-01-01; 7.5: e32219.
Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques
McLean JS, Fansler SJ, Majors PD, McAteer K, Allen LZ, Shirtliff ME, Lux R, Shi W
PMID: 22403637
PloS one. 2012-01-01; 7.5: e42047.
Metagenomic exploration of viruses throughout the Indian Ocean
Williamson SJ, Allen LZ, Lorenzi HA, Fadrosh DW, Brami D, Thiagarajan M, McCrow JP, Tovchigrechko A, Yooseph S, Venter JC
PMID: 23082107
PloS one. 2011-03-23; 6.3: e17722.
Single virus genomics: a new tool for virus discovery
Allen LZ, Ishoey T, Novotny MA, McLean JS, Lasken RS, Williamson SJ
PMID: 21436882
PloS one. 2011-01-01; 6.12: e20388.
Going deeper: metagenome of a hadopelagic microbial community
Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH
PMID: 21629664
Nature. 2010-11-04; 468.7320: 60-6.
Genomic and functional adaptation in surface ocean planktonic prokaryotes
Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, Johnson J, Montgomery R, Ferriera S, Beeson K, Williamson SJ, Tovchigrechko A, Allen AE, Zeigler LA, Sutton G, Eisenstadt E, Rogers YH, Friedman R, Frazier M, Venter JC
PMID: 21048761
Applied and environmental microbiology. 2007-02-01; 73.4: 1146-52.
Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora
Jensen PR, Williams PG, Oh DC, Zeigler L, Fenical W
PMID: 17158611
Collaborator Release

Scientists announce comprehensive regional diagnostic of microbial ocean life using DNA testing

Large-scale ‘metabarcoding’ methods could revolutionize how society understands forces that drive seafood supply, planet’s ability to remove greenhouse gases


Ocean Sampling Day 2018