Bay Paul Publications

Recent Publications

Stevens B. L. F., van Daalen S. F., Blomquist T. J., Gribble K. E., Neubert M. G. (2026). Timing the initiation of sex: Delay mechanisms alter fitness outcomes in a rotifer population model. Journal Of Theoretical Biology. 620. doi: 10.1016/j.jtbi.2025.112333

Corbett L. N., de Vogel F. A., van der Mark P. B. J., Zettler E. R., Mandemaker L. D. B., Weckhuysen B. M., Meirer F., Amaral-Zettler L. A. (2026). Impact of polystyrene nanoplastics on the biodegradation of a polyhydroxyalkanoate and its associated biofilm. Environmental Pollution. 392. doi: 10.1016/j.envpol.2026.127634

van den Akker K., Mandemaker L. D. B., Dorresteijn J. M., Amaral-Zettler L. A., Weckhuysen B. M., Meirer F. (2026). Fluorescent nanoplastics: What steps are needed towards a representative toolkit?. Microplastics And Nanoplastics. 6:4. doi: 10.1186/s43591-025-00159-0

DiSalvo B., Paul B. G., Cardon Z. G. (2026). Complete genome sequence of Thioclava strain BDS19, isolated from coastal marsh sediment. Microbiology Resource Announcements. 15:e00855-e00825. doi: 10.1128/mra.00855-25

Trigodet F., Sachdeva R., Banfield J. F., Eren A. M. (2026). Troubleshooting common errors in assemblies of long-read metagenomes. Nature Biotechnology. doi: 10.1038/s41587-025-02971-8

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., Rappe M. S. (2025). New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the <i>Pelagibacterales</i>. Nature Communications. 17. doi: 10.1038/s41467-025-67043-6

Gattoni G., Lin C.-Y., York J. R., Shew C., Keitley D., Labonne C., Yu J.-K., Gillis J. A., Benito-Gutierrez E. (2025). Evolutionary dynamics of FoxQ2 transcription factors across metazoans reveals three ancient paralogs. Communications Biology. 9. doi: 10.1038/s42003-025-09368-y

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

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

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

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..

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

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

Faure E., Pommellec J., Noel C., Cormier A., Delpech L.-M., Eren M., Fernandez-Guerra A., Vanni C., Fourquez M., Houssais M.-N., Silva C. D., Gavory F., Perdereau A., Labadie K., Wincker P., Poulain J., Hassler C., Lin Y., Cassar N., Maignien L. Water mass specific genes dominate the Southern Ocean microbiome. doi: 10.21203/rs.3.rs-5608865/v1

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

Liang Q., Deng L., Liu X., Xiao X., Xie R., Hou J., Wang J., Sui W., Lu N., Tong Z., Huang D., Wang Y., Han Y., Zhao J., Guo B., Zhang W., Geng M., Ren T., Ye W., Xiong Z., Dong L., Ruff S. E., Meile C., Tao J., Dong X., Wang F. Rapid ecosystem collapse and biofilter formation following seabed methane leakage. doi: 10.64898/2025.12.05.692476