Bay Paul Publications

Recent Publications

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

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: 10.1128/mra.01045-24

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: 10.3389/fmicb.2024.1491488

Hernandez C. M., van Daalen S. F., Liguori A., Neubert M. G., Caswell H., Gribble K. E. (2025). Maternal effect senescence and caloric restriction interact to affect fitness through changes in life history timing. Journal Of Animal Ecology. 94:99-111. doi: 10.1111/1365-2656.14220

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: 10.1038/s41586-024-08405-w

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: 10.1016/j.gca.2025.02.012

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: 10.1186/s40793-025-00663-z

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: 10.1038/s41467-025-56774-1

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: 10.1073/pnas.2406679122

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

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: 10.1038/s41467-025-56212-2

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

Arrington E. C., Tarn J., Kivenson V., Nunn B. L., Liu R. M., Paul B. G., Valentine D. L. (2024). Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus. The Isme Journal: Multidisciplinary Journal Of Microbial Ecology. doi: 10.1093/ismejo/wrae247

Majumder S., Coull B. A., Welch J. L. M., La Riviere P. J., Dewhirst F. E., Starr J. R., Lee K. H. (2024). Multivariate Cluster Point Process to Quantify and Explore Multi‐Entity Configurations: Application to Biofilm Image Data. Statistics In Medicine. 43:5446-5460. doi: 10.1002/sim.10261

Kim J., Buffenstein R., Bronikowski A. M., Vanegas N.-D.P., Rosas L., Agudelo-Garcia P., Mora A. L., Rojas M., Englund D. A., LeBrasseur N. K., Nunes A., Robbins P. D., Kohut M. L., Kothadiya S., Bardhan R., Camell C. D., Sturmlechner I., Goronzy J. J., Yeh C.-Y., Lamming D. W., Huang S., Leiser S. F., Escorcia W., Gill M. S., Taylor J. R., Helfand S. L., Korm S., Gribble K. E., Pehar M., Blaszkiewicz M., Townsend K. L., McGregor E. R., Anderson R. M., Stilgenbauer L., Sadagurski M., Taylor A., McNeill E., Stoeger T., Bai H. (2024). The Fourth Annual Symposium of the Midwest Aging Consortium. The Journals Of Gerontology Series A. 79:glae236. doi: 10.1093/gerona/glae236

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: 10.1101/2024.12.23.630198

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..

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. Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities. doi: 10.1101/2025.01.15.633187