Bay Paul Publications

Recent Publications

Elkassas S. M., Fortunato C. S., Grim S. L., Butterfield D. A., Holden J. F., Vallino J. J., Algar C. K., Zeigler Allen L., Larson B. T., Proskurowski G., Reddington E., Stewart L. C., Topcuoglu B., Huber J. A. (2025). Metabolic and population profiles of active subseafloor autotrophs in young oceanic crust at deep-sea hydrothermal vents. Applied And Environmental Microbiology. doi: 10.1128/aem.01868-25

Gillis J. A., Criswell K. E., Palmer M. A., Baker C. V. H. (2025). The skate spiracular organ develops from a unique neurogenic placode that is distinct from lateral line placodes. Development. 152:dev204767. doi: 10.1242/dev.204767

Worland A. M., Xu V. A., Duran M. F., Gitman P., Hunter-Cevera K., Klemm C., Sun Y., Sanchis D. R., Ledesma-Amaro R., Pomraning K. R., Tanjore D., Blenner M., Tang Y. J. (2025). Staying productive under pressure: systems evaluations of β-carotene production in Yarrowia lipolytica under continuous fermentation. Trends In Biotechnology. doi: 10.1016/j.tibtech.2025.08.019

Stern J. C., Graham H. V., Burcar B., Martin E. S., Noell A., Hand K., Bowman J. S., Doran P., Edgcomb V., Holden J. F., Howells A. E. G., Malaska M. J., Nunn B. L., Radebaugh J., Rodriguez L. E., Borges S., Bower D., Courville S., Diaz M., Hockman B., Huber J., Lawrence J., Vick-Majors T., Nixon C. A., Spear J. R., Steckel A. V., Solomonidou A., Schmerr N., Schmidt B., Schrenk M. O., Seyler L., Smith A. R., Walker C. C., Whelley P., Wolfenbarger N., Vance S. D. (2025). A Comprehensive Framework for Assessing Terrestrial Analogue Field Sites for Ocean Worlds. Journal Of Geophysical Research-Planets. 130. doi: 10.1029/2024JE008803

Mark Welch J. L., Borisy G. G. (2025). Dental plaque Who is in the neighborhood and why it matters. The Journal Of The American Dental Association. 156:674-677. doi: 10.1016/j.adaj.2025.05.005

Theirlynck T., Staat L., Servania D., Engelen A. H., van Tussenbroek B. I., Muyzer G., Visser P. M., Amaral-Zettler L. (2025). Nutrient-driven growth and microbiome shifts in the brown alga <i>Sargassum fluitans</i> III. Journal Of Phycology. 61:933-950. doi: 10.1111/jpy.70045

Eren A. M. (2025). Gifting future scientists the past through well-preserved specimens of modern microbial ecosystems. Nature Communications. 16. doi: 10.1038/s41467-025-62138-6

Paul B. G., DiSalvo B. (2025). Retracing a tangled tree of archaeal evolution. Nature Microbiology. 10:1566-1567. doi: 10.1038/s41564-025-02040-5

Woods P. H., Speth D. R., Laso-Perez R., Utter D. R., Ruff S. E., Orphan V. J. (2025). Identification of key steps in the evolution of anaerobic methanotrophy in <i>Candidatus</i> Methanovorans (ANME-3) archaea. Science Advances. 11. doi: 10.1126/sciadv.adq5232

Little A. S., Younker I. T., Schechter M. S., Bernardino P. N., Meheust R., Stemczynski J., Scorza K., Mullowney M. W., Sharan D., Waligurski E., Smith R., Ramaswamy R., Leiter W., Moran D., Mcmillin M., Odenwald M. A., Iavarone A. T., Sidebottom A. M., Sundararajan A., Pamer E. G., Eren A. M., Light S. H. (2025). Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration (vol 9, pg 55, 2024). Nature Microbiology. 10:1550. doi: 10.1038/s41564-025-02031-6

Appelgate B., Dugan B., Eguchi N., Fornari D., Freudenthal T., Fulton P., Kelley S., Lang S. Q., Manalang D., Mix A., Trask R., Andrys J., Beethe S., Bridgham H., Cabaniss H., Cargill S. K., Conroy C. W., Costa K., Cox A., Cross A., Dwyer D., Dodd J., Donnelly J., Finlayson V., Hashim M., Heaton D., Huber J., Hupp B., Jackson M. G., Jasper C., Kitajima H., Libman-Roshal O., Lowery C. M., Maletic E., Marranzino A. N., Mejia-Mercado B. E., Morrow T., Yobo L. N., Pallone C., Panter K., Patterson M., Peccia A., Ronge T. A., Roth E., Staro A., Stelling K., Todes J. P., Tsang M.-Y., Wieman S. T., Konrad K., Reilly B., Schrenk M., Walczak M., Tominaga M. (2025). The FUTURE of the US Marine Seafloor and Subseafloor Sampling Capabilities. Agu Advances. 6. doi: 10.1029/2024AV001560

Veseli I., Chen Y. T., Schechter M. S., Vanni C., Fogarty E. C., Watson A. R., Jabri B., Blekhman R., Willis A. D., Yu M. K., Fernàndez-Guerra A., Füssel J., Eren A. M. (2025). Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. Elife. 12. doi: 10.7554/elife.89862.3

Veseli I., Chen Y. T., Schechter M. S., Vanni C., Fogarty E. C., Watson A. R., Jabri B., Blekhman R., Willis A. D., Yu M. K., Fernàndez-Guerra A., Füssel J., Eren A. M. (2025). Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. Elife. 12:rp89862. doi: 10.7554/elife.89862

Zhao S., Kvale K. F., Zhu L., Zettler E. R., Egger M., Mincer T. J., Amaral-Zettler L. A., Lebreton L., Niemann H., Nakajima R., Thiel M., Bos R. P., Galgani L., Stubbins A. (2025). The distribution of subsurface microplastics in the ocean. Nature. 641. doi: 10.1038/s41586-025-08818-1

Vallino J. J., Ahern O. M., Huber J. A. Deriving microbial food web structure by maximizing entropy production over variable timescales. doi: 10.1101/2025.04.30.651452

Trigodet F., Sachdeva R., Banfield J. F., Eren A. M. Assemblies of long-read metagenomes suffer from diverse errors. doi: 10.1101/2025.04.22.649783

Stevens B. L. F., van Daalen S., Blomquist T. J., Gribble K. E., Neubert M. G. Timing the initiation of sex: Delay mechanisms alter fitness outcomes in a rotifer population model. doi: 10.1101/2025.04.25.650506

Aparicio N. L., Dryburgh M., McMaken C. M., Liguori A., Gribble K. E. Impact of inhibitors of histone post-translational modifications on lifespan, reproduction, and stress response in the rotifer Brachionus manjavacas. doi: 10.1101/2025.05.03.652051

Ramfelt O., Tucker S. J., Freel K. C., Eren A. M., Rappé M. S. Magnimaribacterales marine bacteria genetically partition across the nearshore to open-ocean in the tropical Pacific Ocean. doi: 10.1101/2025.06.17.660167

Luo E., Pham N. D., Rogers T. J., Vallino J. J., Benner B. E., Trubl G., Huber J. A. Virus-mediated recycling of chemoautotrophic biomass. doi: 10.1101/2025.05.27.656380

Abdelghany S., Helmkampf M., Schechter M. S., Veseli I. A., Leray M., Eren A. M., Puebla O. Proteobacteria with chemosynthetic potential are highly enriched in the gills of Hypoplectrus reef fishes. doi: 10.1101/2025.07.01.662686

Gumnit E., Gattoni G., Woych J., Deryckere A., Bhattarai P., Gillis J. A., Kizil C., Tosches M. A. Evolution of Cajal-Retzius Cells in Vertebrates from an Ancient Class of Tp73+ Neurons. doi: 10.1101/2025.08.21.671508

Gattoni G., Lin C.-Y., York J. R., Keitley D., LaBonne C., Yu J.-K., Gillis J. A., Benito-Gutiérrez E. Evolutionary dynamics of FoxQ2 transcription factors across metazoans: A tale of three ancient paralogs. doi: 10.1101/2025.04.23.650082

Elkassas S. M., Fortunato C. S., Grim S. L., Butterfield D. A., Holden J. F., Vallino J. J., Algar C. K., Allen L. Z., Larson B. T., Proskurowsk G., Reddington E., Stewart L. C., Topçuoğlu B., Huber J. A. Metabolic and Population Profiles of Active Subseafloor Autotrophs in Young Oceanic Crust at Deep-Sea Hydrothermal Vents. doi: 10.1101/2025.04.25.650746

Tucker S. J., Fuessel J., Freel K. C., Kiefl E., Freel E. B., Ramfelt O., Sullivan C. E. S., Gajigan A. P., Mochimaru H., de Souza M. R., Quinn M., Ratum C., Tran L. L., Sobczyk M., Miller S. E., Trigodet F., Lolans K., Morrison H. G., Fallon B., Huettel B., Pan T., Rappé M. S., Eren A. M. A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts. doi: 10.1101/2025.09.15.676277