iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure
Abstract
Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromicsmore »
- Authors:
-
- The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
- Univ. of Arizona, Tucson, AZ (United States). Dept. of Agricultural and Biosystems Engineering
- The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology. Dept. of Civil, Environmental and Geodetic Engineering
- Publication Date:
- Research Org.:
- Univ. of Arizona, Tucson, AZ (United States); The Ohio State Univ., Columbus, OH (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); Gordon and Betty Moore Foundation (United States)
- OSTI Identifier:
- 1473902
- Grant/Contract Number:
- SC0010580; GBMF4491; GBMF4733; GBMF3305; GBMF3790
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The ISME Journal
- Additional Journal Information:
- Journal Volume: 11; Journal ID: ISSN 1751-7362
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; metagenomics; virology
Citation Formats
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., and Sullivan, Matthew B.. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. United States: N. p., 2016.
Web. doi:10.1038/ismej.2016.89.
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., & Sullivan, Matthew B.. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. United States. https://doi.org/10.1038/ismej.2016.89
Bolduc, Benjamin, Youens-Clark, Ken, Roux, Simon, Hurwitz, Bonnie L., and Sullivan, Matthew B.. Fri .
"iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure". United States. https://doi.org/10.1038/ismej.2016.89. https://www.osti.gov/servlets/purl/1473902.
@article{osti_1473902,
title = {iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure},
author = {Bolduc, Benjamin and Youens-Clark, Ken and Roux, Simon and Hurwitz, Bonnie L. and Sullivan, Matthew B.},
abstractNote = {Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.},
doi = {10.1038/ismej.2016.89},
journal = {The ISME Journal},
number = ,
volume = 11,
place = {United States},
year = {2016},
month = {7}
}
Web of Science
Works referenced in this record:
High-Throughput Sequencing Technologies
journal, May 2015
- Reuter, Jason A.; Spacek, Damek V.; Snyder, Michael P.
- Molecular Cell, Vol. 58, Issue 4
Metagenomic Analysis of RNA Viruses in a Fresh Water Lake
journal, September 2009
- Djikeng, Appolinaire; Kuzmickas, Ryan; Anderson, Norman G.
- PLoS ONE, Vol. 4, Issue 9
The iPlant Collaborative: Cyberinfrastructure for Plant Biology
journal, January 2011
- Goff, Stephen A.; Vaughn, Matthew; McKay, Sheldon
- Frontiers in Plant Science, Vol. 2
Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
journal, July 2014
- Hurwitz, B. L.; Westveld, A. H.; Brum, J. R.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 29
CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
journal, June 2012
- Stern, A.; Mick, E.; Tirosh, I.
- Genome Research, Vol. 22, Issue 10
Sequencing platform and library preparation choices impact viral metagenomes
journal, January 2013
- Solonenko, Sergei A.; Ignacio-Espinoza, J.; Alberti, Adriana
- BMC Genomics, Vol. 14, Issue 1
Determinants of community structure in the global plankton interactome
journal, May 2015
- Lima-Mendez, G.; Faust, K.; Henry, N.
- Science, Vol. 348, Issue 6237
Viral metagenomics
journal, May 2005
- Edwards, Robert A.; Rohwer, Forest
- Nature Reviews Microbiology, Vol. 3, Issue 6
CAMERA: A Community Resource for Metagenomics
journal, March 2007
- Seshadri, Rekha; Kravitz, Saul A.; Smarr, Larry
- PLoS Biology, Vol. 5, Issue 3
Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome
journal, August 2014
- Hurwitz, Bonnie L.; Brum, Jennifer R.; Sullivan, Matthew B.
- The ISME Journal, Vol. 9, Issue 2
Bilinear Mixed-Effects Models for Dyadic Data
journal, March 2005
- Hoff, Peter D.
- Journal of the American Statistical Association, Vol. 100, Issue 469
Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes
journal, February 2008
- Lima-Mendez, G.; Van Helden, J.; Toussaint, A.
- Molecular Biology and Evolution, Vol. 25, Issue 4
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
journal, March 2007
- Yooseph, Shibu; Sutton, Granger; Rusch, Douglas B.
- PLoS Biology, Vol. 5, Issue 3
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
journal, January 2014
- Roux, Simon; Tournayre, Jeremy; Mahul, Antoine
- BMC Bioinformatics, Vol. 15, Issue 1
The global virome: not as big as we thought?
journal, October 2013
- Cesar Ignacio-Espinoza, J.; Solonenko, Sergei A.; Sullivan, Matthew B.
- Current Opinion in Virology, Vol. 3, Issue 5
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
Patterns and ecological drivers of ocean viral communities
journal, May 2015
- Brum, J. R.; Ignacio-Espinoza, J. C.; Roux, S.
- Science, Vol. 348, Issue 6237
SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
journal, November 2009
- Rattei, Thomas; Tischler, Patrick; Götz, Stefan
- Nucleic Acids Research, Vol. 38, Issue suppl_1
The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology
journal, February 2013
- Hurwitz, Bonnie L.; Sullivan, Matthew B.
- PLoS ONE, Vol. 8, Issue 2
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
journal, January 2011
- Marçais, Guillaume; Kingsford, Carl
- Bioinformatics, Vol. 27, Issue 6
VIROME: a standard operating procedure for analysis of viral metagenome sequences
journal, July 2012
- Wommack, K. Eric; Bhavsar, Jaysheel; Polson, Shawn W.
- Standards in Genomic Sciences, Vol. 6, Issue 3
Rapid evolution of the human gut virome
journal, July 2013
- Minot, S.; Bryson, A.; Chehoud, C.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 30
Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline
journal, December 2012
- Duhaime, Melissa B.; Sullivan, Matthew B.
- Virology, Vol. 434, Issue 2
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
VirSorter: mining viral signal from microbial genomic data
journal, January 2015
- Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.
- PeerJ, Vol. 3
The EMBL Nucleotide Sequence Database
journal, December 2004
- Kanz, C.
- Nucleic Acids Research, Vol. 33, Issue Database issue
Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
journal, July 2015
- Roux, Simon; Hallam, Steven J.; Woyke, Tanja
- eLife, Vol. 4
Database resources of the National Center for Biotechnology
journal, January 2003
- Wheeler, D. L.
- Nucleic Acids Research, Vol. 31, Issue 1
Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics
journal, March 2012
- Roux, Simon; Enault, Francois; Robin, Agnès
- PLoS ONE, Vol. 7, Issue 3
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Metabolic reprogramming by viruses in the sunlit and dark ocean
journal, January 2013
- Hurwitz, Bonnie L.; Hallam, Steven J.; Sullivan, Matthew B.
- Genome Biology, Vol. 14, Issue 11
Comparative metagenomics of microbial traits within oceanic viral communities
journal, February 2011
- Sharon, Itai; Battchikova, Natalia; Aro, Eva-Mari
- The ISME Journal, Vol. 5, Issue 7
Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community: Halite metagenome
journal, March 2016
- Crits-Christoph, Alexander; Gelsinger, Diego R.; Ma, Bing
- Environmental Microbiology, Vol. 18, Issue 6
Genomic analysis of uncultured marine viral communities
journal, October 2002
- Breitbart, M.; Salamon, P.; Andresen, B.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 22
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
journal, August 2015
- Brum, Jennifer R.; Hurwitz, Bonnie L.; Schofield, Oscar
- The ISME Journal, Vol. 10, Issue 2
The EMBL Nucleotide Sequence Database
journal, January 2000
- Baker, W.
- Nucleic Acids Research, Vol. 28, Issue 1
Erratum: Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
journal, January 2017
- Brum, Jennifer R.; Hurwitz, Bonnie L.; Schofield, Oscar
- The ISME Journal, Vol. 11, Issue 2
The EMBL Nucleotide Sequence Database
journal, January 2002
- Stoesser, G.
- Nucleic Acids Research, Vol. 30, Issue 1
The EMBL Nucleotide Sequence Database
journal, January 2004
- Kulikova, T.
- Nucleic Acids Research, Vol. 32, Issue 90001
The global virome: not as big as we thought?
journal, October 2013
- Cesar Ignacio-Espinoza, J.; Solonenko, Sergei A.; Sullivan, Matthew B.
- Current Opinion in Virology, Vol. 3, Issue 5
High-Throughput Sequencing Technologies
journal, May 2015
- Reuter, Jason A.; Spacek, Damek V.; Snyder, Michael P.
- Molecular Cell, Vol. 58, Issue 4
Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline
journal, December 2012
- Duhaime, Melissa B.; Sullivan, Matthew B.
- Virology, Vol. 434, Issue 2
Comparative metagenomics of microbial traits within oceanic viral communities
journal, February 2011
- Sharon, Itai; Battchikova, Natalia; Aro, Eva-Mari
- The ISME Journal, Vol. 5, Issue 7
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics
journal, August 2015
- Brum, Jennifer R.; Hurwitz, Bonnie L.; Schofield, Oscar
- The ISME Journal, Vol. 10, Issue 2
Rapid evolution of the human gut virome
journal, July 2013
- Minot, S.; Bryson, A.; Chehoud, C.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 30
Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
journal, July 2014
- Hurwitz, B. L.; Westveld, A. H.; Brum, J. R.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 29
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
journal, January 2011
- Marçais, Guillaume; Kingsford, Carl
- Bioinformatics, Vol. 27, Issue 6
Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes
journal, February 2008
- Lima-Mendez, G.; Van Helden, J.; Toussaint, A.
- Molecular Biology and Evolution, Vol. 25, Issue 4
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
Patterns and ecological drivers of ocean viral communities
journal, May 2015
- Brum, J. R.; Ignacio-Espinoza, J. C.; Roux, S.
- Science, Vol. 348, Issue 6237
Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs
journal, September 2015
- Munson-McGee, Jacob H.; Field, Erin K.; Bateson, Mary
- Applied and Environmental Microbiology, Vol. 81, Issue 22
The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
journal, October 2015
- Hannigan, Geoffrey D.; Meisel, Jacquelyn S.; Tyldsley, Amanda S.
- mBio, Vol. 6, Issue 5
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
journal, January 2014
- Roux, Simon; Tournayre, Jeremy; Mahul, Antoine
- BMC Bioinformatics, Vol. 15, Issue 1
Sequencing platform and library preparation choices impact viral metagenomes
journal, January 2013
- Solonenko, Sergei A.; Ignacio-Espinoza, J.; Alberti, Adriana
- BMC Genomics, Vol. 14, Issue 1
Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics
journal, March 2012
- Roux, Simon; Enault, Francois; Robin, Agnès
- PLoS ONE, Vol. 7, Issue 3
The Grand Challenges in Functional Plant Ecology
journal, January 2011
- Körner, Christian
- Frontiers in Plant Science, Vol. 2
Works referencing / citing this record:
An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach
journal, September 2017
- Parmar, Krupa; Dafale, Nishant; Pal, Rajesh
- Current Microbiology, Vol. 75, Issue 2
Virus taxonomy in the age of metagenomics
journal, January 2017
- Simmonds, Peter; Adams, Mike J.; Benkő, Mária
- Nature Reviews Microbiology, Vol. 15, Issue 3
Multiple mechanisms drive phage infection efficiency in nearly identical hosts
journal, March 2018
- Howard-Varona, Cristina; Hargreaves, Katherine R.; Solonenko, Natalie E.
- The ISME Journal, Vol. 12, Issue 6
Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems
journal, February 2019
- Bischoff, Vera; Bunk, Boyke; Meier-Kolthoff, Jan P.
- The ISME Journal, Vol. 13, Issue 6
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
journal, October 2018
- Solden, Lindsey M.; Naas, Adrian E.; Roux, Simon
- Nature Microbiology, Vol. 3, Issue 11
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
journal, May 2019
- Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier
- Nature Biotechnology, Vol. 37, Issue 6
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes
journal, September 2017
- Arndt, David; Marcu, Ana; Liang, Yongjie
- Briefings in Bioinformatics, Vol. 20, Issue 4
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
journal, October 2016
- Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 45, Issue D1
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
journal, May 2019
- Barylski, Jakub; Enault, François; Dutilh, Bas E.
- Systematic Biology
A viral reckoning: viruses emerge as essential manipulators of global ecosystems: Crystal ball
journal, October 2018
- Roux, Simon; Brum, Jennifer R.
- Environmental Microbiology Reports, Vol. 11, Issue 1
Overlooking the smallest matter: viruses impact biological invasions
journal, February 2017
- Faillace, Cara A.; Lorusso, Nicholas S.; Duffy, Siobain
- Ecology Letters, Vol. 20, Issue 4
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
journal, October 2018
- Trubl, Gareth; Jang, Ho Bin; Roux, Simon
- mSystems, Vol. 3, Issue 5
Finer-Scale Phylosymbiosis: Insights from Insect Viromes
journal, December 2018
- Leigh, Brittany A.; Bordenstein, Sarah R.; Brooks, Andrew W.
- mSystems, Vol. 3, Issue 6
The gut virome: the ‘missing link’ between gut bacteria and host immunity?
journal, January 2019
- Mukhopadhya, Indrani; Segal, Jonathan P.; Carding, Simon R.
- Therapeutic Advances in Gastroenterology, Vol. 12
Mining, analyzing, and integrating viral signals from metagenomic data
journal, March 2019
- Zheng, Tingting; Li, Jun; Ni, Yueqiong
- Microbiome, Vol. 7, Issue 1
A Review on Viral Metagenomics in Extreme Environments
journal, October 2019
- Dávila-Ramos, Sonia; Castelán-Sánchez, Hugo G.; Martínez-Ávila, Liliana
- Frontiers in Microbiology, Vol. 10
Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta)
journal, July 2018
- Creasy, Alexandria; Rosario, Karyna; Leigh, Brittany
- Viruses, Vol. 10, Issue 8
Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions
journal, September 2018
- Coy, Samantha; Gann, Eric; Pound, Helena
- Viruses, Vol. 10, Issue 9
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
journal, May 2019
- Kallies, René; Hölzer, Martin; Brizola Toscan, Rodolfo
- Viruses, Vol. 11, Issue 6
vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria
journal, January 2017
- Bolduc, Benjamin; Jang, Ho Bin; Doulcier, Guilhem
- PeerJ, Vol. 5
Putative archaeal viruses from the mesopelagic ocean
journal, January 2017
- Vik, Dean R.; Roux, Simon; Brum, Jennifer R.
- PeerJ, Vol. 5
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
journal, January 2019
- Trubl, Gareth; Roux, Simon; Solonenko, Natalie
- PeerJ, Vol. 7
Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
journal, January 2019
- Bekliz, Meriem; Brandani, Jade; Bourquin, Massimo
- PeerJ, Vol. 7
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages
journal, March 2020
- Lood, Cédric; Danis‐Wlodarczyk, Katarzyna; Blasdel, Bob G.
- Environmental Microbiology, Vol. 22, Issue 6
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
text, January 2019
- Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh
- BioMed Central
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
journal, October 2019
- Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh
- Microbiome, Vol. 7, Issue 1
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
text, January 2020
- Barylski, Jakub; Enault, François; Dutilh, Bas E.
- ETH Zurich
The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract
journal, February 2019
- De Sordi, Luisa; Lourenço, Marta; Debarbieux, Laurent
- Cell Host & Microbe, Vol. 25, Issue 2
Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems
journal, February 2019
- Bischoff, Vera; Bunk, Boyke; Meier-Kolthoff, Jan P.
- The ISME Journal, Vol. 13, Issue 6
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
journal, October 2018
- Solden, Lindsey M.; Naas, Adrian E.; Roux, Simon
- Nature Microbiology, Vol. 3, Issue 11
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
journal, July 2017
- Galiez, Clovis; Siebert, Matthias; Enault, François
- Bioinformatics, Vol. 33, Issue 19
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
journal, November 2018
- Paez-Espino, David; Roux, Simon; Chen, I-Min A.
- Nucleic Acids Research, Vol. 47, Issue D1
Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages
journal, May 2019
- Barylski, Jakub; Enault, François; Dutilh, Bas E.
- Systematic Biology
Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages
journal, March 2020
- Lood, Cédric; Danis‐Wlodarczyk, Katarzyna; Blasdel, Bob G.
- Environmental Microbiology, Vol. 22, Issue 6
Genome Sequence of PM2-Like Phage Cr39582, Induced from a Pseudoalteromonas sp. Isolated from the Gut of Ciona robusta
journal, May 2018
- Leigh, Brittany A.; Breitbart, Mya; Oksanen, Hanna M.
- Genome Announcements, Vol. 6, Issue 21
The gut virome: the ‘missing link’ between gut bacteria and host immunity?
journal, January 2019
- Mukhopadhya, Indrani; Segal, Jonathan P.; Carding, Simon R.
- Therapeutic Advances in Gastroenterology, Vol. 12
Mining, analyzing, and integrating viral signals from metagenomic data
journal, March 2019
- Zheng, Tingting; Li, Jun; Ni, Yueqiong
- Microbiome, Vol. 7, Issue 1
Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
journal, March 2020
- Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh
- Microbiome, Vol. 8, Issue 1
A Review on Viral Metagenomics in Extreme Environments
journal, October 2019
- Dávila-Ramos, Sonia; Castelán-Sánchez, Hugo G.; Martínez-Ávila, Liliana
- Frontiers in Microbiology, Vol. 10
Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions
journal, September 2018
- Coy, Samantha; Gann, Eric; Pound, Helena
- Viruses, Vol. 10, Issue 9
Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches
journal, May 2017
- Hayes, Stephen; Mahony, Jennifer; Nauta, Arjen
- Viruses, Vol. 9, Issue 6
Putative archaeal viruses from the mesopelagic ocean
journal, January 2017
- Vik, Dean R.; Roux, Simon; Brum, Jennifer R.
- PeerJ, Vol. 5