Bay Paul Publications
Recent Publications
Giacomini J. J., Torres-Morales J., Tang J., Dewhirst F. E., Borisy G. G., Mark Welch J. L. (2024). Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.. Microbiology Spectrum. 12:e0401723. doi:
Möller L., Vainshtein Y., Meyer B., Neidhardt J., Eren A. M., Sohn K., Rabus R. (2024). Rich microbial and depolymerising diversity in Antarctic krill gut.. Microbiology Spectrum. 12:e0403523. doi:
Yu M. K., Fogarty E. C., Eren A. M. (2024). Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nature Microbiology. 9:830-847. doi:
McMaken C. M., Gribble K. E. (2024). A free and user-friendly software protocol for the quantification of microfauna swimming behavior. Biotechniques. doi:
Rees J. M., Palmer M. A., Gillis J. A. (2024). Fgf signalling is required for gill slit formation in the skate, Leucoraja erinacea. Developmental Biology. 506:85-94. doi:
Vineis J. H., Reznikoff W. S., Antonopoulos D. A., Koval J., Chang E., Fallon B. R., Paul B. G., Morrison H. G., Sogin M. L. (2024). A novel conjugative transposon carrying an autonomously amplified plasmid. Mbio. 15:e02787-e02723. doi:
Doré H., Eisenberg A. R., Junkins E. N., Leventhal G. E., Ganesh A., Cordero O. X., Paul B. G., Valentine D. L., O’Malley M. A., Wilbanks E. G. (2024). Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proceedings Of The National Academy Of Sciences Of The United States Of America. 121:e2316469121. doi:
Fogarty E. C., Schechter M. S., Lolans K., Sheahan M. L., Veseli I., Moore R. M., Kiefl E., Moody T., Rice P. A., Yu M. K., Mimee M., Chang E. B., Ruscheweyh H.-J., Sunagawa S., Mclellan S. L., Willis A. D., Comstock L. E., Eren A. M. (2024). A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell. 187:1206-1222.e16. doi:
Hu S. K., Anderson R. E., Pachiadaki M. G., Edgcomb V. P., Serres M. H., Sylva S. P., German C. R., Seewald J. S., Lang S. Q., Huber J. A. (2024). Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents. The Isme Journal: Multidisciplinary Journal Of Microbial Ecology. 18:wrae004. doi:
Mullowney M. W., Fiebig A., Schnizlein M. K., McMillin M., Rose A. R., Koval J., Rubin D., Dalal S., Sogin M. L., Chang E. B., Sidebottom A. M., Crosson S. (2024). Microbially catalyzed conjugation of GABA and tyramine to bile acids. Journal Of Bacteriology. 206:e00426-e00423. doi:
Fiebig A., Schnizlein M. K., Pena-Rivera S., Trigodet F., Dubey A. A., Hennessy M. K., Basu A., Pott S., Dalal S., Rubin D., Sogin M. L., Eren A. M., Chang E. B., Crosson S. (2024). Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient. Mbio. 15:e02830-e02823. doi:
Little A. S., Younker I. T., Schechter M. S., Bernardino P. N., Méheust R., Stemczynski J., Scorza K., Mullowney M. W., Sharan D., Waligurski E., Smith R., Ramanswamy R., Leiter W., Moran D., McMillin M., Odenwald M. A., Iavarone A. T., Sidebottom A. M., Sundararajan A., Pamer E. G., Eren A. M., Light S. H. (2024). Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nature Microbiology. 9:55-69. doi:
Mark Welch D. B., Gould T. J., Olins A. L., Olins D. E. (2023). The transcriptome of acute dehydration in myeloid leukemic cells. Postepy Biochem. doi:
Arkhipova I. R., Yushenova I. A. (2023). To Be Mobile or Not: The Variety of Reverse Transcriptases and Their Recruitment by Host Genomes. Biochemistry (Moscow). 88:1754-1762. doi:
Arkhipova I. R., Burns K. H., Chiappinelli K. B., Chuong E. B., Goubert C., Guarné A., Larracuente A. M., Lee E. A., Levin H. L. (2023). Meeting report: transposable elements at the crossroads of evolution, health and disease 2023. Mobile Dna. 14:19. doi:
Schrieke H., Duron O., Trouche B., Eren A. M., Reveillaud J. Multiple Wolbachia subpopulations co-occur in single Culex pipiens mosquito organs. doi:
Mendonça I. R. W., Theirlynck T., Zettler E. R., Amaral-Zettler L. A., Oliveira M. C. Microbiome changes in a stranding simulation of the holopelagic macroalgae Sargassum natans and Sargassum fluitans. doi:
Handa S., Biswas T., Chakraborty J., Paul B. G., Ghosh P. Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement. doi:
Jiang X., Gallager S., Pedrosa Pàmies R., Ruff S. E., Liu Z. Laboratory-Simulated Photoirradiation Reveals Strong Resistance of Primary Macroplastics to Weathering. doi:
Schaible G. A., Jay Z. J., Cliff J., Schulz F., Gauvin C., Goudeau D., Malmstrom R. R., Ruff S. E., Edgcomb V., Hatzenpichler R. Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal. doi:
Rees J. M., Kirk K., Gattoni G., Hockman D., Ritter D. J., Benito-Gutierrez È., Knapik E. W., Crump J. G., Fabian P., Gillis J. A. A pre-vertebrate endodermal origin of calcitonin-producing neuroendocrine cells. doi:
Veseli I., Cooper Z. S., DeMers M. A., Schechter M. S., Miller S., Weber L., Smith C. B., Rodriguez L. T., Schroer W. F., McIlvin M. R., Lopez P. Z., Saito M., Dyhrman S., Eren A. M., Moran M. A., Braakman R. Digital Microbe: A Genome-Informed Data Integration Framework for Collaborative Research on Emerging Model Organisms. doi:
Zhao Y., Zhou R., Xie B., Liu C. Y., Kalski M., Cham C. M., Koval J., Weber C. R., Rubin D. T., Sogin M., Crosson S., Huang J., Fiebig A., Dalal S., Chang E. B., Basu A., Pott S. Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients. 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., Jamouilĺe V., Liu H., Swaminathan V., Nain A., Oldenbourg R., La Rivère P., Shroff H. Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM). doi:
Shan Y., Lake J., Cham C. M., Zhu M., Kaur D., Ringus D., Fei N., Weber C. R., Spedale M., Theriault B., Dalal S., Rubin D. T., Fiebig A., Crosson S., Lolans K., Comstock L., Eren A. M., Basu A., Pott S., Sogin M., Liu C., Chang E. B. Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases. doi: