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For: Roux S, Páez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Reddy TBK, Nayfach S, Schulz F, Call L, Neches RY, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Kyrpides NC. IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. Nucleic Acids Res 2021;49:D764-75. [PMID: 33137183 DOI: 10.1093/nar/gkaa946] [Cited by in Crossref: 31] [Cited by in F6Publishing: 23] [Article Influence: 31.0] [Reference Citation Analysis]
Number Citing Articles
1 Demina TA, Luhtanen A, Roux S, Oksanen HM, Jansson JK. Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages. mBio. [DOI: 10.1128/mbio.00651-22] [Reference Citation Analysis]
2 Bistolas K, Vega Thurber R. Viral discovery in the 'realm' of COVID-19. Environ Microbiol Rep 2021;13:62-7. [PMID: 33258558 DOI: 10.1111/1758-2229.12912] [Reference Citation Analysis]
3 Roux S, Emerson JB. Diversity in the soil virosphere: to infinity and beyond? Trends in Microbiology 2022. [DOI: 10.1016/j.tim.2022.05.003] [Reference Citation Analysis]
4 Gu C, Liang Y, Li J, Shao H, Jiang Y, Zhou X, Gao C, Li X, Zhang W, Guo C, He H, Wang H, Sung YY, Mok WJ, Wong LL, Suttle CA, McMinn A, Tian J, Wang M. Saline lakes on the Qinghai-Tibet Plateau harbor unique viral assemblages mediating microbial environmental adaption. iScience 2021;24:103439. [PMID: 34988389 DOI: 10.1016/j.isci.2021.103439] [Reference Citation Analysis]
5 Abril AG, Carrera M, Notario V, Sánchez-pérez Á, Villa TG. The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics. Antibiotics 2022;11:653. [DOI: 10.3390/antibiotics11050653] [Reference Citation Analysis]
6 Dutilh BE, Varsani A, Tong Y, Simmonds P, Sabanadzovic S, Rubino L, Roux S, Muñoz AR, Lood C, Lefkowitz EJ, Kuhn JH, Krupovic M, Edwards RA, Brister JR, Adriaenssens EM, Sullivan MB. Perspective on taxonomic classification of uncultivated viruses. Curr Opin Virol 2021;51:207-15. [PMID: 34781105 DOI: 10.1016/j.coviro.2021.10.011] [Reference Citation Analysis]
7 Ramos-Barbero MD, Viver T, Zabaleta A, Senel E, Gomariz M, Antigüedad I, Santos F, Martínez-García M, Rosselló-Móra R, Antón J. Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface. Environ Microbiol 2021;23:3477-98. [PMID: 34110059 DOI: 10.1111/1462-2920.15630] [Reference Citation Analysis]
8 Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021;9:1115. [PMID: 34064105 DOI: 10.3390/microorganisms9061115] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
9 Gao C, Xia J, Zhou X, Liang Y, Jiang Y, Wang M, Shao H, Shi X, Guo C, He H, Wang H, He J, Hu D, Wang X, Zhao J, Zhang YZ, Sung YY, Mok WJ, Wong LL, McMinn A, Suttle CA, Wang M. Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas. Appl Environ Microbiol 2021;87:e0116021. [PMID: 34469192 DOI: 10.1128/AEM.01160-21] [Reference Citation Analysis]
10 Zhang W, Liang Y, Zheng K, Gu C, Liu Y, Wang Z, Zhang X, Shao H, Jiang Y, Guo C, He H, Wang H, Sung YY, Mok WJ, Zhang Y, McMinn A, Wang M. Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster. BMC Genomics 2021;22:675. [PMID: 34544379 DOI: 10.1186/s12864-021-07978-4] [Reference Citation Analysis]
11 Finn DR, Maldonado J, de Martini F, Yu J, Penton CR, Fontenele RS, Schmidlin K, Kraberger S, Varsani A, Gile GH, Barker B, Kollath DR, Muenich RL, Herckes P, Fraser M, Garcia-Pichel F. Agricultural practices drive biological loads, seasonal patterns and potential pathogens in the aerobiome of a mixed-land-use dryland. Sci Total Environ 2021;798:149239. [PMID: 34325138 DOI: 10.1016/j.scitotenv.2021.149239] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
12 Wu F, Speth DR, Philosof A, Crémière A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoshechkin IA, Orphan VJ. Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. Nat Microbiol 2022. [PMID: 35027677 DOI: 10.1038/s41564-021-01039-y] [Reference Citation Analysis]
13 Nikulin NA, Zimin AA. Influence of Non-canonical DNA Bases on the Genomic Diversity of Tevenvirinae. Front Microbiol 2021;12:632686. [PMID: 33889139 DOI: 10.3389/fmicb.2021.632686] [Reference Citation Analysis]
14 Wang L, Zhao J, Wang Z, Li N, Song J, Zhang R, Jiao N, Zhang Y. phoH-carrying virus communities responded to multiple factors and their correlation network with prokaryotes in sediments along Bohai Sea, Yellow Sea, and East China Sea in China. Sci Total Environ 2021;:152477. [PMID: 34952046 DOI: 10.1016/j.scitotenv.2021.152477] [Reference Citation Analysis]
15 Chu Q, Li J, Chen J, Yuan Z. HBV induced the discharge of intrinsic antiviral miRNAs in HBV-replicating hepatocytes via extracellular vesicles to facilitate its replication. J Gen Virol 2022;103. [PMID: 35604380 DOI: 10.1099/jgv.0.001744] [Reference Citation Analysis]
16 Merges D, Dal Grande F, Greve C, Otte J, Schmitt I. Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions. Environ Microbiol 2021;23:6637-50. [PMID: 34697892 DOI: 10.1111/1462-2920.15802] [Reference Citation Analysis]
17 Koedooder C, Landou E, Zhang F, Wang S, Basu S, Berman-frank I, Shaked Y, Rubin-blum M. Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Trichodesmium Diversity. Front Microbiol 2022;13:879970. [DOI: 10.3389/fmicb.2022.879970] [Reference Citation Analysis]
18 Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021;11:643214. [PMID: 34150671 DOI: 10.3389/fcimb.2021.643214] [Reference Citation Analysis]
19 Sorensen JW, Zinke LA, Ter Horst AM, Santos-Medellín C, Schroeder A, Emerson JB. DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes. mSystems 2021;6:e0061421. [PMID: 34491084 DOI: 10.1128/mSystems.00614-21] [Reference Citation Analysis]
20 Coclet C, Roux S. Global overview and major challenges of host prediction methods for uncultivated phages. Curr Opin Virol 2021;49:117-26. [PMID: 34126465 DOI: 10.1016/j.coviro.2021.05.003] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
21 Benler S, Koonin EV. Fishing for phages in metagenomes: what do we catch, what do we miss? Curr Opin Virol 2021;49:142-50. [PMID: 34139668 DOI: 10.1016/j.coviro.2021.05.008] [Reference Citation Analysis]
22 Mutalik VK, Arkin AP. A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. iScience 2022;25:104121. [DOI: 10.1016/j.isci.2022.104121] [Reference Citation Analysis]
23 Hsieh SY, Tariq MA, Telatin A, Ansorge R, Adriaenssens EM, Savva GM, Booth C, Wileman T, Hoyles L, Carding SR. Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome. Viruses 2021;13:2093. [PMID: 34696523 DOI: 10.3390/v13102093] [Reference Citation Analysis]
24 Li Z, Pan D, Wei G, Pi W, Zhang C, Wang JH, Peng Y, Zhang L, Wang Y, Hubert CRJ, Dong X. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J 2021;15:2366-78. [PMID: 33649554 DOI: 10.1038/s41396-021-00932-y] [Cited by in Crossref: 1] [Cited by in F6Publishing: 4] [Article Influence: 1.0] [Reference Citation Analysis]
25 Bajaj JS, Ng SC, Schnabl B. Promises of microbiome-based therapies. J Hepatol 2022;76:1379-91. [PMID: 35589257 DOI: 10.1016/j.jhep.2021.12.003] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
26 Lee DY, Bartels C, Mcnair K, Edwards RA, Swairjo MA, Luque A. Predicting the capsid architecture of phages from metagenomic data. Computational and Structural Biotechnology Journal 2022. [DOI: 10.1016/j.csbj.2021.12.032] [Reference Citation Analysis]
27 Roux S, Paul BG, Bagby SC, Nayfach S, Allen MA, Attwood G, Cavicchioli R, Chistoserdova L, Gruninger RJ, Hallam SJ, Hernandez ME, Hess M, Liu WT, McAllister TA, O'Malley MA, Peng X, Rich VI, Saleska SR, Eloe-Fadrosh EA. Ecology and molecular targets of hypermutation in the global microbiome. Nat Commun 2021;12:3076. [PMID: 34031405 DOI: 10.1038/s41467-021-23402-7] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
28 Keown RA, Dums JT, Brumm PJ, Macdonald J, Mead DA, Ferrell BD, Moore RM, Harrison AO, Polson SW, Wommack KE. Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes. Front Microbiol 2022;13:858366. [DOI: 10.3389/fmicb.2022.858366] [Reference Citation Analysis]
29 Mestre MR, Gao LA, Shah SA, López-Beltrán A, González-Delgado A, Martínez-Abarca F, Iranzo J, Redrejo-Rodríguez M, Zhang F, Toro N. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Res 2022:gkac467. [PMID: 35648479 DOI: 10.1093/nar/gkac467] [Reference Citation Analysis]
30 Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A. Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts. Cell Rep 2022;38:110204. [PMID: 35021085 DOI: 10.1016/j.celrep.2021.110204] [Reference Citation Analysis]
31 Forero-junco LM, Alanin KWS, Djurhuus AM, Kot W, Gobbi A, Hansen LH. Bacteriophages Roam the Wheat Phyllosphere. Viruses 2022;14:244. [DOI: 10.3390/v14020244] [Reference Citation Analysis]
32 Mangalea MR, Paez-Espino D, Kieft K, Chatterjee A, Chriswell ME, Seifert JA, Feser ML, Demoruelle MK, Sakatos A, Anantharaman K, Deane KD, Kuhn KA, Holers VM, Duerkop BA. Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell Host Microbe 2021;29:726-739.e5. [PMID: 33957082 DOI: 10.1016/j.chom.2021.03.020] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 3.0] [Reference Citation Analysis]
33 Cook R, Brown N, Redgwell T, Rihtman B, Barnes M, Clokie M, Stekel DJ, Hobman J, Jones MA, Millard A. INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes. PHAGE 2021;2:214-23. [DOI: 10.1089/phage.2021.0007] [Cited by in Crossref: 14] [Cited by in F6Publishing: 9] [Article Influence: 14.0] [Reference Citation Analysis]
34 Cobbin JC, Charon J, Harvey E, Holmes EC, Mahar JE. Current challenges to virus discovery by meta-transcriptomics. Curr Opin Virol 2021;51:48-55. [PMID: 34592710 DOI: 10.1016/j.coviro.2021.09.007] [Cited by in Crossref: 3] [Article Influence: 3.0] [Reference Citation Analysis]
35 Font-Verdera F, Liébana R, Aldeguer-Riquelme B, Gangloff V, Santos F, Viver T, Rosselló-Móra R. Inverted microbial community stratification and spatial-temporal stability in hypersaline anaerobic sediments from the S'Avall solar salterns. Syst Appl Microbiol 2021;44:126231. [PMID: 34332366 DOI: 10.1016/j.syapm.2021.126231] [Reference Citation Analysis]
36 Wang Z, Zhang F, Liang Y, Zheng K, Gu C, Zhang W, Liu Y, Zhang X, Shao H, Jiang Y, Guo C, He H, Wang H, Sung YY, Mok WJ, Wong LL, He J, McMinn A, Wang M. Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus. Microbiol Spectr 2021;9:e0046321. [PMID: 34643440 DOI: 10.1128/Spectrum.00463-21] [Reference Citation Analysis]
37 Johansen J, Plichta DR, Nissen JN, Jespersen ML, Shah SA, Deng L, Stokholm J, Bisgaard H, Nielsen DS, Sørensen SJ, Rasmussen S. Genome binning of viral entities from bulk metagenomics data. Nat Commun 2022;13:965. [PMID: 35181661 DOI: 10.1038/s41467-022-28581-5] [Reference Citation Analysis]
38 Kieft K, Anantharaman K. Virus genomics: what is being overlooked? Current Opinion in Virology 2022;53:101200. [DOI: 10.1016/j.coviro.2022.101200] [Reference Citation Analysis]
39 Alanin KWS, Junco LMF, Jørgensen JB, Nielsen TK, Rasmussen MA, Kot W, Hansen LH. Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay. Viruses 2021;13:959. [PMID: 34064231 DOI: 10.3390/v13060959] [Reference Citation Analysis]
40 Zhao J, Jing H, Wang Z, Wang L, Jian H, Zhang R, Xiao X, Chen F, Jiao N, Zhang Y, Poretsky R. Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench. mSystems. [DOI: 10.1128/msystems.01358-21] [Reference Citation Analysis]
41 Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ. Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity. PeerJ 2022;10:e13084. [PMID: 35345588 DOI: 10.7717/peerj.13084] [Reference Citation Analysis]
42 Rigden DJ, Fernández XM. The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Res 2021;49:D1-9. [PMID: 33396976 DOI: 10.1093/nar/gkaa1216] [Cited by in Crossref: 2] [Cited by in F6Publishing: 5] [Article Influence: 2.0] [Reference Citation Analysis]
43 Pinilla-Redondo R, Russel J, Mayo-Muñoz D, Shah SA, Garrett RA, Nesme J, Madsen JS, Fineran PC, Sørensen SJ. CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. Nucleic Acids Res 2021:gkab859. [PMID: 34606604 DOI: 10.1093/nar/gkab859] [Reference Citation Analysis]
44 Song L, Zhang L, Fang X. Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. Front Microbiol 2021;12:740990. [PMID: 34659174 DOI: 10.3389/fmicb.2021.740990] [Reference Citation Analysis]
45 Benler S, Faure G, Altae-Tran H, Shmakov S, Zheng F, Koonin E. Cargo Genes of Tn7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes. mBio 2021;12:e0293821. [PMID: 34872347 DOI: 10.1128/mBio.02938-21] [Reference Citation Analysis]
46 Chu Y, Zhao Z, Cai L, Zhang G. Viral diversity and biogeochemical potential revealed in different prawn-culture sediments by virus-enriched metagenome analysis. Environmental Research 2022;210:112901. [DOI: 10.1016/j.envres.2022.112901] [Reference Citation Analysis]
47 Hockenberry AJ, Wilke CO. BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains. PeerJ 2021;9:e11396. [PMID: 33996289 DOI: 10.7717/peerj.11396] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 2.0] [Reference Citation Analysis]
48 Oliveira LS, Gruber A. Rational Design of Profile Hidden Markov Models for Viral Classification and Discovery. In: Nakaya HI, editor. Bioinformatics. Exon Publications; 2021. pp. 151-70. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch9] [Reference Citation Analysis]
49 Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol 2021;19:e3001442. [PMID: 34752450 DOI: 10.1371/journal.pbio.3001442] [Reference Citation Analysis]
50 Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiol Mol Biol Rev 2022;:e0000421. [PMID: 35311574 DOI: 10.1128/mmbr.00004-21] [Reference Citation Analysis]