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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:

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:

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:

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:

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:

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:

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:

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:

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:

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..

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:

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: