Bay Paul Publications

Recent Publications

Kennedy S. J., Risser D. D., Paul B. G. (2025). Diel expression dynamics in filamentous cyanobacteria. Mbio. 16. doi: 10.1128/mbio.03779-24

Vidal E., Lindsay M. R., Bradley J. A., Osburn M. R., Ruff S. E. (2025). Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries. Microbial Biotechnology. 18. doi: 10.1111/1751-7915.70286

Freel K. C., Tucker S. J., Freel E. B., Stingl U., Giovannoni S. J., Eren A. M., Rappé M. S. (2025). New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales. Nature Communications. doi: 10.1038/s41467-025-67043-6

Scott W., Ivorra-Molla E., Akhuli D., Massam-Wu T., Lysyganicz P. K., Walsh R., Parent M., Cook J., Song L., Kumar A., Schneider F., Mishima M., Crow A., Balasubramanian M. K. (2025). StayRose: A photostable StayGold derivative redshifted by genetic code expansion. Journal Of Biological Chemistry. 301. doi: 10.1016/j.jbc.2025.110832

Tucker S. J., Fussel 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., Rappe M. S., Eren A. M. (2025). A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts. Scientific Data. 12. doi: 10.1038/s41597-025-06166-3

DiSalvo B., Paul B. G., Cardon Z. G. (2025). Complete genome sequence of Thioclava strain BDS19, isolated from coastal marsh sediment.. Microbiology Resource Announcements. doi: 10.1128/mra.00855-25

Schon I., Chimileski S., Mark Welch J., Martens K. (2025). Vertical transmission of <i>Cardinium</i> bacteria in parthenogenetic non-marine ostracods (Crustacea). Proceedings Of The Royal Society B-Biological Sciences. 292. doi: 10.1098/rspb.2025.1193

Sures K., Esser S. P., Bornemann T. L. V., Moore C. J., Soares A. R., Plewka J., Figueroa-Gonzalez P. A., Ruff S. E., Moraru C., Probst A. J. (2025). Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments. Genome Biology And Evolution. 17. doi: 10.1093/gbe/evaf201

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. 91. doi: 10.1128/aem.01868-25

Paul B. G., Mekalanos J. J. (2025). Natural directed evolution in gut microbiota. Science. 390:129-130. doi: 10.1126/science.aeb8597

Aparicio N. L., Dryburgh M., McMaken C. M., Liguori A., Gribble K. E. (2025). Impact of histone post-translational modification inhibitors on lifespan, reproduction, and stress response in the rotifer Brachionus manjavacas. Plos One. 20:e0324769. doi: 10.1371/journal.pone.0324769

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

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

Olins A. L., Welch D. M., Prudovsky I., Olins D. E. Hyperosmotic Stress of HL-60/S4 Cells: Gene Set Enrichment Analysis and Microscopic Changes. doi: 10.1101/2025.04.22.649232

Olins A. L., Welch D. M., Prudovsky I., Olins D. E. Phenotypic Changes in Undifferentiated and Retinoic Acid Differentiated HL-60/S4 Cells with-or-without LBR Knockdown. doi: 10.1101/2025.02.02.635278

Morillo-Lopez V., Sjaarda A., Islam I., Borisy G. G., Welch J. M. Corncob structures in dental plaque reveal microhabitat taxon specificity. doi: 10.21203/rs.3.rs-769817/v1

Wang S., Wikle C. K., Micheas A. C., Welch J. L. M., Starr J. R., Lee K. H. Inference for Log-Gaussian Cox Point Processes using Bayesian Deep Learning: Application to Human Oral Microbiome Image Data..

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

Perera D., McLean A., Lopez V. M., Cloutier-Leblanc K., Almeida E., Cabana K., Welch J. M., Ramsey M. Mechanisms underlying proximity between oral commensal bacteria. doi: 10.1101/2020.09.29.318816

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

Fuessel J., Miller S., Hecker C., Trigodet F., Dlugosch L., Brinkhoff T., Dittmar T., Eren A. M., Lennartz S., Bunse C. Bacterial interactions shape the molecular composition of dissolved organic matter. doi: 10.21203/rs.3.rs-7321332/v1

Chitale P., Ocke E., Odom A. R., Fan H., Henoch A., Vasco K., Fogarty E. C., Grady C., Lemenze A. D., Kumar P., Manning S., Eren A. M., Johnson W. E., Alland D. Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence. doi: 10.1101/2025.11.03.686283

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