Predicting the evolution of complex phage-host interactions

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

A social niche breadth score reveals niche range strategies of generalists and specialists

Autores: F.A. Bastiaan von Meijenfeldt, Paulien Hogeweg, and Bas E. Dutilh
Publicado en: Nature Ecology & Evolution, Edición 7, 2023, Página(s) 768–781, ISSN 2397-334X
Editor: Springer Nature
DOI: 10.1038/s41559-023-02027-7

Stability of the human gut virome and effect of gluten-free diet

Autores: Sanzhima Garmaeva, Anastasia Gulyaeva, Trishla Sinha, Andrey N. Shkoporov, Adam G. Clooney, Stephen R. Stockdale, Johanne E. Spreckels, Thomas D. S. Sutton, Lorraine A. Draper, Bas E. Dutilh, Cisca Wijmenga, Alexander Kurilshikov, Jingyuan Fu, Colin Hill, Alexandra Zhernakova
Publicado en: Cell Reports, Edición Volume 35, Edición 7, 2021, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2021.109132

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)

Autores: Francisco Murilo Zerbini, 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, David L. Robertson, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Donald B. Sm
Publicado en: Archives of Virology, Edición 168, 2023, ISSN 0304-8608
Editor: Springer Verlag
DOI: 10.1007/s00705-023-05797-4

Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage

Autores: Patrick A. de Jonge, Bert-Jan H. van den Born, Aeilko H. Zwinderman, Max Nieuwdorp, Bas E. Dutilh, Hilde Herrema
Publicado en: Nature Communications, Edición 15, 2024, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-024-50777-0

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

Autores: Sean Meaden, Ambarish Biswas, Ksenia Arkhipova, Sergio E.Morales, Bas E.Dutilh, Edze R.Westra, Peter C.Fineran
Publicado en: Current Biology, Edición Volume 32, Edición 1, 2022, Página(s) 220-227.e5, ISSN 0960-9822
Editor: Cell Press
DOI: 10.1016/j.cub.2021.10.038

A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology

Autores: Selma L. van Esveld, Lisette Meerstein-Kessel, Cas Boshoven, Jochem F. Baaij, Konstantin Barylyuk, Jordy P. M. Coolen, Joeri van Strien, Ronald A. J. Duim, Bas E. Dutilh, Daniel R. Garza, Marijn Letterie, Nicholas I. Proellochs, Michelle N. de Ridder, Prashanna Balaji Venkatasubramanian, Laura E. de Vries, Ross F. Waller, Taco W. A. Kooij, Martijn A. Huynen
Publicado en: mSphere, Edición Volume 6, Edición 5, 2021, ISSN 2379-5042
Editor: American Society for Microbiology
DOI: 10.1128/msphere.00614-21

Prophages are associated with extensive CRISPR–Cas auto-immunity

Autores: Franklin L. Nobrega, Hielke Walinga, Bas E. Dutilh, Stan J. J. Brouns
Publicado en: Nucleic Acids Research, Edición Volume 48, Edición 21, 2020, Página(s) 12074–12084, ISSN 1362-4962
Editor: Oxford University Press
DOI: 10.1093/nar/gkaa1071

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

Autores: Daniel R. Garza; F. A. Bastiaan von Meijenfeldt; Bram van Dijk; Annemarie Boleij; Martijn A. Huynen; Bas E. Dutilh
Publicado en: BMC Ecology and Evolution, Edición 22, 2022, ISSN 2730-7182
Editor: BioMed Central, part of Springer Nature
DOI: 10.1186/s12862-022-02052-3

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data

Autores: Pilleriin Peets, Aristeidis Litos, Kai Dührkop, Daniel R. Garza, Justin J. J. van der Hooft, Sebastian Böcker, Bas E. Dutilh
Publicado en: Journal of Cheminformatics, Edición 17, 2025, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-025-01031-2

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

Autores: Ling-Yi Wu, Yasas Wijesekara, Gonçalo J. Piedade, Nikolaos Pappas, Corina P. D. Brussaard, Bas E. Dutilh
Publicado en: Genome Biology, Edición 25, 2024, ISSN 1474-760X
Editor: BioMed Central Ltd, Springer Nature
DOI: 10.1186/s13059-024-03236-4

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Autores: 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
Publicado en: Environmental Microbiology, Edición Volume 203, Edición 6, 2020, Página(s) 2834-2857, ISSN 1462-2920
Editor: 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

Autores: Nikolaos Pappas; Bas E. Dutilh
Publicado en: BMC Bioinformatics, 2021, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-021-04343-w

Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

Autores: Piotr Rozwalak, Jakub Barylski, Yasas Wijesekara, Bas E. Dutilh, Andrzej Zielezinski
Publicado en: Nature Communications, 2024, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2023.06.01.543182

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

Autores: Sheinman, Michael; Arkhipova, Ksenia; Arndt, Peter F.; Dutilh, Bas E.; Hermsen, Rutger; Massip, Florian; Theoretical Biology and Bioinformatics; Sub Theoretical Biology; Sub Bioinformatics
Publicado en: eLife, Edición 1, 2021, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.62719

Optimized bacterial DNA isolation method for microbiome analysis of human tissues

Autores: Carlijn E. Bruggeling, Daniel R. Garza, Soumia Achouiti, Wouter Mes, Bas E. Dutilh, Annemarie Boleij
Publicado en: MicrobiologyOpen, Edición Volume 10, Edición 3, 2021, ISSN 2045-8827
Editor: John Wiley and Sons Inc.
DOI: 10.1002/mbo3.1191

Improving Genome-Scale Metabolic Models of Incomplete Genomes with Deep Learning

Autores: Meine D. Boer, Chrats Melkonian, Haris Zafeiropoulos, Andreas F. Haas, Daniel Garza, Bas Dutilh
Publicado en: iScience, 2023, ISSN 2589-0042
Editor: Cell Press
DOI: 10.2139/ssrn.4535250

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024)

Autores: Peter Simmonds, Evelien M. Adriaenssens, Elliot J. Lefkowitz, Hanna M. Oksanen, Stuart G. Siddell, Francisco Murilo Zerbini, Poliane Alfenas-Zerbini, Frank O. Aylward, Donald M. Dempsey, Bas E. Dutilh, Juliana Freitas-Astúa, María Laura García, R. Curtis Hendrickson, Holly R. Hughes, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Małgorzata Łobocka, Arcady R. Mushegian, Judit Pe
Publicado en: Archives of Virology, Edición 169, 2024, ISSN 0304-8608
Editor: Springer Verlag
DOI: 10.1007/s00705-024-06143-y

Graphite: painting genomes using a colored de Bruijn graph

Autores: Rick Beeloo, Aldert L Zomer, Sebastian Deorowicz, Bas E Dutilh
Publicado en: NAR Genomics and Bioinformatics, Edición 6, 2024, ISSN 2631-9268
Editor: Oxford University Press
DOI: 10.1093/nargab/lqae142

Perspective on taxonomic classification of uncultivated viruses.

Autores: 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
Publicado en: Current Opinion in Virology, 2021, ISSN 1879-6257
Editor: Elsevier BV
DOI: 10.1016/j.coviro.2021.10.011

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria

Autores: Katarina Hrovat, Bas E Dutilh, Marnix H Medema, Chrats Melkonian
Publicado en: ISME Communications, Edición 4, 2024, ISSN 2730-6151
Editor: Oxford academic
DOI: 10.1093/ismeco/ycae034

Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity

Autores: Amruta Nair, Swapnil Prakash Doijad, Mangesh Vasant Suryavanshi, Anwesha Dey, Satya Veer Singh Malik, Bas E. Dutilh, Sukhadeo Baliram Barbuddhe
Publicado en: Microbiology Research, Edición 16, 2025, Página(s) 54, ISSN 2036-7481
Editor: MDPI AG
DOI: 10.3390/microbiolres16030054

Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome

Autores: Patrick A. de Jonge, Koen Wortelboer, Torsten P.M. Scheithauer, Bert-Jan H. van den Born, Aeilko H. Zwinderman, Franklin L. Nobrega, Bas E. Dutilh, Max Nieuwdorp, Hilde Herrema
Publicado en: Nature Communications, Edición 13, 2022, Página(s) 3594, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31390-5

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

Autores: Dann Turner; Andrey N. Shkoporov; Cédric Lood; Andrew D. Millard; Bas E. Dutilh; Poliane Alfenas-Zerbini; Leonardo J. van Zyl; Ramy K. Aziz; Hanna M. Oksanen; Minna M. Poranen; Andrew M. Kropinski; Jakub Barylski; J Rodney Brister; Nina Chanisvili; Rob A. Edwards; François Enault; Annika Gillis; Petar Knezevic; Mart Krupovic; Ipek Kurtböke; Alla Kushkina; Rob Lavigne; Susan Lehman; Malgorzata L
Publicado en: Archives of Virology, Edición 168/74, 2023, ISSN 1432-8798
Editor: Springer Nature
DOI: 10.1007/s00705-022-05694-2

Evolutionary Study of the Crassphage Virus at Gene Level

Autores: Alessandro Rossi, Laura Treu, Stefano Toppo, Henrike Zschach, Stefano Campanaro, Bas E. Dutilh
Publicado en: Viruses, Edición Volume 12, Edición 9, 2021, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12091035

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

Autores: Rahwa Taddese, Clara Belzer, Steven Aalvink, Marien I. de Jonge, Iris D. Nagtegaal, Bas E. Dutilh, Annemarie Boleij
Publicado en: Journal of Microbiological Methods, Edición Volume 184, 2021, ISSN 0167-7012
Editor: Elsevier BV
DOI: 10.1016/j.mimet.2021.106208

Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons

Autores: Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh, Arthur Gruber
Publicado en: Viruses, Edición 15/2/519, 2023, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15020519

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

Autores: Tatiana Demina, Heli Marttila, Igor S Pessi, Minna K Mannisto, Bas E Dutilh, Simon Roux, Jenni Hultman
Publicado en: Microbiome, 2025, ISSN 2049-2618
Editor: BioMed Central
DOI: 10.1101/2024.08.08.607240

Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids

Autores: Laura Villanueva, A. Bastiaan von Meijenfeldt, Alexander B. Westbye, Subhash Yadav, Ellen C. Hopmans, Bas E. Dutilh, Jaap S. Sinninghe Damsté
Publicado en: The ISME Journal, Edición 15, 2021, Página(s) 168 - 182, ISSN 1751-7370
Editor: International Society for Microbial Ecology
DOI: 10.1038/s41396-020-00772-2

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

Autores: Felipe Hernandes Coutinho, Asier Zaragoza-Solas, Mario López-Pérez, Jakub Barylski, Andrzej Zielezinski, Bas E. Dutilh, Robert Edwards, Francisco Rodriguez-Valera
Publicado en: Patterns, Edición Volume 2, Edición 7, 2021, ISSN 2666-3899
Editor: 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

Autores: 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
Publicado en: Journal of Virology, Edición Vol. 94, No. 23, 2020, ISSN 1098-5514
Editor: 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

Autores: 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.;
Publicado en: Archives of Virology, Edición 166, 2021, Página(s) 3239–3244, ISSN 0304-8608
Editor: Springer Verlag
DOI: 10.1007/s00705-021-05205-9

IPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

Autores: Simon Roux, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt
Publicado en: PLoS Biology, Edición 21, 2023, ISSN 1545-7885
Editor: PLoS
DOI: 10.1371/journal.pbio.3002083

Growth rate is a dominant factor predicting the rhizosphere effect

Autores: José L López, Arista Fourie, Sanne W M Poppeliers, Nikolaos Pappas, Juan J Sánchez-Gil, Ronnie de Jonge, Bas E Dutilh
Publicado en: The ISME Journal, Edición 17, 2024, Página(s) 1396-1405, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1038/s41396-023-01453-6

Lifestyle of sponge symbiont phages by host prediction and correlative microscopy

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

Differentiating between viruses and virus species by writing their names correctly

Autores: 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
Publicado en: Archives of Virology, Edición 167, 2022, Página(s) 1231–1234, ISSN 0304-8608
Editor: Springer Verlag
DOI: 10.1007/s00705-021-05323-4

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Autores: Daniel Loos, Ailton Pereira da Costa Filho, Bas E. Dutilh, Amelia E. Barber, Gianni Panagiotou
Publicado en: Cell Reports, 2024, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1101/2022.11.15.515575

A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater

Autores: Ernestina Hauptfeld, Jordi Pelkmans, Terry T. Huisman, Armin Anocic, Basten L. Snoek, F. A. Bastiaan von Meijenfeldt, Jan Gerritse, Johan van Leeuwen, Gert Leurink, Arie van Lit, Ruud van Uffelen, Margot C. Koster, Bas E. Dutilh
Publicado en: Water Research, Edición Volume 221, 2022, ISSN 1879-2448
Editor: Elsevier Inc.
DOI: 10.1016/j.watres.2022.118767

Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis

Autores: Carlijn E Bruggeling, Maarten te Groen, Daniel R Garza, Famke van Heeckeren tot Overlaer, Joyce P M Krekels, Basma-Chick Sulaiman, Davy Karel, Athreyu Rulof, Anne R Schaaphok, Daniel L A H Hornikx, Iris D Nagtegaal, Bas E Dutilh, Frank Hoentjen, Annemarie Boleij
Publicado en: Journal of Crohn's and Colitis, Edición 17, 2024, Página(s) 1870-1881, ISSN 1873-9946
Editor: Elsevier Science
DOI: 10.1093/ecco-jcc/jjad092

SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks

Autores: Abraham L van Eijnatten, Luc van Zon, Eleni Manousou, Margarita Bikineeva, E R Jasper Wubs, Wim H van der Putten, Elly Morriën, Bas E Dutilh, L Basten Snoek
Publicado en: ISME Communications, 2025, ISSN 2730-6151
Editor: Oxford University Press (OUP)
DOI: 10.1093/ismeco/ycaf036

Novel high-resolution targeted sequencing of the cervicovaginal microbiome

Autores: 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
Publicado en: BMC Biology, 2021, ISSN 1741-7007
Editor: BioMed Central
DOI: 10.1186/s12915-021-01204-z

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

Autores: Patrick A.de Jonge, F. A. Bastiaan von Meijenfeldt, Ana Rita Costa, Franklin L. Nobrega, Stan J. J. Brouns, Bas E. Dutilh
Publicado en: iScience, Edición Volume 23, Edición 9, 2021, ISSN 2589-0042
Editor: Cell Press Elsevier Inc.
DOI: 10.1016/j.isci.2020.101439

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

Autores: Evelien M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cédric Lood, Elliot J. Lefkowitz, Matthew B. Sullivan, Robert A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. Dutilh
Publicado en: Nature Biotechnology, Edición 41, 2023, Página(s) 898-902, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.1038/s41587-023-01844-2

Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype

Autores: Aldert Zomer, Colin J. Ingham, F. A. Bastiaan von Meijenfeldt, Álvaro Escobar Doncel, Gea T. van de Kerkhof, Raditijo Hamidjaja, Sanne Schouten, Lukas Schertel, Karin H. Müller, Laura Catón, Richard L. Hahnke, Henk Bolhuis, Silvia Vignolini, Bas E. Dutilh
Publicado en: Proceedings of the National Academy of Sciences, Edición 121, 2024, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2309757121

Guidance for creating individual and batch latinized binomial virus species names

Autores: Thomas S. Postler, Luisa Rubino, Evelien M. Adriaenssens, Bas E. Dutilh, Balázs Harrach, Sandra Junglen, Andrew M. Kropinski, Mart Krupovic, Jiro Wada, Anya Crane, Jens H. Kuhn, Arcady Mushegian, Jānis Rūmnieks, Sead Sabanadzovic, Peter Simmonds, Arvind Varsani, F. Murilo Zerbini, Julie Callanan, Lorraine A. Draper, Colin Hill, Stephen R. Stockdale
Publicado en: Journal of General Virology, Edición 103/12, 2022, ISSN 1465-2099
Editor: Microbiology Society
DOI: 10.1099/jgv.0.001800

Four principles to establish a universal virus taxonomy

Autores: Peter Simmonds; Evelien M. Adriaenssens; F. Murilo Zerbini; Nicola G. A. Abrescia; Pakorn Aiewsakun; Poliane Alfenas-Zerbini; Yiming Bao; Jakub Barylski; Christian Drosten; Siobain Duffy; W. Paul Duprex; Bas E. Dutilh; Santiago F. Elena; Maria Laura García; Sandra Junglen; Aris Katzourakis; Eugene V. Koonin; Mart Krupovic; Jens H. Kuhn; Amy J. Lambert; Elliot J. Lefkowitz; Małgorzata Łobocka; C
Publicado en: Plos Biology, Edición 21/2, 2023, ISSN 1545-7885
Editor: PLOS
DOI: 10.1371/journal.pbio.3001922

Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

Autores: Bram van Dijk, Pauline Buffard, Andrew D Farr, Franz Giersdorf, Jeroen Meijer, Bas E Dutilh, Paul B Rainey
Publicado en: ISME Communications, Edición 3, 2024, ISSN 2730-6151
Editor: Springer Nature
DOI: 10.1038/s43705-023-00294-w

Virus Taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Autores: Stuart G. Siddell, Donald B. Smith, Evelien Adriaenssens, Poliane Alfenas-Zerbini, Bas E. Dutilh, Maria Laura Garcia, Sandra Junglen, Mart Krupovic, Jens H. Kuhn, Amy J. Lambert, Elliot J. Lefkowitz, Małgorzata Łobocka, Arcady R. Mushegian, Hanna M. Oksanen, David L. Robertsonn, Luisa Rubino, Sead Sabanadzovic, Peter Simmonds, Nobuhiro Suzuki, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvi
Publicado en: Journal of General Virology, Edición Vol. 104, Edición 5, 2023, ISSN 1465-2099
Editor: Microbiology Society
DOI: 10.1099/jgv.0.001840

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape

Autores: Gonçalo J. Piedade, Max E. Schön, Cédric Lood, Mikhail V. Fofanov, Ella M. Wesdorp, Tristan E.G. Biggs, Lingyi Wu, Henk Bolhuis, Matthias G. Fischer, Natalya Yutin, Bas E. Dutilh, Corina P. D. Brussaard
Publicado en: Nature Communications, 2024, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.21203/rs.3.rs-3778832/v1

Integration of taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes

Autores: Ernestina Hauptfeld, Nikolaos Pappas, Sandra van Iwaarden, Basten L. Snoek, Andrea Aldas-Vargas, Bas E. Dutilh, FA Bastiaan von Meijenfeldt
Publicado en: Nature Communications, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2023.03.22.533753

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

Autores: Stijn P. Andeweg, Can Keşmir, Bas E. Dutilh
Publicado en: mSphere, Edición Volume 6, Edición 4, 2021, ISSN 2379-5042
Editor: 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).

Autores: 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;
Publicado en: Archives of Virology, 2021, ISSN 0304-8608
Editor: Springer Verlag
DOI: 10.1007/s00705-020-04752-x

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

Autores: 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
Publicado en: Archives of Virology, Edición 167, 2022, ISSN 1432-8798
Editor: Springer Nature
DOI: 10.1007/s00705-022-05516-5

Bacterial biofilms in early colon carcinogenesis: A study in Lynch syndrome and ulcerative colitis

Autores: Bruggeling, C.E.
Publicado en: Edición 1, 2023
Editor: Radboud University

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