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Predicting the evolution of complex phage-host interactions

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Publications

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

Author(s): Sean Meaden, Ambarish Biswas, Ksenia Arkhipova, Sergio E.Morales, Bas E.Dutilh, Edze R.Westra, Peter C.Fineran
Published in: Current Biology, Volume 32, Issue 1, 2022, Page(s) 220-227.e5, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2021.10.038

Prophages are associated with extensive CRISPR–Cas auto-immunity

Author(s): Franklin L. Nobrega, Hielke Walinga, Bas E. Dutilh, Stan J. J. Brouns
Published in: Nucleic Acids Research, Volume 48, Issue 21, 2020, Page(s) 12074–12084, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1071

Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes

Author(s): Daniel R. Garza; F. A. Bastiaan von Meijenfeldt; Bram van Dijk; Annemarie Boleij; Martijn A. Huynen; Bas E. Dutilh
Published in: BMC Ecology and Evolution, 22, 2022, ISSN 2730-7182
Publisher: BioMed Central, part of Springer Nature
DOI: 10.1186/s12862-022-02052-3

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Author(s): Daan M. van Vliet, F. A. Bastiaan von Meijenfeldt, Bas E. Dutilh, Laura Villanueva, Jaap S. Sinninghe Damsté, Alfons J.M. Stams, Irene Sánchez-Andrea
Published in: Environmental Microbiology, Volume 203, Issue 6, 2020, Page(s) 2834-2857, ISSN 1462-2920
Publisher: Society for Applied Microbiology and John Wiley & Sons Ltd
DOI: 10.1111/1462-2920.15265

Finding functional associations between prokaryotic virus orthologous groups: a proof of concept

Author(s): Nikolaos Pappas; Bas E. Dutilh
Published in: BMC Bioinformatics, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04343-w

Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain.

Author(s): Sheinman, Michael; Arkhipova, Ksenia; Arndt, Peter F.; Dutilh, Bas E.; Hermsen, Rutger; Massip, Florian; Theoretical Biology and Bioinformatics; Sub Theoretical Biology; Sub Bioinformatics
Published in: eLife, 1, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.62719

Perspective on taxonomic classification of uncultivated viruses.

Author(s): Bas E. Dutilh; Arvind Varsani; Arvind Varsani; Yigang Tong; Peter Simmonds; Sead Sabanadzovic; Luisa Rubino; Simon Roux; Alejandro Reyes Muñoz; Cédric Lood; Elliot J. Lefkowitz; Jens H. Kuhn; Mart Krupovic; Robert Edwards; J. Rodney Brister; Evelien M. Adriaenssens; Matthew B. Sullivan
Published in: Current Opinion in Virology, 2021, ISSN 1879-6257
Publisher: Elsevier BV
DOI: 10.1016/j.coviro.2021.10.011

Production of inactivated gram-positive and gram-negative species with preserved cellular morphology and integrity

Author(s): Rahwa Taddese, Clara Belzer, Steven Aalvink, Marien I. de Jonge, Iris D. Nagtegaal, Bas E. Dutilh, Annemarie Boleij
Published in: Journal of Microbiological Methods, Volume 184, 2021, ISSN 0167-7012
Publisher: Elsevier BV
DOI: 10.1016/j.mimet.2021.106208

RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content

Author(s): Felipe Hernandes Coutinho, Asier Zaragoza-Solas, Mario López-Pérez, Jakub Barylski, Andrzej Zielezinski, Bas E. Dutilh, Robert Edwards, Francisco Rodriguez-Valera
Published in: Patterns, Volume 2, Issue 7, 2021, ISSN 2666-3899
Publisher: Cell Press Elsevier Inc.
DOI: 10.1016/j.patter.2021.100274

Development of Styrene Maleic Acid Lipid Particles as a Tool for Studies of Phage-Host Interactions

Author(s): Patrick A. de Jonge, Dieuwke J. C. Smit Sibinga, Oliver A. Boright, Ana Rita Costa, Franklin L. Nobrega, Stan J. J. Brouns, Bas E. Dutilh
Published in: Journal of Virology, Vol. 94, No. 23, 2020, ISSN 1098-5514
Publisher: American Society for Microbiology
DOI: 10.1128/jvi.01559-20

Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021

Author(s): Krupovic, Mart; Turner, Dann; Morozova, Vera; Dyall-Smith, Mike; Oksanen, Hanna M.; Edwards, Rob; Dutilh, Bas E.; Lehman, Susan M.; Reyes, Alejandro; Baquero, Diana P.; Sullivan, Matthew B.; Uchiyama, Jumpei; Nakavuma, Jesca; Barylski, Jakub; Young, Mark J.; Du, Shishen; Alfenas-Zerbini, Poliane; Kushkina, Alla; Kropinski, Andrew M.; Kurtboke, Ipek; Brister, J. Rodney; Lood, Cedric; Sarkar, B. L.;
Published in: Archives of Virology, 166, 2021, Page(s) 3239–3244, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-021-05205-9

Lifestyle of sponge symbiont phages by host prediction and correlative microscopy

Author(s): M. T. Jahn, T. Lachnit, S. M. Markert, C. Stigloher, L. Pita, M. Ribes, B. E. Dutilh, U. Hentschel
Published in: The ISME Journal, 15, 2021, Page(s) 2001 - 2011, ISSN 1751-7370
Publisher: International Society for Microbial Ecology
DOI: 10.1038/s41396-021-00900-6

Differentiating between viruses and virus species by writing their names correctly

Author(s): Francisco Murilo Zerbini, Stuart G. Siddell, Arcady R. Mushegian, Peter J. Walker, Elliot J. Lefkowitz, Evelien M. Adriaenssens, Poliane Alfenas‑Zerbini, Bas E. Dutilh, María Laura García, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Małgorzata Łobocka, Hanna M. Oksanen, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorsla
Published in: Archives of Virology, 167, 2022, Page(s) 1231–1234, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-021-05323-4

Novel high-resolution targeted sequencing of the cervicovaginal microbiome

Author(s): Karolina M. Andralojc; Mariano A. Molina; Mengjie Qiu; Bram Spruijtenburg; Menno Rasing; Bernard Pater; Martijn A. Huynen; Bas E. Dutilh; Thomas H. A. Ederveen; Duaa Elmelik; Albert G. Siebers; Diede Loopik; Ruud L. M. Bekkers; William P. J. Leenders; Willem J. G. Melchers
Published in: BMC Biology, 2021, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-021-01204-z

Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts

Author(s): Patrick A.de Jonge, F. A. Bastiaan von Meijenfeldt, Ana Rita Costa, Franklin L. Nobrega, Stan J. J. Brouns, Bas E. Dutilh
Published in: iScience, Volume 23, Issue 9, 2021, ISSN 2589-0042
Publisher: Cell Press Elsevier Inc.
DOI: 10.1016/j.isci.2020.101439

Quantifying the Impact of Human Leukocyte Antigen on the Human Gut Microbiota

Author(s): Stijn P. Andeweg, Can Keşmir, Bas E. Dutilh
Published in: mSphere, Volume 6, Issue 4, 2021, ISSN 2379-5042
Publisher: American Society for Microbiology
DOI: 10.1128/msphere.00476-21

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

Author(s): 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;
Published in: Archives of Virology, 2021, ISSN 0304-8608
Publisher: Springer Verlag
DOI: 10.1007/s00705-020-04752-x

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

Author(s): Peter J. Walker; Stuart G. Siddell; Elliot J. Lefkowitz; Arcady R. Mushegian; Evelien M. Adriaenssens; Poliane Alfenas-Zerbini; Donald M. Dempsey; Bas E. Dutilh; María Laura García; R. Curtis Hendrickson; Sandra Junglen; Mart Krupovic; Jens H. Kuhn; Amy J. Lambert; Małgorzata Łobocka; Hanna M. Oksanen; Richard J. Orton; David L. Robertson; Luisa Rubino; Sead Sabanadzovic; Peter Simmonds; Donal
Published in: Archives of Virology, 167, 2022, ISSN 1432-8798
Publisher: Springer Nature
DOI: 10.1007/s00705-022-05516-5