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:
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:
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:
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:
Elkassas S. M., Serres M. H., Navarro M., Patterson A., Zhivkova T., Petersen M., Weeks K., Lang S., Seewald J., Wheat G., Trembath-Reichert E., Huber J. A. (2025). Draft genome sequences of six high pH adapted Marinobacter shengliensis strains isolated from Mariana forearc serpentinite mud volcanoes. Microbiology Resource Announcements. 14:e01045-e01024. doi:
Hinkle J. E., Chanton J. P., Moynihan M. A., Ruff S. E., Teske A. (2025). Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq). Frontiers In Microbiology. 15. doi:
Handa S., Biswas T., Chakraborty J., Ghosh G., Paul B. G., Ghosh P. (2025). RNA control of reverse transcription in a diversity-generating retroelement. Nature. doi:
Gu S., Berthelot H., Lin Y., Tang W., Robidart J., Eren A. M., Ducklow H. W., Cassar N. (2025). Evidence of limited N<sub>2</sub> fixation in the Southern Ocean. Communications Earth & Environment. 6. doi:
Walter S. R. S., Wood L. J., Yoshimura K. M., Gonski S. F., Cai W.-J., Huber J. A., Trembath-Reichert E., Girguis P. R. (2025). Drivers of inorganic and organic carbon removal in aged oceanic crust. Geochimica Et Cosmochimica Acta. 394:1-14. doi:
Manral D., Gomez-Navarro L., Denes M. C., Iovino D., Fogli P. G., Masina S., Hernandez-Carrasco I., Amaral-Zettler L., Vichi M., van Sebille E. (2025). Separation Timescales of Vertically Migrating Zooplankton and Other (a)Biotic Materials in the Benguela System. Journal Of Geophysical Research-Oceans. 130. doi:
Sow S. L. S., van de Poll W. H., Eveleth R., Rich J. J., Ducklow H. W., Rozema P. D., Luria C. M., Bolhuis H., Meredith M. P., Amaral-Zettler L. A., Engelmann J. C. (2025). Spatial and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula. Environmental Microbiome. 20. doi:
Jiang Q., Cao L., Han Y., Li S., Zhao R., Zhang X., Ruff S. E., Zhao Z., Peng J., Liao J., Zhu B., Wang M., Lin X., Dong X. (2025). Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla. Nature Communications. 16. doi:
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:
Chandler T., Guo M., Su Y., Chen J., Wu Y., Liu J., Agashe A., Fischer R. S., Mehta S. B., Kumar A., Baskin T. I., Jaumouille V., Liu H., Swaminathan V., Nain A. S., Oldenbourg R., La Riviere P. J., Shroff H. (2025). Volumetric imaging of the 3D orientation of cellular structures with a polarized fluorescence light-sheet microscope. Proceedings Of The National Academy Of Sciences Of The United States Of America. 122. doi:
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:
Zhao Y., Zhou R., Xie B., Liu C. Y., Kalski M., Cham C. M., Jiang Z., Koval J., Weber C. R., Rubin D. T., Sogin M., Crosson S., Chen M., Huang J., Fiebig A., Dalal S., Chang E. B., Basu A., Pott S. (2025). Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients. Nature Communications. 16:904. doi:
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:
Vallino J. J., Ahern O. M., Huber J. A. Deriving microbial food web structure by maximizing entropy production over variable timescales. doi:
Trigodet F., Sachdeva R., Banfield J. F., Eren A. M. Assemblies of long-read metagenomes suffer from diverse errors. doi:
Tucker S. J., Freel K. C., Eren A. M., Rappé M. S. Habitat-specificity in SAR11 is associated with a handful of genes under high selection. doi:
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:
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..
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:
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:
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: