Computational approaches to predict bacteriophage–host relationships
Edwards, Robert A., McNair, Katelyn, Faust, Karoline, Raes, Jeroen, Dutilh, Bas E.
Published in FEMS microbiology reviews (01.03.2016)
Published in FEMS microbiology reviews (01.03.2016)
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Book Review
Eleven grand challenges in single-cell data science
Lähnemann, David, Köster, Johannes, Szczurek, Ewa, McCarthy, Davis J, Hicks, Stephanie C, Robinson, Mark D, Vallejos, Catalina A, Campbell, Kieran R, Beerenwinkel, Niko, Mahfouz, Ahmed, Pinello, Luca, Skums, Pavel, Stamatakis, Alexandros, Attolini, Camille Stephan-Otto, Aparicio, Samuel, Baaijens, Jasmijn, Balvert, Marleen, Barbanson, Buys de, Cappuccio, Antonio, Corleone, Giacomo, Dutilh, Bas E, Florescu, Maria, Guryev, Victor, Holmer, Rens, Jahn, Katharina, Lobo, Thamar Jessurun, Keizer, Emma M, Khatri, Indu, Kielbasa, Szymon M, Korbel, Jan O, Kozlov, Alexey M, Kuo, Tzu-Hao, Lelieveldt, Boudewijn P F, Mandoiu, Ion I, Marioni, John C, Marschall, Tobias, Mölder, Felix, Niknejad, Amir, Rączkowska, Alicja, Reinders, Marcel, Ridder, Jeroen de, Saliba, Antoine-Emmanuel, Somarakis, Antonios, Stegle, Oliver, Theis, Fabian J, Yang, Huan, Zelikovsky, Alex, McHardy, Alice C, Raphael, Benjamin J, Shah, Sohrab P, Schönhuth, Alexander
Published in Genome Biology (07.02.2020)
Published in Genome Biology (07.02.2020)
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Journal Article
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
Roux, Simon, Camargo, Antonio Pedro, Coutinho, Felipe H, Dabdoub, Shareef M, Dutilh, Bas E, Nayfach, Stephen, Tritt, Andrew
Published in PLoS biology (21.04.2023)
Published in PLoS biology (21.04.2023)
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Journal Article
Targeting mechanisms of tailed bacteriophages
Nobrega, Franklin L., Vlot, Marnix, de Jonge, Patrick A., Dreesens, Lisa L., Beaumont, Hubertus J. E., Lavigne, Rob, Dutilh, Bas E., Brouns, Stan J. J.
Published in Nature reviews. Microbiology (01.12.2018)
Published in Nature reviews. Microbiology (01.12.2018)
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Journal Article
Towards the human colorectal cancer microbiome
Marchesi, Julian R, Dutilh, Bas E, Hall, Neil, Peters, Wilbert H M, Roelofs, Rian, Boleij, Annemarie, Tjalsma, Harold
Published in PloS one (24.05.2011)
Published in PloS one (24.05.2011)
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Journal Article
Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)
Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Davison, Andrew J., Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Harrach, Balázs, Harrison, Robert L., Hendrickson, R. Curtis, Junglen, Sandra, Knowles, Nick J., Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Nibert, Max L., Oksanen, Hanna M., Orton, Richard J., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Dooerslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, Francisco Murilo
Published in Archives of virology (01.09.2021)
Published in Archives of virology (01.09.2021)
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Journal Article
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
Silva, Genivaldo Gueiros Z, Green, Kevin T, Dutilh, Bas E, Edwards, Robert A
Published in Bioinformatics (01.02.2016)
Published in Bioinformatics (01.02.2016)
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Journal Article
Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee
Turner, Dann, Shkoporov, Andrey N., Lood, Cédric, Millard, Andrew D., Dutilh, Bas E., Alfenas-Zerbini, Poliane, van Zyl, Leonardo J., Aziz, Ramy K., Oksanen, Hanna M., Poranen, Minna M., Kropinski, Andrew M., Barylski, Jakub, Brister, J Rodney, Chanisvili, Nina, Edwards, Rob A., Enault, François, Gillis, Annika, Knezevic, Petar, Krupovic, Mart, Kurtböke, Ipek, Kushkina, Alla, Lavigne, Rob, Lehman, Susan, Lobocka, Malgorzata, Moraru, Cristina, Moreno Switt, Andrea, Morozova, Vera, Nakavuma, Jesca, Reyes Muñoz, Alejandro, Rūmnieks, Jānis, Sarkar, BL, Sullivan, Matthew B., Uchiyama, Jumpei, Wittmann, Johannes, Yigang, Tong, Adriaenssens, Evelien M.
Published in Archives of virology (01.02.2023)
Published in Archives of virology (01.02.2023)
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Journal Article
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
Roux, Simon, Brum, Jennifer R., Dutilh, Bas E., Sunagawa, Shinichi, Duhaime, Melissa B., Loy, Alexander, Poulos, Bonnie T., Solonenko, Natalie, Lara, Elena, Poulain, Julie, Pesant, Stéphane, Kandels-Lewis, Stefanie, Dimier, Céline, Picheral, Marc, Searson, Sarah, Cruaud, Corinne, Alberti, Adriana, Duarte, Carlos M., Gasol, Josep M., Vaqué, Dolors, Bork, Peer, Acinas, Silvia G., Wincker, Patrick, Sullivan, Matthew B.
Published in Nature (London) (29.09.2016)
Published in Nature (London) (29.09.2016)
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Journal Article
Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022)
Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dempsey, Donald M., Dutilh, Bas E., García, María Laura, Curtis Hendrickson, R., Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Łobocka, Małgorzata, Oksanen, Hanna M., Orton, Richard J., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, Francisco Murilo
Published in Archives of virology (01.11.2022)
Published in Archives of virology (01.11.2022)
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Journal Article
Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)
Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Adriaenssens, Evelien M., Dempsey, Donald M., Dutilh, Bas E., Harrach, Balázs, Harrison, Robert L., Hendrickson, R. Curtis, Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max, Orton, Richard J., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Smith, Donald B., Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J.
Published in Archives of virology (01.11.2020)
Published in Archives of virology (01.11.2020)
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Journal Article
Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)
Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Dempsey, Donald M., Dutilh, Bas E., Harrach, Balázs, Harrison, Robert L., Hendrickson, R. Curtis, Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J.
Published in Archives of virology (01.09.2019)
Published in Archives of virology (01.09.2019)
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Journal Article
Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
Coutinho, Felipe H., Silveira, Cynthia B., Gregoracci, Gustavo B., Thompson, Cristiane C., Edwards, Robert A., Brussaard, Corina P. D., Dutilh, Bas E., Thompson, Fabiano L.
Published in Nature communications (05.07.2017)
Published in Nature communications (05.07.2017)
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Journal Article
Nitrite-driven anaerobic methane oxidation by oxygenic bacteria
Ettwig, Katharina F, Strous, Marc, Butler, Margaret K, Le Paslier, Denis, Pelletier, Eric, Mangenot, Sophie, Kuypers, Marcel M. M, Schreiber, Frank, Dutilh, Bas E, Zedelius, Johannes, de Beer, Dirk, Gloerich, Jolein, Wessels, Hans J. C. T, van Alen, Theo, Luesken, Francisca, Wu, Ming L, van de Pas-Schoonen, Katinka T, Op den Camp, Huub J. M, Janssen-Megens, Eva M, Francoijs, Kees-Jan, Stunnenberg, Henk, Weissenbach, Jean, Jetten, Mike S. M
Published in Nature (London) (25.03.2010)
Published in Nature (London) (25.03.2010)
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Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)
King, Andrew M. Q., Lefkowitz, Elliot J., Mushegian, Arcady R., Adams, Michael J., Dutilh, Bas E., Gorbalenya, Alexander E., Harrach, Balázs, Harrison, Robert L., Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max L., Rubino, Luisa, Sabanadzovic, Sead, Sanfaçon, Hélène, Siddell, Stuart G., Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, Davison, Andrew J.
Published in Archives of virology (01.09.2018)
Published in Archives of virology (01.09.2018)
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Journal Article
The human gut microbiome and health inequities
Amato, Katherine R., Arrieta, Marie-Claire, Azad, Meghan B., Bailey, Michael T., Broussard, Josiane L., Bruggeling, Carlijn E., Claud, Erika C., Costello, Elizabeth K., Davenport, Emily R., Dutilh, Bas E., Ewald, Holly A. Swain, Ewald, Paul, Hanlon, Erin C., Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F., Miller, Gregory E., Preidis, Geoffrey A., Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, Kuzawa, Christopher W.
Published in Proceedings of the National Academy of Sciences - PNAS (22.06.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (22.06.2021)
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