Publications
From the lab (KGI, 2023–present)
† trainee author
Chen CY†, Wang X†, Yan Y†, Escobar R†, Ignacio-Espinoza JC (2026). Complete genome sequences of three co-occurring Pseudomonas isolates from California Botanic Garden topsoil. Microbiology Resource Announcements e00793-26.
Stroebel BM, Jimenez A†, Lindquist KJ, Torgerson D, Longoria KD, Ignacio-Espinoza JC, Flowers E (2026). Considering microRNAs as measures of extrinsic domains of risk in the context of underlying genetic characteristics: type 2 diabetes as an exemplar. Frontiers in Genetics 17:1934355.
Ignacio-Espinoza JC, Zou Y†, Hou S, Long AM, Needham DM, Fichot E, Fuhrman JA (2026). In situ bacterioplankton growth distribution by high-resolution metatranscriptomics. Environmental Microbiology Reports, 18 (4), e70385
Laperriere S, Minch B, Weissman JL, Hou S, Yeh YC, Ignacio-Espinoza JC, Ahlgren NA, Moniruzzaman M, Fuhrman JA (2025). Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series. ISME Communications, 5(1):ycaf217
Preprints
Moon J, Ignacio-Espinoza JC, Puzantian T. Disparities, perceived discrimination, and patient–clinician communication in alcohol use disorder treatment: an All of Us cohort study.
Selected publications
Long AM, Hou S, Ignacio-Espinoza JC, Fuhrman JA (2021). Benchmarking microbial growth rate predictions from metagenomes. The ISME Journal 15:183–195.
Ignacio-Espinoza JC, Ahlgren NA, Fuhrman JA (2020). Long-term stability and Red Queen-like strain dynamics in marine viruses. Nature Microbiology 5:265–271.
Sieradzki ET, Ignacio-Espinoza JC, Needham DM, Fichot E, Fuhrman JA (2019). Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nature Communications 10:1169.
Brum JR*, Ignacio-Espinoza JC*, Kim EH*, et al. (2016). Illuminating structural proteins in viral "dark matter" with metaproteomics. PNAS 113:2436–2441.
Brum JR*, Ignacio-Espinoza JC*, Roux S*, et al. (2015). Patterns and ecological drivers of ocean viral communities. Science 348:1261498.
Deng L*, Ignacio-Espinoza JC*, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 513:242–245.
For the complete list, see Google Scholar.