Bay Paul Publications

Recent Publications

Giacomini J. J., Torres-Morales J., Dewhirst F. E., Borisy G. G., Welch J. L. M. (2025). Spatial ecology of the Neisseriaceae family in the human oral cavity. Microbiology Spectrum. 13:e03275-e03224. doi: 10.1128/spectrum.03275-24

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

Sebastian H., Robador A., Ray D., Angermeyer A., D’Hondt S., Huber J. A., Finkel S. E. (2025). Identifying potential nutrient acquisition mechanisms for long-term survival: adaptive evolution of Halomonas isolated from subseafloor crustal fluids. Frontiers In Microbiology. 16:1511421. doi: 10.3389/fmicb.2025.1511421

Thiruppathy M., Teubner L., Roberts R. R., Lasser M. C., Moscatello A., Chen Y.-W., Hochstim C., Ruffins S., Sarkar A., Tassey J., Evseenko D., Lozito T. P., Willsey H. R., Gillis J. A., Crump J. G. (2025). Repurposing of a gill gene regulatory program for outer-ear evolution. Nature. 639:682-690. doi: 10.1038/s41586-024-08577-5

Lee K. H., Coull B. A., Majumder S., La Riviere P. J., Welch J. L. M., Starr J. R. (2025). A Bayesian Multivariate Spatial Point Pattern Model: Application to Oral Microbiome FISH Image Data. doi: 10.48550/arxiv.2502.10513

Simon S. A., Soares A. R., Bornemann T. L. V., Lange A., Griesdorn L., Fuentes A., Dieckmann M., Krok B. A., Ruff S. E., Hügler M., Moraru C., Probst A. J. (2025). Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing. Isme Communications. 5:ycaf041. doi: 10.1093/ismeco/ycaf041

Kananen K., Veseli I., Quiles Pérez C. J., Miller S. E., Eren A. M., Bradley P. H. (2024). Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes. Bioinformatics Advances. 5:vbaf039. doi: 10.1093/bioadv/vbaf039

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

Freel K. C., Tucker S. J., Freel E. B., Giovannoni S. J., Eren A. M., Rappé M. S. New isolate genomes and global marine metagenomes resolve ecologically relevant units of SAR11. doi: 10.1101/2024.12.24.630191

Lee K. H., Coull B. A., Majumder S., Riviere P. J. L., Welch J. L. M., Starr J. R. A Bayesian Multivariate Spatial Point Pattern Model: Application to Oral Microbiome FISH Image Data..

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

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

Schechter M. S., Trigodet F., Veseli I. A., Miller S. E., Klein M. L., Sever M., Maignien L., Delmont T. O., Light S. H., Eren A. M. Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo. doi: 10.1101/2025.01.15.633187

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., Proskurowski 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