The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
Open accessAbstract
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Fortunato, S. (2010) · Physics Reports · doi:10.1016/j.physrep.2009.11.002 · Cited by 11,293
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128
Using network analysis to explore co-occurrence patterns in soil microbial communities
Barberán, A., Bates, S. T., Casamayor, E. O., & Fierer, N. (2012) · The ISME Journal · doi:10.1038/ismej.2011.119 · Cited by 3,044
Computing topological parameters of biological networks
Assenov, Y., Ramírez, F., Schelhorn, S.-E., Lengauer, T., & Albrecht, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm554 · Cited by 1,826
Schaeffer, S. E. (2007) · Computer Science Review · doi:10.1016/j.cosrev.2007.05.001 · Cited by 1,639
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease
Norman, J. M., Handley, S. A., Baldridge, M. T., Droit, L., Liu, C. Y., Keller, B. C., Kambal, A., Monaco, C. L., Zhao, G., Fleshner, P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.002 · Cited by 1,285
Detecting overlapping protein complexes in protein-protein interaction networks
Nepusz, T., Yu, H., & Paccanaro, A. (2012) · Nature Methods · doi:10.1038/nmeth.1938 · Cited by 1,245
Paez-Espino, D., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Thomas, A. D., Huntemann, M., Mikhailova, N., Rubin, E., Ivanova, N. N., & Kyrpides, N. C. (2016) · Nature · doi:10.1038/nature19094 · Cited by 1,170
A review of long-branch attraction
Bergsten, J. (2005) · Cladistics · doi:10.1111/j.1096-0031.2005.00059.x · Cited by 1,162
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Coordinators, T. O., Roux, S., Brum, J. R., Dutilh, B. E., Sunagawa, S., Duhaime, M. B., Loy, A., Poulos, B. T., Solonenko, N., Lara, E., et al. (2016) · Nature · doi:10.1038/nature19366 · Cited by 865
Self-citationWang, J., Tang, H., Zhang, C., Zhao, Y., Derrien, M., Rocher, E., van-Hylckama Vlieg, J. E. T., Strissel, K., Zhao, L., Obin, M., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2014.99 · Cited by 836
Edwards, R. A., & Rohwer, F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1163 · Cited by 820
Patterns and ecological drivers of ocean viral communities
Brum, J. R., Ignacio-Espinoza, J. C., Roux, S., Doulcier, G., Acinas, S. G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J. M., et al. (2015) · Science · doi:10.1126/science.1261498 · Cited by 785
Self-citationVirus taxonomy in the age of metagenomics
Simmonds, P., Adams, M. J., Benkő, M., Breitbart, M., Brister, J. R., Carstens, E. B., Davison, A. J., Delwart, E., Gorbalenya, A. E., Harrach, B., et al. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.177 · Cited by 741
Self-citationThe Phage Proteomic Tree: a Genome-Based Taxonomy for Phage
Rohwer, F., & Edwards, R. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.16.4529-4535.2002 · Cited by 605
Manrique, P., Bolduc, B., Walk, S. T., van der Oost, J., de Vos, W. M., & Young, M. J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1601060113 · Cited by 545
Self-citationViral dark matter and virus–host interactions resolved from publicly available microbial genomes
Roux, S., Hallam, S. J., Woyke, T., & Sullivan, M. B. (2015) · eLife · doi:10.7554/elife.08490 · Cited by 478
Self-citationSullivan, M. B., Lindell, D., Lee, J. A., Thompson, L. R., Bielawski, J. P., & Chisholm, S. W. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040234 · Cited by 474
Self-citationThe iPlant Collaborative: Cyberinfrastructure for Plant Biology
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., et al. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00034 · Cited by 442
Pope, W. H., Bowman, C. A., Russell, D. A., Jacobs-Sera, D., Asai, D. J., Cresawn, S. G., Jacobs, W. R., Hendrix, R. W., Lawrence, J. G., Hatfull, G. F., et al. (2015) · eLife · doi:10.7554/elife.06416 · Cited by 310
Metabolic reprogramming by viruses in the sunlit and dark ocean
Hurwitz, B. L., Hallam, S. J., & Sullivan, M. B. (2013) · Genome Biology · doi:10.1186/gb-2013-14-11-r123 · Cited by 276
Self-citationClassification of Myoviridae bacteriophages using protein sequence similarity
Lavigne, R., Darius, P., Summer, E. J., Seto, D., Mahadevan, P., Nilsson, A. S., Ackermann, H. W., & Kropinski, A. M. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-224 · Cited by 269
Imbroglios of Viral Taxonomy: Genetic Exchange and Failings of Phenetic Approaches
Lawrence, J. G., Hatfull, G. F., & Hendrix, R. W. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.17.4891-4905.2002 · Cited by 268
Network analyses structure genetic diversity in independent genetic worlds
Halary, S., Leigh, J. W., Cheaib, B., Lopez, P., & Bapteste, E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908978107 · Cited by 263
Grose, J. H., & Casjens, S. R. (2014) · Virology · doi:10.1016/j.virol.2014.08.024 · Cited by 250
Ågren, J., Sundström, A., Håfström, T., & Segerman, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039107 · Cited by 249
International Committee on Taxonomy of Viruses and the 3,142 unassigned species
Fauquet, C., & Fargette, D. (2005) · Virology Journal · doi:10.1186/1743-422x-2-64 · Cited by 244
Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton
Labonté, J. M., Swan, B. K., Poulos, B., Luo, H., Koren, S., Hallam, S. J., Sullivan, M. B., Woyke, T., Eric Wommack, K., & Stepanauskas, R. (2015) · The ISME Journal · doi:10.1038/ismej.2015.48 · Cited by 239
Self-citationReticulate Representation of Evolutionary and Functional Relationships between Phage Genomes
Lima-Mendez, G., Van Helden, J., Toussaint, A., & Leplae, R. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn023 · Cited by 231
Roux, S., Hawley, A. K., Torres Beltran, M., Scofield, M., Schwientek, P., Stepanauskas, R., Woyke, T., Hallam, S. J., & Sullivan, M. B. (2014) · eLife · doi:10.7554/elife.03125 · Cited by 223
Self-citationEvolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life
Prangishvili, D., Garrett, R. A., & Koonin, E. V. (2006) · Virus Research · doi:10.1016/j.virusres.2006.01.007 · Cited by 217
ACLAME: A CLAssification of Mobile genetic Elements
Leplae, R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh084 · Cited by 213
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space
Deng, L., Ignacio-Espinoza, J. C., Gregory, A. C., Poulos, B. T., Weitz, J. S., Hugenholtz, P., & Sullivan, M. B. (2014) · Nature · doi:10.1038/nature13459 · Cited by 209
Self-citationHurwitz, B. L., Brum, J. R., & Sullivan, M. B. (2015) · The ISME Journal · doi:10.1038/ismej.2014.143 · Cited by 196
Self-citationThe Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing
Iranzo, J., Krupovic, M., & Koonin, E. V. (2016) · mBio · doi:10.1128/mbio.00978-16 · Cited by 188
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
Paez-Espino, D., Chen, I.-M. A., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V. M., Nielsen, T., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1030 · Cited by 187
Self-citationNovel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation
Keen, E. C., Bliskovsky, V. V., Malagón, F., Baker, J. D., Prince, J. S., Klaus, J. S., & Adhya, S. L. (2017) · mBio · doi:10.1128/mbio.02115-16 · Cited by 153
Millard, A. D., Zwirglmaier, K., Downey, M. J., Mann, N. H., & Scanlan, D. J. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01966.x · Cited by 152
A reevaluation of the higher taxonomy of viruses based on RNA polymerases
Zanotto, P. M. D. A., Gibbs, M. J., Gould, E. A., & Holmes, E. C. (1996) · Journal of Virology · doi:10.1128/jvi.70.9.6083-6096.1996 · Cited by 149
Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome
Drees, K. P., Lorch, J. M., Puechmaille, S. J., Parise, K. L., Wibbelt, G., Hoyt, J. R., Sun, K., Jargalsaikhan, A., Dalannast, M., Palmer, J. M., et al. (2017) · mBio · doi:10.1128/mbio.01941-17 · Cited by 127
The involvement of survival signaling pathways in rubella-virus induced apoptosis
Cooray, S., Jin, L., & Best, J. M. (2005) · Virology Journal · doi:10.1186/1743-422x-2-1 · Cited by 126
Identifying functional modules in interaction networks through overlapping Markov clustering
Shih, Y.-K., & Parthasarathy, S. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts370 · Cited by 124
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution
Corel, E., Lopez, P., Méheust, R., & Bapteste, E. P. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2015.12.003 · Cited by 124
The Grand Challenges in Functional Plant Ecology
Körner, C. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00001 · Cited by 118
Genomes of marine cyanopodoviruses reveal multiple origins of diversity
Labrie, S. J., Moniz, K., Osburne, M. S., Kelly, L., Roggensack, S. E., Sullivan, M. B., Gearin, G., Zeng, Q., FitzGerald, M. G., Henn, M. R., et al. (2012) · Environmental Microbiology · doi:10.1111/1462-2920.12053 · Cited by 117
Self-citationBolduc, B., Youens‐Clark, K., Roux, S., Hurwitz, B. L., & Sullivan, M. B. (2016) · The ISME Journal · doi:10.1038/ismej.2016.89 · Cited by 112
Self-citationMethods for virus classification and the challenge of incorporating metagenomic sequence data
Peter Simmonds, K. (2014) · Journal of General Virology · doi:10.1099/jgv.0.000016 · Cited by 110
Redder, P., Peng, X., Brügger, K., Shah, S. A., Roesch, F., Greve, B., She, Q., Schleper, C., Forterre, P., Garrett, R. A., et al. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02009.x · Cited by 107
Iranzo, J., Koonin, E. V., Prangishvili, D. A., & Krupovìč, M. (2016) · Journal of Virology · doi:10.1128/jvi.01622-16 · Cited by 102
Comeau, A., & Krisch, H. M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn080 · Cited by 84
Dagan, T. (2011) · Trends in Microbiology · doi:10.1016/j.tim.2011.07.001 · Cited by 82
Filée, J., Bapteste, É., Susko, E., & Krisch, H. (2006) · Molecular biology and evolution · doi:10.1093/molbev/msl036 · Cited by 80
Niu, Y. D., McAllister, T. A., Nash, J. J., Kropinski, A. M., & Stanford, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100426 · Cited by 71
Goulet, A., Blangy, S., Redder, P., Prangishvili, D. A., Felisberto‐Rodrigues, C., Forterre, P., Campanacci, V., & Cambillau, C. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909893106 · Cited by 54
Recombination and microdiversity in coastal marine cyanophages
Marston, M. F., & Amrich, C. G. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02037.x · Cited by 53
Eriksson, H., Maciejewska, B., Łątka, A., Majkowska-Skrobek, G., Hellstrand, M., Melefors, Ö., Wang, J., Kropinski, A. M., Drulis‐Kawa, Z., & Nilsson, A. S. (2015) · Viruses · doi:10.3390/v7041804 · Cited by 48
Gutiérrez, D., Adriaenssens, E. M., Martínez, B., Rodríguez, A., Lavigne, R., Kropinski, A. M., & García, P. (2013) · Archives of Virology · doi:10.1007/s00705-013-1833-1 · Cited by 26
Cited by
Phage diversity, genomics and phylogeny
Dion, M. B., Oechslin, F., & Moineau, S. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0311-5 · Cited by 960
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
Gregory, A. C., Zayed, A. A., Conceição-Neto, N., Temperton, B., Bolduc, B., Alberti, A., Ardyna, M., Arkhipova, K., Carmichael, M., Cruaud, C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.040 · Cited by 826
Self-citationBacteriophages 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 767
Minimum Information about an Uncultivated Virus Genome (MIUViG)
Roux, S., Adriaenssens, E. M., Dutilh, B. E., Koonin, E. V., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Lavigne, R., Brister, J. R., Varsani, A., et al. (2019) · Nature Biotechnology · doi:10.1038/nbt.4306 · Cited by 732
Self-citationThe Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
Gregory, A. C., Zablocki, O., Zayed, A. A., Howell, A., Bolduc, B., & Sullivan, M. B. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.08.003 · Cited by 658
Self-citation
Metadata
- Authors
- Bolduc, B., Jang, H. B., Doulcier, G., You, Z.-Q., Roux, S., & Sullivan, M. B.
- Venue
- PeerJ
- Publisher
- PeerJ
- Published
- 2017-05-03
- Volume
- 5
- Pages
- e3243
- ISSN
- 2167-8359 (ISSN-L)
- OpenAlex
- W2610784236
- Cited by
- 287
- References
- 58
- FWCI
- 15.23
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
