Search Results - Bas E. Dutilh

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  1. 1

    Beyond research: a primer for considerations on using viral metagenomics in the field and clinic by Richard J Hall, Jenny eDraper, Fiona eNielsen, Bas E. Dutilh, Bas E. Dutilh, Bas E. Dutilh

    Published in Frontiers in Microbiology (2015-03-01)
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  2. 2

    Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons by Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh, Arthur Gruber

    Published in Viruses (2023-02-01)
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  3. 3

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

    Published in Nature Communications (2024-01-01)
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  4. 4

    Evolutionary Study of the Crassphage Virus at Gene Level by Alessandro Rossi, Laura Treu, Stefano Toppo, Henrike Zschach, Stefano Campanaro, Bas E. Dutilh

    Published in Viruses (2020-09-01)
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  5. 5

    FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares by Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Bas E. Dutilh, Robert A. Edwards

    Published in PeerJ (2014-06-01)
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  6. 6

    Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain by Michael Sheinman, Ksenia Arkhipova, Peter F Arndt, Bas E Dutilh, Rutger Hermsen, Florian Massip

    Published in eLife (2021-06-01)
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  7. 7

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

    Published in Cell Reports (2024-04-01)
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  8. 8

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

    Published in Microbiome (2025-03-01)
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  9. 9

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

    Published in iScience (2024-12-01)
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  10. 10

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

    Published in Genome Biology (2024-04-01)
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  11. 11

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

    Published in PLoS ONE (2011-01-01)
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  12. 12

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

    Published in PLoS Biology (2023-04-01)
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  13. 13

    Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review by Felipe H. Coutinho, Pedro M. Meirelles, Ana Paula B. Moreira, Rodolfo P. Paranhos, Bas E. Dutilh, Fabiano L. Thompson

    Published in PeerJ (2015-06-01)
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  14. 14

    Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes by 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 (2022-08-01)
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  15. 15

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

    Published in Nature Communications (2024-11-01)
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  16. 16

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

    Published in Nature Communications (2024-07-01)
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  17. 17

    Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity by Amruta Nair, Swapnil Prakash Doijad, Mangesh Vasant Suryavanshi, Anwesha Dey, Satya Veer Singh Malik, Bas E. Dutilh, Sukhadeo Baliram Barbuddhe

    Published in Microbiology Research (2025-02-01)
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  18. 18

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

    Published in Journal of Cheminformatics (2025-05-01)
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  19. 19

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

    Published in Nature Communications (2024-04-01)
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  20. 20

    Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis by Carolien Ruesen, Lidya Chaidir, Arjan van Laarhoven, Sofiati Dian, Ahmad Rizal Ganiem, Hanna Nebenzahl-Guimaraes, Martijn A. Huynen, Bachti Alisjahbana, Bas E. Dutilh, Reinout van Crevel

    Published in BMC Genomics (2018-02-01)
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