Detecting contamination in viromes using ViromeQC

Marine viruses — major players in the global ecosystem

Suttle, C. (2007) · Nature Reviews Microbiology · doi:10.1038/nrmicro1750 · Cited by 3,054 · see citing works

The Sequence Read Archive

Leinonen, R., Sugawara, H., & Shumway, M. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1019 · Cited by 2,760 · see citing works

Shotgun metagenomics, from sampling to analysis

Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202 · see citing works

Viruses in the faecal microbiota of monozygotic twins and their mothers

Reyes, A., Haynes, M. R., Hanson, N., Angly, F. E., Heath, A. C., Rohwer, F. L., & Gordon, J. I. (2010) · Nature · doi:10.1038/nature09199 · Cited by 1,198 · see citing works

VirSorter: mining viral signal from microbial genomic data

Roux, S., Enault, F., Hurwitz, B. L., & Sullivan, M. B. (2015) · PeerJ · doi:10.7717/peerj.985 · Cited by 1,074 · see citing works

The human gut virome: inter-individual variation and dynamic response to diet

Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2011) · Genome Research · doi:10.1101/gr.122705.111 · Cited by 935 · see citing works

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Roux, S., Brum, J. R., Dutilh, B. E., Sunagawa, S., Duhaime, M. B., Loy, A., Poulos, B. T., Solonenko, N., Lara, E., Poulain, J., et al. (2016) · Nature · doi:10.1038/nature19366 · Cited by 866 · see citing works

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

Shkoporov, A. N., & Hill, C. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.017 · Cited by 760 · see citing works

The International Nucleotide Sequence Database Collaboration

Karsch‐Mizrachi, I., Nakamura, Y., & Cochrane, G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1006 · Cited by 717 · see citing works

Cryptic prophages help bacteria cope with adverse environments

Wang, X., Kim, Y., Ma, Q., Hong, S. H., Pokusaeva, K., Sturino, J. M., & Wood, T. K. (2010) · Nature Communications · doi:10.1038/ncomms1146 · Cited by 677 · see citing works

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

Ren, J., Ahlgren, N. A., Lu, Y. Y., Fuhrman, J. A., & Sun, F. (2017) · Microbiome · doi:10.1186/s40168-017-0283-5 · Cited by 633 · see citing works

Laboratory procedures to generate viral metagenomes

Thurber, R. L. V., Haynes, M. R., Breitbart, M., Wegley, L., & Rohwer, F. L. (2009) · Nature Protocols · doi:10.1038/nprot.2009.10 · Cited by 600 · see citing works

Rapid evolution of the human gut virome

Minot, S. S., Bryson, A. L., Chehoud, C., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300833110 · Cited by 594 · see citing works

Accessible, curated metagenomic data through ExperimentHub

Pasolli, E., Schiffer, L., Manghi, P., Renson, A., Obenchain, V., Truong, D. T., Beghini, F., Malik, F., Ramos, M., Dowd, J. B., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4468 · Cited by 514 · see citing works

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

Wu, M., & Scott, A. J. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts079 · Cited by 453 · see citing works

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

Reyes, A., Blanton, L. V., Cao, S., Zhao, G., MANARY, M. J., Trehan, I., Smith, M. I., Wang, D., Virgin, H. W., Rohwer, F. L., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514285112 · Cited by 321 · see citing works

The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome

Hannigan, G. D., Meisel, J. S., Tyldsley, A. S., Zheng, Q., Hodkinson, B. P., SanMiguel, A. J., Minot, S. S., Bushman, F. D., & Grice, E. A. (2015) · mBio · doi:10.1128/mbio.01578-15 · Cited by 312 · see citing works

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

Roux, S., Enault, F., Robin, A., Ravet, V., Personnic, S., Theil, S., Colombet, J., Sime‐Ngando, T., & Debroas, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033641 · Cited by 240 · see citing works

Reproducible protocols for metagenomic analysis of human faecal phageomes

Shkoporov, A. N., Ryan, F. J., Draper, L. A., Forde, A., Stockdale, S. R., Daly, K. M., McDonnell, S. A., Nolan, J. A., Sutton, T., Dalmasso, M., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0446-z · Cited by 195 · see citing works

DESMAN: a new tool for de novo extraction of strains from metagenomes

Quince, C., Delmont, T., Raguideau, S., Alneberg, J., Darling, A., Collins, G., & Eren, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1309-9 · Cited by 175 · see citing works

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences

Roux, S., Krupovìč, M., Debroas, D., Forterre, P., & Enault, F. (2013) · Open Biology · doi:10.1098/rsob.130160 · Cited by 152 · see citing works

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

McCann, A., Ryan, F. J., Stockdale, S. R., Dalmasso, M., Blake, T., Ryan, C. A., Stanton, C., Mills, S., Ross, P. R., & Hill, C. (2018) · PeerJ · doi:10.7717/peerj.4694 · Cited by 129 · see citing works

Numerous cultivated and uncultivated viruses encode ribosomal proteins

Mizuno, C. M., Guyomar, C., Roux, S., Lavigne, R., Rodríguez‐Valera, F., Sullivan, M. B., Gillet, R., Forterre, P., & Krupovìč, M. (2019) · Nature Communications · doi:10.1038/s41467-019-08672-6 · Cited by 114 · see citing works

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

Zolfo, M., Tett, A., Jousson, O., Donati, C., & Segata, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw837 · Cited by 105 · see citing works

Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly

Emerson, J., Thomas, B. C., Andrade, K., Allen, E. E., Heidelberg, K. B., & Banfield, J. F. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.01212-12 · Cited by 102 · see citing works

Metagenomic Investigation of Viral Communities in Ballast Water

Kim, Y., Aw, T. G., Teal, T. K., & Rose, J. B. (2015) · Environmental Science & Technology · doi:10.1021/acs.est.5b01633 · Cited by 75 · see citing works

Generating viral metagenomes from the coral holobiont

Weynberg, K. D., Wood‐Charlson, E. M., Suttle, C. A., & van Oppen, M. J. H. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00206 · Cited by 74 · see citing works

Transmission of viruses via our microbiomes

Ly, M., Jones, M. B., Abeles, S. R., Santiago-Rodríguez, T. M., Gao, J., Chan, I. Y. F., Ghose, C., & Pride, D. T. (2016) · Microbiome · doi:10.1186/s40168-016-0212-z · Cited by 63 · see citing works

Diversity of DNA and RNA Viruses in Indoor Air As Assessed via Metagenomic Sequencing

Rosario, K., Fierer, N., Miller, S. L., Luongo, J. C., & Breitbart, M. (2018) · Environmental Science & Technology · doi:10.1021/acs.est.7b04203 · Cited by 61 · see citing works

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

Watkins, S. C., Kuehnle, N., Ruggeri, C. A., Malki, K., Bruder, K., Elayyan, J., Damisch, K., Vahora, N., O’Malley, P., Ruggles-Sage, B., et al. (2015) · Marine and Freshwater Research · doi:10.1071/mf15172 · Cited by 37 · see citing works

Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula

de Cárcer, D. A., López-Bueno, A., Alonso-Lobo, J. M., Quesada, A., & Alcamı́, A. (2016) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw074 · Cited by 31 · see citing works

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works

The human virome: assembly, composition and host interactions

Liang, G., & Bushman, F. D. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00536-5 · Cited by 629 · see citing works

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00928-6 · Cited by 580 · see citing works

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma

Lee, K. A., Thomas, A. M., Bolte, L. A., Björk, J. R., de Ruijter, L. K., Armanini, F., Asnicar, F., Blanco-Miguez, A., Board, R., Calbet-Llopart, N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01695-5 · Cited by 464 · see citing works

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

Zepeda-Rivera, M., Minot, S. S., Bouzek, H., Wu, H., Blanco-Míguez, A., Manghi, P., Jones, D. S., LaCourse, K. D., Wu, Y., McMahon, E. F., et al. (2024) · Nature · doi:10.1038/s41586-024-07182-w · Cited by 451 · see citing works

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

Cook, R., Hooton, S., Trivedi, U. H., King, L., Dodd, C. E. R., Hobman, J. L., Stekel, D. J., Jones, M. A., & Millard, A. D. (2021) · Microbiome · doi:10.1186/s40168-021-01010-3 · Cited by 318 · see citing works

A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

Tisza, M. J., & Buck, C. B. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023202118 · Cited by 254 · see citing works

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

Moon, K., Jeon, J. H., Kang, I., Park, K. S., Lee, K., Cha, C., Lee, S. H., & Cho, J. (2020) · Microbiome · doi:10.1186/s40168-020-00863-4 · Cited by 216 · see citing works

Discovery of several thousand highly diverse circular DNA viruses

Tisza, M. J., Pastrana, D. V., Welch, N. L., Stewart, B. M., Peretti, A., Starrett, G. J., Pang, Y.-Y. S., Krishnamurthy, S. R., Pesavento, P. A., McDermott, D. H., et al. (2020) · eLife · doi:10.7554/elife.51971 · Cited by 188 · see citing works

Mutualistic interplay between bacteriophages and bacteria in the human gut

Shkoporov, A. N., Turkington, C. J. R., & Hill, C. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00755-4 · Cited by 188 · see citing works

Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

Karcher, N., Nigro, E., Punčochář, M., Blanco-Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02427-7 · Cited by 159 · see citing works

Cenote-Taker 2 democratizes virus discovery and sequence annotation

Tisza, M. J., Belford, A. K., Domínguez‐Huerta, G., Bolduc, B., Sullivan, M. B., & Buck, C. B. (2020) · Virus Evolution · doi:10.1093/ve/veaa100 · Cited by 146 · see citing works

Expanding known viral diversity in the healthy infant gut

Shah, S. A., Deng, L., Thorsen, J., Pedersen, A. G., Dion, M. B., Castro-Mejía, J. L., Silins, R., Romme, F. O., Sausset, R., Jessen, L. E., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01345-7 · Cited by 141 · see citing works

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

Pratama, A. A., Bolduc, B., Zayed, A. A., Zhong, Z.-P., Guo, J., Vik, D. R., Gazitúa, M. C., Wainaina, J. M., Roux, S., & Sullivan, M. B. (2021) · PeerJ · doi:10.7717/peerj.11447 · Cited by 122 · see citing works

Genome binning of viral entities from bulk metagenomics data

Johansen, J., Plichta, D., Nissen, J., Jespersen, M., Shah, S. A., Deng, L., Stokholm, J., Bisgaard, H., Nielsen, D. S., Sørensen, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-022-28581-5 · Cited by 105 · see citing works

Shining Light on Human Gut Bacteriophages

Guerin, E., & Hill, C. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00481 · Cited by 84 · see citing works

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

Trubl, G., Hyman, P., Roux, S., & Abedon, S. T. (2020) · Soil Systems · doi:10.3390/soilsystems4020023 · Cited by 87 · see citing works

Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives

Jurasz, H., Pawłowski, T., & Perlejewski, K. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.745076 · Cited by 83 · see citing works

Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions

Blanco‐Míguez, A., Gálvez, E. J. C., Pasolli, E., Filippis, F. D., Amend, L., Huang, K. D., Manghi, P., Lesker, T.-R., Riedel, T., Cova, L., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.09.013 · Cited by 80 · see citing works

Viral biogeography of the mammalian gut and parenchymal organs

Shkoporov, A. N., Stockdale, S. R., Lavelle, A., Kondova, I. I., Hueston, C. M., Upadrasta, A., Khokhlova, E. V., van der Kamp, I., Ouwerling, B., Draper, L. A., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01178-w · Cited by 68 · see citing works

In-depth characterization of food and environmental microbiomes across different meat processing plants

Barcenilla, C., Cobo-Díaz, J. F., Puente, A., Valentino, V., Filippis, F. D., Ercolini, D., Carlino, N., Pinto, F., Segata, N., Maradona, M. P., et al. (2024) · Microbiome · doi:10.1186/s40168-024-01856-3 · Cited by 57 · see citing works

The gut virome in inflammatory bowel diseases

Liang, G., Güemes, A. G. C., Albenberg, L. G., & Bushman, F. D. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.10.005 · Cited by 53 · see citing works

Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages rarely carry antibiotic resistance genes

Billaud, M., Lamy-Besnier, Q., Lossouarn, J., Moncaut, E., Dion, M. B., Moineau, S., Traoré, F., Chatelier, E. L., Denis, C., Estellé, J., et al. (2021) · ISME Communications · doi:10.1038/s43705-021-00054-8 · Cited by 52 · see citing works

Single-virus genomics and beyond

Martínez, J. M., Martinez-Hernandez, F., & Martínez-García, M. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00444-0 · Cited by 37 · see citing works

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

Wu, L., Pappas, N., Wijesekara, Y., Piedade, G. J., Brussaard, C. P. D., & Dutilh, B. E. (2024) · Genome biology · doi:10.1186/s13059-024-03236-4 · Cited by 42 · see citing works

Administration of 25,000 IU vitamin A doses at routine immunisation in young infants.

Rahman, M. M., Mahalanabis, D., Wahed, M. A., Islam, M. A., & Habte, D. (1995) · PubMed · Cited by 40 · see citing works

The food-associated resistome is shaped by processing and production environments

Quijada, N. M., Cobo-Díaz, J. F., Valentino, V., Barcenilla, C., Filippis, F. D., Cabrera‐Rubio, R., Carlino, N., Pinto, F., Dzieciol, M., Calvete‐Torre, I., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02059-8 · Cited by 39 · see citing works

mMGE: a database for human metagenomic extrachromosomal mobile genetic elements

Lai, S., Jia, L., Subramanian, B., Pan, S., Zhang, J., Dong, Y., Chen, W.-H., & Zhao, X. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa869 · Cited by 38 · see citing works

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape

Piedade, G. J., Schön, M. E., Lood, C., Fofanov, M. V., Wesdorp, E. M., Biggs, T. E. G., Wu, L., Bolhuis, H., Fischer, M., Yutin, N., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53317-y · Cited by 35 · see citing works

Viromics approaches for the study of viral diversity and ecology in microbiomes

Roux, S., & Coclet, C. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00871-w · Cited by 39 · see citing works

Emerging technologies in the study of the virome

Smith, S. E., Huang, W., Tiamani, K., Unterer, M., Mirzaei, M. K., & Deng, L. (2022) · Current Opinion in Virology · doi:10.1016/j.coviro.2022.101231 · Cited by 32 · see citing works

Comprehensive Evaluation of RNA and DNA Viromic Methods Based on Species Richness and Abundance Analyses Using Marmot Rectal Samples

Sun, Y., Qu, Y., Yan, X., Yan, G., Chen, J., Wang, G., Zhao, Z., Liu, Y., Tu, C., & He, B. (2022) · mSystems · doi:10.1128/msystems.00430-22 · Cited by 31 · see citing works

Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways

Walsh, L. H., Coakley, M., Walsh, A. M., Crispie, F., O’Toole, P. W., & Cotter, P. D. (2023) · iScience · doi:10.1016/j.isci.2023.108004 · Cited by 29 · see citing works

Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin

Jackson, E. W., Wilhelm, R. C., Johnson, M. R., Lutz, H. L., Danforth, I., Gaydos, J. K., Hart, M. W., & Hewson, I. (2020) · Journal of Virology · doi:10.1128/jvi.01594-20 · Cited by 29 · see citing works

Insights into the global freshwater virome

Elbehery, A. H. A., & Deng, L. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.953500 · Cited by 27 · see citing works

Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea

Moon, K., Kim, S., Kang, I., & Cho, J. (2020) · Scientific Data · doi:10.1038/s41597-020-00695-9 · Cited by 27 · see citing works

Global Composition of the Bacteriophage Community in Honey Bees

Busby, T. J., Miller, C. R., Moran, N. A., & Leuven, J. T. V. (2022) · mSystems · doi:10.1128/msystems.01195-21 · Cited by 27 · see citing works

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data

Ciciani, M., Demozzi, M., Pedrazzoli, E., Visentin, E., Pezzè, L., Signorini, L. F., Blanco‐Míguez, A., Zolfo, M., Asnicar, F., Casini, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34213-9 · Cited by 24 · see citing works

Illuminating the Virosphere Through Global Metagenomics

Call, L., Nayfach, S., & Kyrpides, N. C. (2021) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-012221-095114 · Cited by 25 · see citing works

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samplesPreprint

Zolfo, M., Silverj, A., Blanco‐Míguez, A., Manghi, P., Rota‐Stabelli, O., Heidrich, V., Jensen, J., Maharjan, S., Franzosa, E. A., Menni, C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.19.580813 · Cited by 24 · see citing works

Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities

Filippis, F. D., Valentino, V., Yap, M., Cabrera‐Rubio, R., Barcenilla, C., Carlino, N., Cobo-Díaz, J. F., Quijada, N. M., Calvete‐Torre, I., Ruas‐Madiedo, P., et al. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00541-5 · Cited by 21 · see citing works

Droplet Microfluidics for High-Resolution Virology

Jing, W., & Han, H. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c00615 · Cited by 20 · see citing works

Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics

Ngo, V. Q. H., Enault, F., Midoux, C., Mariadassou, M., Chapleur, O., Mazéas, L., Loux, V., Bouchez, T., Krupovìč, M., & Bize, A. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.16120 · Cited by 19 · see citing works

High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia

Medina, J. E., Castañeda, S., Páez-Triana, L., Camargo, M., García-Corredor, D. J., Gómez, M., Luna, N., Ramírez, A., Pulido-Medellín, M. O., Muñoz, M., et al. (2023) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2023.105543 · Cited by 19 · see citing works

Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis

Chen, J., Sun, Y., Yan, X., Ren, Z., Wang, G., Liu, Y., Zhao, Z., Yi, L., Tu, C., & He, B. (2022) · mSystems · doi:10.1128/msystems.00907-22 · Cited by 19 · see citing works

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Lücking, D., Mercier, C., Alarcón-Schumacher, T., & Erdmann, S. (2023) · ISME Communications · doi:10.1038/s43705-023-00317-6 · Cited by 17 · see citing works

grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories

Taylor, L. J., Abbas, A. A., & Bushman, F. D. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa167 · Cited by 17 · see citing works

Ecological drivers and potential functions of viral communities in flooded arsenic-contaminated paddy soils

Gao, R., Ma, B., Hu, M., Fang, L., Chen, G., Zhang, W., Wang, Y., Song, X., & Li, F. (2023) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2023.162289 · Cited by 17 · see citing works

Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations

Gao, S., Fei, H., Li, Q., Lan, L., Huang, L., & Fan, P. (2024) · Nature Communications · doi:10.1038/s41467-024-45663-8 · Cited by 17 · see citing works

Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

Hsieh, S.-Y., Tariq, M., Telatin, A., Ansorge, R., Adriaenssens, E. M., Savva, G. M., Booth, C., Wileman, T., Hoyles, L., & Carding, S. R. (2021) · Viruses · doi:10.3390/v13102093 · Cited by 16 · see citing works

Hundreds of viral families in the healthy infant gutPreprint

Shah, S. A., Deng, L., Thorsen, J., Pedersen, A. G., Dion, M. B., Castro-Mejía, J. L., Silins, R., Romme, F. O., Sausset, R., Ndela, É. O., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.02.450849 · Cited by 16 · see citing works

The gut virome in two indigenous populations from Malaysia

Lee, C. Z., Zoqratt, M. Z. H. M., Phipps, M. E., Barr, J. J., Lal, S. K., Ayub, Q., & Rahman, S. (2022) · Scientific Reports · doi:10.1038/s41598-022-05656-3 · Cited by 14 · see citing works

Genome binning of viral entities from bulk metagenomics dataPreprint

Johansen, J., Plichta, D. R., Nissen, J. N., Jespersen, M. L., Shah, S. A., Deng, L., Stokholm, J., Bisgaard, H. F., Nielsen, D. S., Sørensen, S. J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.07.451412 · Cited by 14 · see citing works

Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens

Rubio‐Portillo, E., Robertson, S. E., & Antón, J. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae017 · Cited by 13 · see citing works

Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease

Boix-Amorós, A., Monaco, H., Sambataro, E., & Clemente, J. C. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2107866 · Cited by 13 · see citing works

Identification of antimicrobial resistance genes in intestinal content from Coyote (Canis latrans)

López-Islas, J. J., Méndez-Olvera, E. T., Cruz, T. R., & Martínez-Gómez, D. (2023) · Polish Journal of Veterinary Sciences · doi:10.24425/pjvs.2023.145016 · Cited by 12 · see citing works

Does the Human Gut Virome Contribute to Host Health or Disease?

Pavia, G., Marascio, N., Matera, G., & Quirino, A. (2023) · Viruses · doi:10.3390/v15112271 · Cited by 12 · see citing works

Influence of dengue virus serotypes on the abundance of Aedes aegypti insect-specific viruses (ISVs)

Gómez, M., Martínez, D., Páez-Triana, L., Luna, N., Ramírez, A., Medina, J. E., Cruz‐Saavedra, L., Hernández, C., Castañeda, S., Melo, R. B., et al. (2023) · Journal of Virology · doi:10.1128/jvi.01507-23 · Cited by 11 · see citing works

Optimisation and Application of a Novel Method to Identify Bacteriophages in Maternal Milk and Infant Stool Identifies Host-Phage Communities Within Preterm Infant Gut

Young, G. R., Yew, W. C., Nelson, A., Bridge, S. H., Berrington, J. E., Embleton, N. D., & Smith, D. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2022.856520 · Cited by 10 · see citing works

RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data

Tang, X., Shang, J., & Sun, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac011 · Cited by 9 · see citing works

NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland – a study protocol

Zimmermann, P., Kurth, S., Giannoukos, S., Stocker, M., & Bokulich, N. A. (2025) · BMJ Open · doi:10.1136/bmjopen-2024-092938 · Cited by 9 · see citing works

Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India

Mukhopadhyay, A., Choudhury, S., & Kumar, M. (2023) · Virus Research · doi:10.1016/j.virusres.2023.199110 · Cited by 9 · see citing works

IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning

Yin, H., Wu, S., Tan, J., Guo, Q., Li, M., Guo, J., Wang, Y., Jiang, X., & Zhu, H. (2024) · GigaScience · doi:10.1093/gigascience/giae018 · Cited by 9 · see citing works

Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools

Malukiewicz, J., D’arc, M., Dias, C. A., Cartwright, R. A., Grativol, A. D., Moreira, S. B., Souza, A. R., Tavares, M. C. H., Pissinatti, A., Ruiz-Miranda, C. R., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-42059-4 · Cited by 8 · see citing works

Host specificity and cophylogeny in the “animal-gut bacteria-phage” tripartite system

Feng, Y., Wei, R., Chen, Q., Shang, T., Zhou, N., Wang, Z., Chen, Y., Chen, G., Zhang, G., Dong, K., et al. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00557-x · Cited by 8 · see citing works

Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut

Park, J.-W., Yun, Y.-E., Cho, J. A., Yoon, S.-I., In, S.-A., Park, E., & Kim, M. (2025) · Nature Communications · doi:10.1038/s41467-025-58856-6 · Cited by 7 · see citing works

Insights into the human gut virome by sampling a population from the Indian subcontinent

Bhardwaj, K., Garg, A., Pandey, A. D., Sharma, H., Kumar, M., & Vrati, S. (2022) · Journal of General Virology · doi:10.1099/jgv.0.001774 · Cited by 5 · see citing works

Role of Transposons Inverted Repeat in Balancing Drought Tolerance and Yield Related Trait in Maize

(2023) · Trends in Animal and Plant Sciences · doi:10.62324/taps/2023.008 · Cited by 6 · see citing works

Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle

Medina, J. E., Castañeda, S., Camargo, M., García-Corredor, D. J., Muñoz, M., & Ramírez, J. D. (2024) · Veterinary Research Communications · doi:10.1007/s11259-024-10403-2 · Cited by 7 · see citing works

Dynamic nature of viral and bacterial communities in human faeces

Shkoporov, A. N., O’Regan, O., Smith, L., Khokhlova, E. V., Draper, L. A., Ross, R. P., & Hill, C. (2023) · iScience · doi:10.1016/j.isci.2023.108778 · Cited by 6 · see citing works

Construction and characterization of DNA libraries from cultured phages and environmental viromes

Liu, C. G., Thompson, B. E., Chang, J. D., Min, L., & Maresso, A. W. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01171-24 · Cited by 5 · see citing works

Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics

Trubl, G., Roux, S., Kellom, M., Vyshenska, D., Tomatsu, A., Singh, K., Kimbrel, J. A., Eloe‐Fadrosh, E. A., Malmstrom, R. R., Pett‐Ridge, J., et al. (2026) · mSystems · doi:10.1128/msystems.01136-25 · Cited by 5 · see citing works

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach

Dovrolis, N., Kassela, K., Konstantinidis, K., Kouvela, A., Veletza, S. V., & Karakasiliοtis, I. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009304 · Cited by 5 · see citing works

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogensPreprint

Cook, R., Hooton, S., Trivedi, U. H., King, L., Dodd, C. E. R., Hobman, J. L., Stekel, D. J., Jones, M. A., & Millard, A. D. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.08.329714 · Cited by 5 · see citing works

Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands

Hemmat-Jou, M. H., Li, F., Wang, D., Gao, R., Zhou, X., Chen, Y., & Fang, L. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.140469 · Cited by 3 · see citing works

De-heterogeneity of the eukaryotic viral reference database (EVRD) improves the accuracy and efficiency of viromic analysisPreprint

Chen, J., Yan, X., Sun, Y., Ren, Z., Yan, G., Wang, G., Liu, Y., Zhao, Z., Liu, Y., Tu, C., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.03.482774 · Cited by 3 · see citing works

Impact of diet in shaping gut virome of grain-fed and grass-fed beef cattle revealed by a comparative metagenomic study

Zhang, Y., Liao, Y., Fang, L., Li, R. W., & Wu, V. C. H. (2025) · Microbiome · doi:10.1186/s40168-025-02163-1 · Cited by 2 · see citing works

A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samplesPreprint

Pinto, F., Zolfo, M., Beghini, F., Armanini, F., Asnicar, F., Silverj, A., Boscaini, A., Salmaso, N., & Segata, N. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.17.302836 · Cited by 2 · see citing works

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequencesPreprint

Wijesekara, Y., Wu, L., Beeloo, R., Rozwalak, P., Hauptfeld, E., Doijad, S. P., Dutilh, B. E., & Kaderali, L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.24.612722 · Cited by 2 · see citing works

A comparison of methods for the optimal recovery of the human fecal virome

Chiara, L. D., Doughty, R., Estévez‐Gómez, N., Gallego‐García, P., Alvariño, P., Díez‐Martín, A. I., Dávila-Piñón, P., Treangen, T. J., Cubiella, J., & Posada, D. (2026) · ISME Communications · doi:10.1093/ismeco/ycag090 · Cited by 1 · see citing works

ViromeXplore: integrative workflows for complete and reproducible virome characterization

Hernández-Velázquez, R., Ziemski, M., & Bokulich, N. A. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf638 · Cited by 1 · see citing works

iVirP: An integrative, efficient, and user-friendly pipeline to annotate viral contigs from raw reads of metagenome or VLP sequencingPreprint

Li, B., Jiao, X., & Liang, G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.21.576577 · Cited by 1 · see citing works

Life-Stage Transitions Drive Distinct Gut Viral Communities in Dairy CattlePreprint

Cook, R., Blanchard, A. M., Marsh, C., Ponsero, A. J., Reynolds, J., Adriaenssens, E. M., Hudson, C. D., Hobman, J. L., Stekel, D. J., Jones, M. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.24.655612 · Cited by 1 · see citing works

Peer Review #1 of "Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation (v0.2)"

(2021) · PeerJ · doi:10.7287/peerj.11447v0.2/reviews/1

Peer Review #1 of "Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.11447v0.1/reviews/1

Peer Review #2 of "Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.11447v0.1/reviews/2

Peer Review #2 of "Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation (v0.2)"

(2021) · PeerJ · doi:10.7287/peerj.11447v0.2/reviews/2

Understanding virus–bacteria–human tripartite interactions: strategies and challenges

Yadav, A., Shinde, P. B., Ahlawat, S., & Sharma, K. K. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-95332-0.00006-5

Clinical insights into the efficacy of immune checkpoint inhibitors in patients with cancer

de Ruijter, L. K. (2024) · doi:10.33612/diss.952617592

Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey

Senel, E., Ramos‐Barbero, M. D., Santos, F., Villamor, J., Mutlu, M. B., & Antón, J. (2025) · Archives of Virology · doi:10.1007/s00705-025-06449-5

Additional file 2 of Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

Karcher, N., Nigro, E., Punčochář, M., Blanco‐Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14984999

Additional file 3 of Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

Wu, L., Wijesekara, Y., Piedade, G. J., Pappas, N., Brussaard, C. P. D., & Dutilh, B. E. (2024) · Figshare · doi:10.6084/m9.figshare.26707020

Additional file 3 of Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

Karcher, N., Nigro, E., Punčochář, M., Blanco‐Míguez, A., Ciciani, M., Manghi, P., Zolfo, M., Cumbo, F., Manara, S., Golzato, D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14985002

Additional file 1 of Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

Wu, L., Wijesekara, Y., Piedade, G. J., Pappas, N., Brussaard, C. P. D., & Dutilh, B. E. (2024) · Figshare · doi:10.6084/m9.figshare.25608690

Additional file 2 of Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

Wu, L., Wijesekara, Y., Piedade, G. J., Pappas, N., Brussaard, C. P. D., & Dutilh, B. E. (2024) · UvA-DARE (University of Amsterdam) · doi:10.6084/m9.figshare.25608862

Additional file 3 of Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

Cook, R., Hooton, S., Trivedi, U., King, L., R., D. C. E., Hobman, J. L., Stekel, D. J., Jones, M. A., & Millard, A. D. (2021) · Figshare · doi:10.6084/m9.figshare.14253440

Effects of marine heatwaves on the dynamics of marine coastal microbial communities

Haro-Moreno, J. M., Diaz-Arinero, E., Aldeguer‐Riquelme, B., & Rubio‐Portillo, E. (2026) · Environmental Microbiome · doi:10.1186/s40793-026-00861-3

Bactériophages et vésicules extracellulaires du microbiote intestinal : développement de nouveaux outils d’étude et rôles dans les Maladies Inflammatoires Chroniques de l’Intestin (MICI)

Sausset, R. (2022) · doi:10.70675/cbe2ca53z6c38z4615zafe0z731fbdda12a4

Studying viral genome and protein diversity : bioinformatic developments and analysis of families of interest

Ndela, É. O. (2023) · doi:10.70675/17b72026z076az4622za540z38bfb251dd02

Paired viromics resolves the modular ecological architecture of the swine nasopharyngeal phageomePreprint

Mencía‐Ares, Ó., Deneke, C., Martínez-Martínez, S., Malorny, B., Gutiérrez-Martín, C. B., & Grützke, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.28.728360

CONTAMINATOR – detect contaminating sequences in high-throughput sequencing data

Glatting, K., Budak, G., Sieverling, L., & Hotz‐Wagenblatt, A. (2013) · F1000Research · doi:10.7490/f1000research.1094020.1

Monitoring cross-contamination in viral metagenomic data using an alien-control

Rollin, J., Rong, W., & Massart, S. (2023) · Open Repository and Bibliography (University of Liège)

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

Kostic, A. D., Ojesina, A. I., Pedamallu, C. S., Jung, J., Verhaak, R. G. W., Getz, G. A., & Meyerson, M. M. (2011) · Nature Biotechnology · doi:10.1038/nbt.1868 · Cited by 317 · see citing works

ViralQC: a tool for assessing completeness and contamination of predicted viral contigs

Peng, C., Shang, J., Guan, J., & Sun, Y. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag463 · Cited by 1 · see citing works

Cont-ID: detection of cross-contamination in metagenomic data

Rollin, J., Rong, W., & Massart, S. (2021) · Open Repository and Bibliography (University of Liège)