Bay Paul Publications

Recent Publications

Gillis J. A. (2023). Scales, scutes, and embryonic origins of the vertebrate dermal skeleton.. Proceedings Of The National Academy Of Sciences Of The United States Of America. 120:e2310552120. doi: 10.1073/pnas.2310552120

Mincer T. J., Bos R. P., Zettler E. R., Zhao S., Asbun A. A., Orsi W. D., Guzzetta V. S., Amaral-Zettler L. A. (2023). Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat. Water Research. 242:120033. doi: 10.1016/j.watres.2023.120033

Armitage D. W., Aruda A., Blasiak L., Buchwald C., Cregger M., Cappelletti M., Cordero O. X., Gallagher K., Glass J., Holmes J., Hurley S., Hemp J., Ma P., Rampersaud R., Ruff E., Salman V., Schick M., Shade A., Vuono D., Youngblut N. (2023). Microbial Diversity: Marine Biological Laboratory 2011 Final Reports. public url: https://hdl.handle.net/1912/66531

Itano M. S., Kumar A., Maddox P. S. (2023). Editorial: Live cell imaging: Cell and developmental research bridging education, optical engineering, industry, software, shared facilities. Frontiers In Cell And Developmental Biology. 11:1191235. doi: 10.3389/fcell.2023.1191235

Richter N., Hopmans E. C., Mitrović D., Raposeiro P. M., Gonçalves V., Costa A. C., Amaral-Zettler L. A., Villanueva L., Rush D. (2023). Distributions of bacteriohopanepolyols in lakes and coastal lagoons of the Azores Archipelago. Biogeosciences. 20:2065-2098. doi: 10.5194/bg-20-2065-2023

Ruff S. E., Humez P., de Angelis I. H., Diao M., Nightingale M., Cho S., Connors L., Kuloyo O. O., Seltzer A., Bowman S., Wankel S. D., McClain C. N., Mayer B., Strous M. (2023). Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems. Nature Communications. 14:3194. doi: 10.1038/s41467-023-38523-4

Hauer M. A., Breusing C., Trembath-Reichert E., Huber J. A., Beinart R. A. (2023). Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts. Microbiome. 11:106. doi: 10.1186/s40168-023-01493-2

Gollnisch R., Wallenius J., Gribble K. E., Ahrén D., Rengefors K. (2023). SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes. Molecular Biology And Evolution. 40:msad095. doi: 10.1093/molbev/msad095

Zhao Y., Zhou R., Xie B., Liu C. Y., Cham C. M., Koval J., Kalski M., Rubin D. T., Huang J., Sogin M., Weber C., Fiebig A., Crosson S., Dalal S., Chang E. B., Basu A., Pott S. (2023). Sa1797 SINGLE-CELL GENE EXPRESSION AND CHROMATIN ACCESSIBILITY PROFILING REVEALS PROFOUND CELLULAR AND EPIGENETIC PLASTICITY OF INTESTINAL POUCHES FROM ULCERATIVE COLITIS PATIENTS. Gastroenterology. 164:s-436. doi: 10.1016/s0016-5085(23)02011-5

Lundgren S. N., Madan J. C., Karagas M. R., Morrison H. G., Christensen B. C., Hoen A. G. (2023). Human milk-associated bacterial communities associate with the infant gut microbiome over the first year of life. Frontiers In Microbiology. 14:1164553. doi: 10.3389/fmicb.2023.1164553

Ghousein A., Tutagata J., Schrieke H., Etienne M., Chaumeau V., Boyer S., Pages N., Roiz D., Eren A. M., Cambray G., Reveillaud J. (2023). pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex pipiens and Culex quinquefasciatus mosquitoes worldwide. Isme Communications. 3:40. doi: 10.1038/s43705-023-00248-2

Amaral-Zettler L. (2023). Algae. doi: 10.1007/978-3-662-65093-6_48

Amaral-Zettler L. (2023). Eukarya. doi: 10.1007/978-3-662-65093-6_537

Hamilton B. R., Hunter-Cevera K. R. Effective concentration of marine nanoflagellates with a microfluidic device. doi: 10.1101/2023.04.03.534374

Gillis J. A., Criswell K. E., Baker C. V. H. The skate spiracular organ develops from a unique neurogenic placode, distinct from lateral line placodes. doi: 10.1101/2023.03.17.533203

Rees J. M., Palmer M. A., Gillis J. A. Fgf signalling is required for gill slit formation in the skate, Leucoraja erinacea. doi: 10.1101/2023.08.20.554054

Attenborough T., Rawlinson K. A., Soria C. L. D., Ambridge K., Sankaranarayanan G., Graham J., Doyle S. R., Rinaldi G., Berriman M. A single-cell atlas of the free-living miracidium larva of Schistosoma mansoni. doi: 10.1101/2023.03.27.533868

Soria C. L. D., Attenborough T., Lu Z., Graham J., Hall C., Thompson S., Andrews T. G. R., Rawlinson K. A., Berriman M., Rinaldi G. Single cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem cell regulators. doi: 10.1101/2023.05.02.538881

Minařík M., Modrell M. S., Gillis J. A., Campbell A. S., Fuller I., Lyne R., Micklem G., Gela D., Pšenička M., Baker C. V. H. Identification of multiple transcription factor genes potentially involved in the development of electrosensory versus mechanosensory lateral line organs. doi: 10.1101/2023.04.14.536701

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. Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents: Implications for deep-sea carbon cycling. doi: 10.1101/2023.08.11.552852

Castro S. P., Peredo E. L., Mason O. U., Vineis J., Bowen J., Mortazavi B., Ganesh A., Ruff S. E., Paul B. G., Giblin A. E., Cardon Z. G. Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes. doi: 10.1101/2023.06.08.544202

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. Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. doi: 10.1101/2023.05.10.540289

Fiebig A., Schnizlein M., Pena-Rivera S., Trigodet F., Dubey A. A., Hennessy M., Basu A., Pott S., Dalal S., Rubin D., Sogin M. L., Eren A. M., Chang E. B., Crosson S. Multi-omics analysis of a Bacteroides fragilis isolate from an ulcerative colitis patient defines genetic determinants of fitness in bile. doi: 10.1101/2023.05.11.540287

Fogarty E. C., Schechter M. S., Lolans K., Sheahan M. L., Veseli I., Moore R., Kiefl E., Moody T., Rice P. A., Yu M. K., Mimee M., Chang E. B., Mclellan S. L., Willis A. D., Comstock L. E., Eren A. M. A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut. doi: 10.1101/2023.03.25.534219

Fernandez-Guerra A., Borrel G., Delmont T. O., Elberling B., Eren A. M., Gribaldo S., Jochheim A., Henriksen R. A., Hinrichs K.-U., Korneliussen T. S., Krupovic M., Larsen N. K., Laso-Pérez R., Pedersen M. W., Pedersen V. K., Sand K. K., Sikora M., Steinegger M., Veseli I., Wörmer L., Zhao L., Žure M., Kjær K., Willerslev E. A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland. doi: 10.1101/2023.06.10.544454