John M. Eppley
University of Hawaii
42 Papers
180 Citations
John M. Eppley is an academic researcher from University of Hawaii. The author has contributed to research in topics: Biology & Metagenomics. The author has an hindex of 23, co-authored 34 publications. Previous affiliations of John M. Eppley include Massachusetts Institute of Technology & University of California, Berkeley.
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Papers
Community-led, integrated, reproducible multi-omics with anvi'o.
A. Murat Eren,Evan Kiefl,Alon Shaiber,Iva Veseli,Samuel E. Miller,Matthew S. Schechter,Isaac Fink,Jessica N. Pan,Mahmoud Yousef,Emily Fogarty,Florian Trigodet,Andrea R. Watson,Özcan C. Esen,Ryan M Moore,Quentin Clayssen,Michael D. Lee,Veronika Kivenson,Elaina D. Graham,Bryan D. Merrill,Antti Karkman,Daniel Blankenberg,Daniel Blankenberg,John M. Eppley,Andreas Sjödin,Jarrod J. Scott,Xabier Vázquez-Campos,Luke J. McKay,Elizabeth A. McDaniel,Sarah L. R. Stevens,Rika E. Anderson,Jessika Fuessel,Antonio Fernandez-Guerra,Lois Maignien,Lois Maignien,Tom O. Delmont,Amy D. Willis +35 more
TL;DR: The workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked as discussed by the authors, but the workflows can also be difficult to adapt to real-world applications.
552
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean
TL;DR: The data support the utility of coupled DNA and cDNA analyses for describing taxonomic and functional attributes of microbial communities in their natural habitats.
Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages
Elizabeth A. Ottesen,Elizabeth A. Ottesen,Elizabeth A. Ottesen,Curtis R. Young,Curtis R. Young,Scott M. Gifford,Scott M. Gifford,John M. Eppley,John M. Eppley,Roman Marin,Stephan C. Schuster,Christopher A. Scholin,Edward F. DeLong,Edward F. DeLong +13 more
TL;DR: Time-resolved whole-genome transcriptome profiles of multiple, naturally occurring oceanic bacterial populations sampled in situ over 3 days show pronounced diel periodicity in the cyanobacterial transcriptome, and several different heterotrophic bacterioplankton groups also displayed diel cycling in many of their gene transcripts.
Pattern and synchrony of gene expression among sympatric marine microbial populations
Elizabeth A. Ottesen,Curtis R. Young,John M. Eppley,John P. Ryan,Francisco P. Chavez,Christopher A. Scholin,Edward F. DeLong +6 more
TL;DR: A day in the life of wild planktonic microbial species using robotic sampling coupled with genome-wide gene expression analysis showed that closely related populations, as well as very different bacterial and archaeal species, displayed remarkably similar time-variable synchronous patterns of gene expression over 2 d.
215
Microbial community transcriptional networks are conserved in three domains at ocean basin scales
Frank O. Aylward,John M. Eppley,Jason M. Smith,Francisco P. Chavez,Christopher A. Scholin,Edward F. DeLong,Edward F. DeLong +6 more
TL;DR: It is reported that common temporal and ecological dynamics underpin disparate marine microbial communities, providing the first evidence that trans-Pacific diurnal transcriptional patterns in these communities may regulate ecological and biogeochemical processes across the ocean.
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