A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions Camargo, A.P., Baltoumas, F.A., Ndela, E.O., Fiamenghi, M.B., Merrill, B.D., Carter, M.M., Pinto, Y., Chakraborty, M., Andreeva, A., Ghiotto, G., Shaw, J., Proal, A.D., Sonnenburg, J.L., Bhatt, A.S., Roux, S., Pavlopoulos, G.A., Nayfach, S., & Kyrpides, N.C.
bioRxiv (2025). doi:10.1101/2025.11.01.686033.

Meta-Virus Resource (MetaVR): Expanding the Frontiers of Viral Diversity with 24 million Uncultivated Virus Genomes Fiamenghi MB, Camargo AP, Chasapi IN, Baltoumas F, Roux S, Egorov A, Aplakidou E, Ndela EO, Vasquez YM, Chen I-M, Palaniappan K, Reddy TBK, Mukherjee S, Ivanova N, Schulz F, Woyke T, Eloe-Fadrosh E, Pavlopoulos GA, Kyrpides N.
Nucleic Acids Res. 2025 Nov 28:gkaf1283. doi:10.1093/nar/gkaf1283. PMID:41312645.

metagRoot: A comprehensive database of protein families associated with plant root microbiomes Chasapi MN, Chasapi IN, Aplakidou E, Baltoumas FA, Karatzas E, Iliopoulos I, Stravopodis DJ, Emiris IZ, Buluç A, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA.
Nucleic Acids Res. 2025 Sep 1:gkaf862. doi: 10.1093/nar/gkaf862. PMID: 40888850.

Unraveling the functional dark matter through global metagenomics Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E; Novel Metagenome Protein Families Consortium; Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A, Kyrpides NC.
Nature. 2023 Oct;622(7983):594-602. doi: 10.1038/s41586-023-06583-7. Epub 2023 Oct 11. PMID: 37821698

NMPFamsDB: A database of novel protein families from microbial metagenomes and metatranscriptomes Baltoumas FA, Karatzas E, Liu S, Ovchinnikov S, Sofianatos Y, Chen IM, Kyrpides NC, Pavlopoulos GA.
Nucleic Acids Res. 2024 Jan 5;52(D1):D502-D512. doi: 10.1093/nar/gkad800. PMID: 37811892