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iVirus publications and where iVirus is making a difference

Authorship and Citation

iVirus is built on tools developed by the Sullivan and Hurwitz labs, and expanded through inclusion of other, 3rd party tools. Anyone using iVirus tools (and the underlying programs) are asked to cite:

Bolduc, B. et al. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. ISME Commun. 1, (2021).
An update to the original work. Here, iVirus expands to KBase, in addition to adding more data and tools to CyVerse.
Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B. L. & Sullivan, M. B. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. ISME J. 11, 7–14 (2017)
The original paper. Check here to see how it all started.

Additionally, nearly all tools have some sort of reference that can be cited. These should be cited where appropriate. Citation information is included with every app, and here as well. If an author wishes to update their tool’s citation or adjust how it’s used, please let us know.

Publications Using iVirus

Below are a featured list of publications that are funded or associated with iVirus products. Publications using data are not listed here, check out the Data page for that! Also not included are those publications that only reference iVirus as "a resource."
Warwick-Dugdale, J., Solonenko, N., Moore, K., Chittick, L., Gregory, A. C., Allen, M. J., … Temperton, B. (2019). Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ, 7, e6800. https://doi.org/10.7717/peerj.6800
iVirus and long-read viromics!
Gregory, A. C., Zayed, A. A., Conceição-Neto, N., Temperton, B., Bolduc, B., Alberti, A., … Wincker, P. (2019). Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell, 177(5), 1109-1123.e14. https://doi.org/10.1016/j.cell.2019.03.040
Using iVirus tools to examine single-amplified viruses and tracking them in the oceans
Martinez-Hernandez, F., Fornas, O., Lluesma Gomez, M., Bolduc, B., de la Cruz Peña, M. J. M. J., Martínez, J. M. J. M., … Martinez-Garcia, M. (2017). Single-virus genomics reveals hidden cosmopolitan and abundant viruses. Nature Communications, 8(May), 15892. https://doi.org/10.1038/ncomms15892
Using iVirus tools to examine single-amplified viruses and tracking them in the oceans
Trubl, G., Jang, H. Bin, Roux, S., Emerson, J. B., Solonenko, N., Vik, D. R., … Rich, V. I. (2018). Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. MSystems, 3(5), 338103. https://doi.org/10.1128/mSystems.00076-18
Using iVirus tools to examine viruses found in soil.
Zhong, Z.-P., Rapp, J. Z., Wainaina, J. M., Solonenko, N. E., Maughan, H., Carpenter, S. D., … Sullivan, M. B. (2020). Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice. MSystems, 5(3), 1–17. https://doi.org/10.1128/mSystems.00246-20
Using iVirus tools to analyze
Bin Jang, H., Bolduc, B., Zablocki, O., Kuhn, J. H., Roux, S., Adriaenssens, E. M., … Sullivan, M. B. (2019). Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology, 37(6), 632–639. https://doi.org/10.1038/s41587-019-0100-8
An update to the original vConTACT tool.
Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B. L., & Sullivan, M. B. (2017). iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal, 11(1), 7–14. https://doi.org/10.1038/ismej.2016.89
Our introductory manuscript, showcasing the first round of data products brought alive through iVirus!
Vik, D. R., Roux, S., Brum, J. R., Bolduc, B., Emerson, J. B., Padilla, C. C. C., … Sullivan, M. B. (2017). Putative archaeal viruses from the mesopelagic ocean. PeerJ, 5(6), e3428. https://doi.org/10.7717/peerj.3428
A tool for identifying archaeal viruses, integrated into CyVerse
Bolduc, B., Jang, H. B. H. B., Doulcier, G., You, Z.-Q. Z., Roux, S., & Sullivan, M. B. M. B. (2017). vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ, 5(5), e3243. https://doi.org/10.7717/peerj.3243
Though it predates iVirus proper, this tool serves as a foundational one in many iVirus pipelines
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