Publications
Fiamenghi MB, Camargo AP, Chasapi IN, Baltoumas FA, Roux S, Egorov AA, Aplakidou E, Ndela EO, Vasquez YM, Chen IA, Palaniappan K, Reddy TBK, Mukherjee S, Ivanova NN, Schulz F, Woyke T, Eloe-Fadrosh EA, Pavlopoulos GA, Kyrpides NC. Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes. Nucleic Acids Res. 2026 Jan 6;54(D1):D801-D812. doi: 10.1093/nar/gkaf1283. PMID: 41312645; PMCID: PMC12807716.
Hernandez-Kapila YL, Kim RY, Gokhale SS, Lin YL, Dommisch H, Slots J, Weisenberger DJ. Oral virome in health and disease. J Am Dent Assoc. 2026 Apr 21:S0002-8177(26)00112-1. doi: 10.1016/j.adaj.2026.01.019. Epub ahead of print. PMID: 42012437; PMCID: PMC13101916.
Merenstein C, Litichevskiy L, Thaiss C, Collman RG, Bushman FD. Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction. Microbiome. 2026 Mar 3;14(1):86. doi: 10.1186/s40168-026-02362-4. PMID: 41772715; PMCID: PMC12983593.
Munteanu V, Saldana MA, Dreifuss D, Ouyang WO, Ferdous J, Mohebbi F, Roseberry JS, Ciorba D, Bostan V, Gordeev V, Drabcinski N, Su JM, Kasianchuk N, Sharma NK, Knyazev S, Aßmann E, Lobiuc A, Covasa M, Crandall KA, Wu NC, Mason CE, Tierney BT, Lucaci AG, Ophoff RA, Gibas C, Rzymski P, Skums P, Solo-Gabriele H, Niko B, Zelikovsky A, Hölzer M, Smith A, Mangul S. SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities. Genome Biol. 2026 Jan 12;27(1):1. doi: 10.1186/s13059-025-03927-6. PMID: 41526978; PMCID: PMC12794521.
Nyeo SS, Cumming EM, Burren OS, Pagadala MS, Gutierrez JC, Ali TA, Kida LC, Chen Y, Chu H, Hu F, Zou XZ, Hollis B, Fabre MA, MacArthur S, Wang Q, Ludwig LS, Dey KK, Petrovski S, Dhindsa RS, Lareau CA. Population-scale sequencing resolves determinants of persistent EBV DNA. Nature. 2026 Feb;650(8102):664-672. doi: 10.1038/s41586-025-10020-2. Epub 2026 Jan 28. PMID: 41606327; PMCID: PMC12888827.
Wirbel J, Hickey AS, Chang D, Enright NJ, Dvorak M, Chanin RB, Schmidtke DT, Bhatt AS. Long-read metagenomics reveals phage dynamics in the human gut microbiome. Nature. 2026 Jan;649(8098):982-990. doi: 10.1038/s41586-025-09786-2. Epub 2025 Nov 26. PMID: 41299176; PMCID: PMC12823448.
Camargo AP, Baltoumas FA, Ndela EO, Fiamenghi MB, Merrill BD, Carter MM, Pinto Y, Chakraborty M, Andreeva A, Ghiotto G, Shaw J, Proal AD, Sonnenburg JL, Bhatt AS, Roux S, Pavlopoulos GA, Nayfach S, Kyrpides NC. A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions. bioRxiv [Preprint]. 2025 Nov 2:2025.11.01.686033. doi: 10.1101/2025.11.01.686033. PMID: 41279291; PMCID: PMC12636319.
Campbell DE, Wu X, Hall LR, Lawrence D, Molleston JM, Schriefer LA, Droit L, Weagley JS, Olson BS, Rimmer J, Parkes M, Handley SA, Baldridge MT. Single cell viral tagging of Faecalibacterium prausnitzii reveals rare bacteriophages omitted by other techniques. Gut Microbes. 2025 Dec;17(1):2526719. doi: 10.1080/19490976.2025.2526719. Epub 2025 Aug 3. PMID: 40754853; PMCID: PMC12323421.
Cano P, Seltzer T, Seltzer J, Peng A, Landis J, Pluta L, Dittmer DP. Viral Load Measurements for Kaposi Sarcoma Herpesvirus (KSHV/HHV8): Review and an Updated Assay. J Med Virol. 2024 Dec;96(12):e70105. doi: 10.1002/jmv.70105. PMID: 39648698; PMCID: PMC12042282.
Weagley JS, Chica Cárdenas LA, Romani A, Sullender ME, Aggarwal S, Makimaa H, Hogarty MP, Rodgers R, Kennedy EA, Foster L, Schriefer LA, Baldridge MT. Differential microbial community assembly following co-housing versus microbiota transplant. ISME J. 2025 Jan 2;19(1):wraf256. doi: 10.1093/ismejo/wraf256. PMID: 41247324; PMCID: PMC12694414.