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MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets.
Published in:
ISME Communications, 2023, v. 3, n. 1, p. 1, doi. 10.1038/s43705-023-00295-9
By:
- Vik, Dean;
- Bolduc, Benjamin;
- Roux, Simon;
- Sun, Christine L.;
- Pratama, Akbar Adjie;
- Krupovic, Mart;
- Sullivan, Matthew B.
Publication type:
Article
Cenote-Taker 2 democratizes virus discovery and sequence annotation.
Published in:
Virus Evolution, 2021, v. 7, n. 1, p. 1, doi. 10.1093/ve/veaa100
By:
- Tisza, Michael J;
- Belford, Anna K;
- Domínguez-Huerta, Guillermo;
- Bolduc, Benjamin;
- Buck, Christopher B
Publication type:
Article
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.
Published in:
Nature Biotechnology, 2019, v. 37, n. 6, p. 632, doi. 10.1038/s41587-019-0100-8
By:
- 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;
- Sullivan, Matthew B.
Publication type:
Article
Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis.
Published in:
ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 10, p. 2162, doi. 10.1038/ismej.2015.28
By:
- Bolduc, Benjamin;
- Wirth, Jennifer F;
- Mazurie, Aurélien;
- Young, Mark J
Publication type:
Article
Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs.
Published in:
Microbial Ecology, 2015, v. 70, n. 2, p. 411, doi. 10.1007/s00248-015-0576-9
By:
- Menzel, Peter;
- Gudbergsdóttir, Sóley;
- Rike, Anne;
- Lin, Lianbing;
- Zhang, Qi;
- Contursi, Patrizia;
- Moracci, Marco;
- Kristjansson, Jakob;
- Bolduc, Benjamin;
- Gavrilov, Sergey;
- Ravin, Nikolai;
- Mardanov, Andrey;
- Bonch-Osmolovskaya, Elizaveta;
- Young, Mark;
- Krogh, Anders;
- Peng, Xu
Publication type:
Article
Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.
Published in:
Microbiome, 2024, v. 12, n. 1, p. 1, doi. 10.1186/s40168-024-01876-z
By:
- Tian, Funing;
- Wainaina, James M.;
- Howard-Varona, Cristina;
- Domínguez-Huerta, Guillermo;
- Bolduc, Benjamin;
- Gazitúa, Maria Consuelo;
- Smith, Garrett;
- Gittrich, Marissa R.;
- Zablocki, Olivier;
- Cronin, Dylan R.;
- Eveillard, Damien;
- Hallam, Steven J.;
- Sullivan, Matthew B.
Publication type:
Article
MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations.
Published in:
Microbiome, 2022, v. 10, n. 1, p. 1, doi. 10.1186/s40168-022-01231-0
By:
- Gregory, Ann C.;
- Gerhardt, Kenji;
- Zhong, Zhi-Ping;
- Bolduc, Benjamin;
- Temperton, Ben;
- Konstantinidis, Konstantinos T.;
- Sullivan, Matthew B.
Publication type:
Article
MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations.
Published in:
Microbiome, 2022, v. 10, n. 1, p. 1, doi. 10.1186/s40168-022-01231-0
By:
- Gregory, Ann C.;
- Gerhardt, Kenji;
- Zhong, Zhi-Ping;
- Bolduc, Benjamin;
- Temperton, Ben;
- Konstantinidis, Konstantinos T.;
- Sullivan, Matthew B.
Publication type:
Article
Single-virus genomics reveals hidden cosmopolitan and abundant viruses.
Published in:
Nature Communications, 2017, v. 8, n. 6, p. 15892, doi. 10.1038/ncomms15892
By:
- Martinez-Hernandez, Francisco;
- Fornas, Oscar;
- Lluesma Gomez, Monica;
- Bolduc, Benjamin;
- de la Cruz Peña, Maria Jose;
- Martínez, Joaquín Martínez;
- Anton, Josefa;
- Gasol, Josep M.;
- Rosselli, Riccardo;
- Rodriguez-Valera, Francisco;
- Sullivan, Matthew B.;
- Acinas, Silvia G.;
- Martinez-Garcia, Manuel
Publication type:
Article
The Prevalence of STIV c92-Like Proteins in Acidic Thermal Environments.
Published in:
Advances in Virology, 2011, v. 2011, p. 1, doi. 10.1155/2011/650930
By:
- Snyder, Jamie C.;
- Bolduc, Benjamin;
- Bateson, Mary M.;
- Young, Mark J.
Publication type:
Article
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation.
Published in:
PeerJ, 2021, p. 1, doi. 10.7717/peerj.11447
By:
- Pratama, Akbar Adjie;
- Bolduc, Benjamin;
- Zayed, Ahmed A.;
- Zhi-Ping Zhong;
- Jiarong Guo;
- Vik, Dean R.;
- Gazitúa, Maria Consuelo;
- Wainaina, James M.;
- Roux, Simon;
- Sullivan, Matthew B.
Publication type:
Article
The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research.
Published in:
PeerJ, 2020, p. 1, doi. 10.7717/peerj.9467
By:
- Bolduc, Benjamin;
- Hodgkins, Suzanne B.;
- Varner, Ruth K.;
- Crill, Patrick M.;
- McCalley, Carmody K.;
- Chanton, Jeffrey P.;
- Tyson, Gene W.;
- Riley, William J.;
- Palace, Michael;
- Duhaime, Melissa B.;
- Hough, Moira A.;
- Saleska, Scott R.;
- Sullivan, Matthew B.;
- Rich, Virginia I.
Publication type:
Article
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils.
Published in:
PeerJ, 2019, p. 1, doi. 10.7717/peerj.7265
By:
- Trubl, Gareth;
- Roux, Simon;
- Solonenko, Natalie;
- Li, Yueh-Fen;
- Bolduc, Benjamin;
- Rodríguez-Ramos, Josué;
- Eloe-Fadrosh, Emiley A.;
- Rich, Virginia I.;
- Sullivan, Matthew B.
Publication type:
Article
Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient.
Published in:
Frontiers in Microbiology, 2020, v. 11, p. 1, doi. 10.3389/fmicb.2020.00796
By:
- Hough, Moira;
- McClure, Amelia;
- Bolduc, Benjamin;
- Dorrepaal, Ellen;
- Saleska, Scott;
- Klepac-Ceraj, Vanja;
- Rich, Virginia
Publication type:
Article
DRAM for distilling microbial metabolism to automate the curation of microbiome function.
Published in:
Nucleic Acids Research, 2020, v. 48, n. 16, p. 8883, doi. 10.1093/nar/gkaa621
By:
- Shaffer, Michael;
- Borton, Mikayla A;
- McGivern, Bridget B;
- Zayed, Ahmed A;
- La Rosa, Sabina Leanti;
- Solden, Lindsey M;
- Liu, Pengfei;
- Narrowe, Adrienne B;
- Rodríguez-Ramos, Josué;
- Bolduc, Benjamin;
- Gazitúa, M Consuelo;
- Daly, Rebecca A;
- Smith, Garrett J;
- Vik, Dean R;
- Pope, Phil B;
- Sullivan, Matthew B;
- Roux, Simon;
- Wrighton, Kelly C
Publication type:
Article
Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient.
Published in:
Environmental Microbiology, 2024, v. 26, n. 8, p. 1, doi. 10.1111/1462-2920.16665
By:
- Sun, Christine L.;
- Pratama, Akbar Adjie;
- Gazitúa, Maria Consuelo;
- Cronin, Dylan;
- McGivern, Bridget B.;
- Wainaina, James M.;
- Vik, Dean R.;
- Zayed, Ahmed A.;
- Bolduc, Benjamin;
- Wrighton, Kelly C.;
- Rich, Virginia I.;
- Sullivan, Matthew B.
Publication type:
Article

Found: 16