iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria von Roux, Simon, Camargo, Antonio Pedro, Coutinho, Felipe H, Dabdoub, Shareef M, Dutilh, Bas E, Nayfach, Stephen, Tritt, Andrew

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Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT von von Meijenfeldt, F A Bastiaan, Arkhipova, Ksenia, Cambuy, Diego D, Coutinho, Felipe H, Dutilh, Bas E

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Computational approaches to predict bacteriophage–host relationships von Edwards, Robert A., McNair, Katelyn, Faust, Karoline, Raes, Jeroen, Dutilh, Bas E.

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Towards the human colorectal cancer microbiome von Marchesi, Julian R, Dutilh, Bas E, Hall, Neil, Peters, Wilbert H M, Roelofs, Rian, Boleij, Annemarie, Tjalsma, Harold

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A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects von Tjalsma, Harold, Boleij, Annemarie, Marchesi, Julian R., Dutilh, Bas E.

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Targeting mechanisms of tailed bacteriophages von 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.

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Eleven grand challenges in single-cell data science von 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

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Natural supramolecular protein assemblies von Pieters, Bas J. G. E, van Eldijk, Mark B, Nolte, Roeland J. M, Mecinovi, Jasmin

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Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system von Speth, Daan R., in ’t Zandt, Michiel H., Guerrero-Cruz, Simon, Dutilh, Bas E., Jetten, Mike S. M.

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The human gut microbiome and health inequities von 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.

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From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems von Garza, Daniel R., Dutilh, Bas E.

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Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021) von 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

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Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee von 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.

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SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data von Silva, Genivaldo Gueiros Z, Green, Kevin T, Dutilh, Bas E, Edwards, Robert A

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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses von 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.

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Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022) von 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

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Metagenomics and future perspectives in virus discovery von Mokili, John L, Rohwer, Forest, Dutilh, Bas E

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Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020) von 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.

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Finding functional associations between prokaryotic virus orthologous groups: a proof of concept von Pappas, Nikolaos, Dutilh, Bas E

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Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019) von 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.

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