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

The Sequence Read Archive

Leinonen, R., Sugawara, H., & Shumway, M. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1019 · Cited by 2,872

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

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 1,230

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

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

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 863

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 783

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

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

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

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 652

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

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

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

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 320

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 260

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

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 193

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 200

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

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 145

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 148

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

Genome binning of viral entities from bulk metagenomics data

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. (2022) · Nature Communications · doi:10.1038/s41467-022-28581-5 · Cited by 116

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 88

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

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 89

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 86

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 71

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

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

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

Single-virus genomics and beyond

Martínez, J. M., Martinez‐Hernández, F., & Martínez‐García, M. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00444-0 · Cited by 46

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 46

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

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 41

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

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

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

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 35

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

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

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

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

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

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

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 25

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

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

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 24

Droplet Microfluidics for High-Resolution Virology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 9

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 7

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

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

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

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

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

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

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 3

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

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

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

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

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

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

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) · University of Groningen research database (University of Groningen / Centre for Information Technology) · 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 · Cited by 1

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) · theses.fr (ABES) · doi:10.70675/cbe2ca53z6c38z4615zafe0z731fbdda12a4

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

Ndela, É. O. (2023) · theses.fr (ABES) · 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 312

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 2

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

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