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Your search keyword '"Brister, J Rodney"' showing total 5 results
Start Over Author "Brister, J Rodney" Journal nature biotechnology
5 results on '"Brister, J Rodney"'

1. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author

Adriaenssens, Evelien M, Roux, Simon, Brister, J Rodney, Karsch-Mizrachi, Ilene, Kuhn, Jens H, Varsani, Arvind, Yigang, Tong, Reyes, Alejandro, Lood, Cédric, Lefkowitz, Elliot J, Sullivan, Matthew B, Edwards, Robert A, Simmonds, Peter, Rubino, Luisa, Sabanadzovic, Sead, Krupovic, Mart, and Dutilh, Bas E

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Genome, Viral, Phylogeny, Databases, Factual
Published
2023

2. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author

Bin Jang, Ho, Bolduc, Benjamin, Zablocki, Olivier, Kuhn, Jens H, Roux, Simon, Adriaenssens, Evelien M, Brister, J Rodney, Kropinski, Andrew M, Krupovic, Mart, Lavigne, Rob, Turner, Dann, and Sullivan, Matthew B

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Biotechnology, Genetics, Infection, Bacteriophages, Classification, Gene Regulatory Networks, Genome, Viral, Metagenome, Metagenomics, Phylogeny, Prokaryotic Cells, Viruses
Abstract

Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.

Published
2019

3. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

4. Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author

Adriaenssens, Evelien M., primary, Roux, Simon, additional, Brister, J. Rodney, additional, Karsch-Mizrachi, Ilene, additional, Kuhn, Jens H., additional, Varsani, Arvind, additional, Yigang, Tong, additional, Reyes, Alejandro, additional, Lood, Cédric, additional, Lefkowitz, Elliot J., additional, Sullivan, Matthew B., additional, Edwards, Robert A., additional, Simmonds, Peter, additional, Rubino, Luisa, additional, Sabanadzovic, Sead, additional, Krupovic, Mart, additional, and Dutilh, Bas E., additional

Published
2023
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5. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, primary, Adriaenssens, Evelien M, additional, Dutilh, Bas E, additional, Koonin, Eugene V, additional, Kropinski, Andrew M, additional, Krupovic, Mart, additional, Kuhn, Jens H, additional, Lavigne, Rob, additional, Brister, J Rodney, additional, Varsani, Arvind, additional, Amid, Clara, additional, Aziz, Ramy K, additional, Bordenstein, Seth R, additional, Bork, Peer, additional, Breitbart, Mya, additional, Cochrane, Guy R, additional, Daly, Rebecca A, additional, Desnues, Christelle, additional, Duhaime, Melissa B, additional, Emerson, Joanne B, additional, Enault, François, additional, Fuhrman, Jed A, additional, Hingamp, Pascal, additional, Hugenholtz, Philip, additional, Hurwitz, Bonnie L, additional, Ivanova, Natalia N, additional, Labonté, Jessica M, additional, Lee, Kyung-Bum, additional, Malmstrom, Rex R, additional, Martinez-Garcia, Manuel, additional, Mizrachi, Ilene Karsch, additional, Ogata, Hiroyuki, additional, Páez-Espino, David, additional, Petit, Marie-Agnès, additional, Putonti, Catherine, additional, Rattei, Thomas, additional, Reyes, Alejandro, additional, Rodriguez-Valera, Francisco, additional, Rosario, Karyna, additional, Schriml, Lynn, additional, Schulz, Frederik, additional, Steward, Grieg F, additional, Sullivan, Matthew B, additional, Sunagawa, Shinichi, additional, Suttle, Curtis A, additional, Temperton, Ben, additional, Tringe, Susannah G, additional, Thurber, Rebecca Vega, additional, Webster, Nicole S, additional, Whiteson, Katrine L, additional, Wilhelm, Steven W, additional, Wommack, K Eric, additional, Woyke, Tanja, additional, Wrighton, Kelly C, additional, Yilmaz, Pelin, additional, Yoshida, Takashi, additional, Young, Mark J, additional, Yutin, Natalya, additional, Allen, Lisa Zeigler, additional, Kyrpides, Nikos C, additional, and Eloe-Fadrosh, Emiley A, additional

Published
2018
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