Publications by authors named "Bas E Dutilh"

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

PLoS Biol· April 2023

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VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses.
Shahram Saghaei, Malte Siemers, Kilian L Ossetek, Stephan Richter, Robert A Edwards, Bas E Dutilh

Nucleic Acids Res· December 2025

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Machine learning enables scalable and systematic hierarchical virus taxonomy.
Benjamin Bolduc, Olivier Zablocki, Dann Turner, Ho Bin Jang, Jiarong Guo, Bas E Dutilh

Nat Biotechnol· December 2025

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Computational function prediction of bacteria and phage proteins.
Susanna R Grigson, George Bouras, Bas E Dutilh, Robert D Olson, Robert A Edwards

Microbiol Mol Biol Rev· September 2025

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Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.
Dann Turner, Evelien M Adriaenssens, Rudolf I Amann, Pavol Bardy, Nina Bartlau, Bas E Dutilh

J Gen Virol· July 2025

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Ultrafast and accurate sequence alignment and clustering of viral genomes.
Andrzej Zielezinski, Adam Gudyś, Jakub Barylski, Krzysztof Siminski, Piotr Rozwalak, Bas E Dutilh

Nat Methods· June 2025

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Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data.
Pilleriin Peets, Aristeidis Litos, Kai Dührkop, Daniel R Garza, Justin J J van der Hooft, Bas E Dutilh

J Cheminform· May 2025

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Examining the healthy human microbiome concept.
Raphaela Joos, Katy Boucher, Aonghus Lavelle, Manimozhiyan Arumugam, Martin J Blaser, Bas E Dutilh

Nat Rev Microbiol· March 2025

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Author Correction: Examining the healthy human microbiome concept.
Raphaela Joos, Katy Boucher, Aonghus Lavelle, Manimozhiyan Arumugam, Martin J Blaser, Bas E Dutilh

Nat Rev Microbiol· March 2025

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Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.
Tatiana Demina, Heli Marttila, Igor S Pessi, Minna K Männistö, Bas E Dutilh

Microbiome· March 2025

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SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.
Abraham L van Eijnatten, Luc van Zon, Eleni Manousou, Margarita Bikineeva, E R Jasper Wubs, Bas E Dutilh

ISME Commun· January 2025

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Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development.
Yujun Zhong, Yingyue Zhang, José Luis López Arcondo, Ruoyi Xu, Mark Radosevich, Bas E Dutilh

ISME Commun· January 2025

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Improving genome-scale metabolic models of incomplete genomes with deep learning.
Meine D Boer, Chrats Melkonian, Haris Zafeiropoulos, Andreas F Haas, Daniel R Garza, Bas E Dutilh

iScience· December 2024

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Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024).
Peter Simmonds, Evelien M Adriaenssens, Elliot J Lefkowitz, Hanna M Oksanen, Stuart G Siddell, Bas E Dutilh

Arch Virol· November 2024

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Author Correction: Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage.
Patrick A de Jonge, Bert-Jan H van den Born, Aeilko H Zwinderman, Max Nieuwdorp, Bas E Dutilh

Nat Commun· November 2024

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Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape.
Gonçalo J Piedade, Max E Schön, Cédric Lood, Mikhail V Fofanov, Ella M Wesdorp, Bas E Dutilh

Nat Commun· October 2024

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Graphite: painting genomes using a colored de Bruijn graph.
Rick Beeloo, Aldert L Zomer, Sebastian Deorowicz, Bas E Dutilh

NAR Genom Bioinform· September 2024

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Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.
Aldert Zomer, Colin J Ingham, F A Bastiaan von Meijenfeldt, Álvaro Escobar Doncel, Gea T van de Kerkhof, Bas E Dutilh

Proc Natl Acad Sci U S A· July 2024

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Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage.
Patrick A de Jonge, Bert-Jan H van den Born, Aeilko H Zwinderman, Max Nieuwdorp, Bas E Dutilh

Nat Commun· July 2024

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A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.
Daniel Loos, Ailton Pereira da Costa Filho, Bas E Dutilh, Amelia E Barber, Gianni Panagiotou

Cell Rep· April 2024

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Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.
Ling-Yi Wu, Yasas Wijesekara, Gonçalo J Piedade, Nikolaos Pappas, Corina P D Brussaard, Bas E Dutilh

Genome Biol· April 2024

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Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.
Ernestina Hauptfeld, Nikolaos Pappas, Sandra van Iwaarden, Basten L Snoek, Andrea Aldas-Vargas, Bas E Dutilh

Nat Commun· April 2024

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Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces.
Piotr Rozwalak, Jakub Barylski, Yasas Wijesekara, Bas E Dutilh, Andrzej Zielezinski

Nat Commun· January 2024

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Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria.
Katarina Hrovat, Bas E Dutilh, Marnix H Medema, Chrats Melkonian

ISME Commun· January 2024

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Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023).
Francisco Murilo Zerbini, Stuart G Siddell, Elliot J Lefkowitz, Arcady R Mushegian, Evelien M Adriaenssens, Bas E Dutilh

Arch Virol· October 2023

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Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.
Bram van Dijk, Pauline Buffard, Andrew D Farr, Franz Giersdorf, Jeroen Meijer, Bas E Dutilh

ISME Commun· August 2023

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