All Stories

  1. Metagenomics in Virology

    Article • January 2019, Elsevier

    Prof. Dr. Bas E. Dutilh

  2. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

    Article • Archives of Virology, May 2018, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Jens H. Kuhn

  3. Towards predicting the environmental metabolome from metagenomics with a mechanistic model

    Article • Nature Microbiology, March 2018, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  4. Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

    Article • Frontiers in Cellular and Infection Microbiology, February 2018, Frontiers

    Prof. Dr. Bas E. Dutilh, Prof dr. John W Rossen

  5. Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis

    Article • BMC Genomics, February 2018, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  6. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

    Article • Archives of Virology, January 2018, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Hanna M Oksanen, Dr Robert A Edwards, Dr Jens H. Kuhn

  7. Phage Genome Annotation Using the RAST Pipeline

    Article • November 2017, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  8. Ecogenomics and Taxonomy of Cyanobacteria Phylum

    Article • Frontiers in Microbiology, November 2017, Frontiers

    Prof. Dr. Bas E. Dutilh

  9. Temporal dynamics of uncultured viruses: a new dimension in viral diversity

    Article • The ISME Journal, October 2017, Nature

    Prof. Dr. Bas E. Dutilh

  10. Editorial: Virus Discovery by Metagenomics: The (Im)possibilities

    Article • Frontiers in Microbiology, September 2017, Frontiers

    Prof. Dr. Bas E. Dutilh, Professor Alejandro Reyes

  11. Induction of differentiation and metabolic reprogramming in human hepatoma cells by adult human serum

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Prof. Dr. Bas E. Dutilh

  12. Preservation of bacterial DNA in 10-year-old guaiac FOBT cards and FIT tubes

    Article • Journal of Clinical Pathology, August 2017, BMJ

    Prof. Dr. Bas E. Dutilh

  13. Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

    Article • Nature Communications, July 2017, Nature

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  14. Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses

    Article • Viruses, June 2017, MDPI AG

    Prof. Dr. Bas E. Dutilh

  15. Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses

    Article • Frontiers in Microbiology, March 2017, Frontiers

    Prof. Dr. Bas E. Dutilh

  16. Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

    Article • Microbial Ecology, January 2017, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Ilias Lagkouvardos

  17. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee

    Article • Archives of Virology, December 2016, Springer Science + Business Media

    Dr Robert A Edwards, Prof. Dr. Bas E. Dutilh, Dr Hanna M Oksanen, Dr Jens H. Kuhn

  18. Computational pan-genomics: status, promises and challenges

    Article • Briefings in Bioinformatics, October 2016, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh

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

    Article • Nature, September 2016, Nature

    Prof. Dr. Bas E. Dutilh

  20. Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

    Article • May 2016, Cold Spring Harbor Laboratory Press

    Prof. Dr. Bas E. Dutilh

  21. Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

    Article • Nature Communications, March 2016, Nature

    Prof. Dr. Bas E. Dutilh

  22. FOCUS2: agile and sensitive classification of metagenomics data using a reduced database

    Article • March 2016, Cold Spring Harbor Laboratory Press

    Prof. Dr. Bas E. Dutilh

  23. Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon

    Article • Frontiers in Microbiology, January 2016, Frontiers

    Prof. Dr. Bas E. Dutilh, Prof. Dr. Koen Venema

  24. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

    Article • Archives of Virology, January 2016, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards, Dr Jens H. Kuhn

  25. Computational approaches to predict bacteriophage–host relationships

    Article • FEMS Microbiology Reviews, December 2015, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  26. Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

    Article • PLoS Medicine, November 2015, PLOS

    Prof. Dr. Bas E. Dutilh

  27. Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm

    Article • Environmental Microbiology, October 2015, Wiley

    Prof. Dr. Bas E. Dutilh

  28. SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

    Article • Bioinformatics, October 2015, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  29. Sequence specificity between interacting and non-interacting homologs identifies interface residues – a homodimer and monomer use case

    Article • BMC Bioinformatics, October 2015, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  30. From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

    Article • Cellular and Molecular Life Sciences, August 2015, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  31. Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next-generation sequencing

    Article • Histopathology, June 2015, Wiley

    Prof. Dr. Bas E. Dutilh

  32. Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review

    Article • PeerJ, June 2015, PeerJ

    Prof. Dr. Bas E. Dutilh

  33. Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum

    Article • PLoS ONE, June 2015, PLOS

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  34. Copper tolerance and distribution of epibiotic bacteria associated with giant kelp Macrocystis pyrifera in southern California

    Article • Ecotoxicology, April 2015, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  35. Beyond research: a primer for considerations on using viral metagenomics in the field and clinic

    Article • Frontiers in Microbiology, March 2015, Frontiers

    Prof. Dr. Bas E. Dutilh

  36. Draft Genome Sequence of Anammox Bacterium “Candidatus Scalindua brodae,” Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments

    Article • Genome Announcements, January 2015, ASM Journals

    Prof. Dr. Bas E. Dutilh, Dr. Huub JM Op den Camp, Professor Mike Jetten

  37. Colorectal Cancer-Associated Microbiota

    Article • January 2015, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  38. Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

    Article • Archives of Microbiology, December 2014, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Professor Martin Polz, Dr Robert A Edwards

  39. Metagenomic ventures into outer sequence space

    Article • Bacteriophage, December 2014, Taylor & Francis

    Prof. Dr. Bas E. Dutilh

  40. Microbial community diversity and physical–chemical features of the Southwestern Atlantic Ocean

    Article • Archives of Microbiology, September 2014, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  41. Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

    Article • PeerJ, August 2014, PeerJ

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  42. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

    Article • Nature Communications, July 2014, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  43. Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics

    Article • OMICS A Journal of Integrative Biology, July 2014, Mary Ann Liebert Inc

    Prof. Dr. Bas E. Dutilh

  44. Cell Wall Modifications during Conidial Maturation of the Human Pathogenic Fungus Pseudallescheria boydii

    Article • PLoS ONE, June 2014, PLOS

    Prof. Dr. Bas E. Dutilh

  45. FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

    Article • PeerJ, June 2014, PeerJ

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  46. Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

    Article • BMC Genomics, January 2014, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards, Iruka Okeke

  47. Faculty of 1000 evaluation for Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes.

    Article • August 2013, Faculty of 1000, Ltd.

    Prof. Dr. Bas E. Dutilh

  48. Explaining microbial phenotypes on a genomic scale: GWAS for microbes

    Article • Briefings in Functional Genomics, April 2013, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  49. Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness

    Article • PLoS ONE, March 2013, PLOS

    Prof. Dr. Bas E. Dutilh

  50. Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer

    Article • Best Practice & Research Clinical Gastroenterology, February 2013, Elsevier

    Prof. Dr. Bas E. Dutilh

  51. Combining de novo and reference-guided assembly with scaffold_builder

    Article • Source Code for Biology and Medicine, January 2013, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  52. Colorectal Cancer-Associated Microbiota

    Article • January 2013, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  53. Discovery of a hapE Mutation That Causes Azole Resistance in Aspergillus fumigatus through Whole Genome Sequencing and Sexual Crossing

    Article • PLoS ONE, November 2012, PLOS

    Prof. Dr. Bas E. Dutilh

  54. Reference-independent comparative metagenomics using cross-assembly: crAss

    Article • Bioinformatics, October 2012, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  55. Oxygen minimum zones harbour novel viral communities with low diversity

    Article • Environmental Microbiology, October 2012, Wiley

    Prof. Dr. Bas E. Dutilh

  56. Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

    Article • PLoS ONE, July 2012, PLOS

    Prof. Dr. Bas E. Dutilh, Dr. Gisele Lôbo Hajdu, Dr Robert A Edwards

  57. A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects

    Article • Nature Reviews Microbiology, June 2012, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  58. Bacterial Responses to a Simulated Colon Tumor Microenvironment

    Article • Molecular & Cellular Proteomics, June 2012, American Society for Biochemistry & Molecular Biology (ASBMB)

    Prof. Dr. Bas E. Dutilh

  59. Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic

    Article • PLoS ONE, May 2012, PLOS

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  60. Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9

    Article • Journal of Bacteriology, May 2012, ASM Journals

    Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  61. The metagenome of the marine anammox bacterium ‘CandidatusScalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium

    Article • Environmental Microbiology, May 2012, Wiley

    Prof. Dr. Bas E. Dutilh, Dr. Huub JM Op den Camp, Professor Mike Jetten, Dr Susannah Green Tringe

  62. Metagenomics and future perspectives in virus discovery

    Article • Current Opinion in Virology, February 2012, Elsevier

    Prof. Dr. Bas E. Dutilh

  63. Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.)

    Article • AMB Express, November 2011, Springer Science + Business Media

    Dr Peter H.M. Klaren, Prof. Dr. Bas E. Dutilh, Dr. Huub JM Op den Camp, Professor Mike Jetten

  64. Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia

    Article • Journal of Bacteriology, September 2011, ASM Journals

    Dr Michel Abanto Marin, Prof. Dr. Bas E. Dutilh, Dr Robert A Edwards

  65. Faculty of 1000 evaluation for A global network of coexisting microbes from environmental and whole-genome sequence data.

    Article • August 2011, Faculty of 1000, Ltd.

    Prof. Dr. Bas E. Dutilh

  66. FACIL: Fast and Accurate Genetic Code Inference and Logo

    Article • Bioinformatics, June 2011, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh, Dr. Huub JM Op den Camp

  67. Towards the Human Colorectal Cancer Microbiome

    Article • PLoS ONE, May 2011, PLOS

    Prof. Dr. Bas E. Dutilh

  68. Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog

    Article • Environmental Microbiology Reports, May 2011, Wiley

    Prof. Dr. Bas E. Dutilh, Dr. Huub JM Op den Camp, Professor Mike Jetten

  69. Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly

    Article • May 2011, Wiley

    Prof. Dr. Bas E. Dutilh

  70. Mass Spectrometry Analysis of Hepcidin Peptides in Experimental Mouse Models

    Article • PLoS ONE, March 2011, PLOS

    Prof. Dr. Bas E. Dutilh

  71. The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis

    Article • Molecular Biology and Evolution, March 2011, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh

  72. Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation

    Article • Journal of Endocrinology, February 2011, Bioscientifica

    Prof. Dr. Bas E. Dutilh, Prof James C Neil

  73. Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus

    Article • PLoS Genetics, August 2010, PLOS

    Prof. Dr. Bas E. Dutilh

  74. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

    Article • Nature, March 2010, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh, Dr. Huub JM Op den Camp, Professor Mike Jetten

  75. Faculty of 1000 evaluation for Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence.

    Article • January 2010, Faculty of 1000, Ltd.

    Prof. Dr. Bas E. Dutilh

  76. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

    Article • Bioinformatics, June 2009, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh

  77. Faculty of 1000 evaluation for Presence of a latent mitochondrial targeting signal in gene on mitochondrial genome.

    Article • April 2009, Faculty of 1000, Ltd.

    Prof. Dr. Bas E. Dutilh

  78. The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus

    Article • BMC Genomics, January 2009, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  79. Asymmetric relationships between proteins shape genome evolution

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  80. Faculty of 1000 evaluation for Gene-boosted assembly of a novel bacterial genome from very short reads.

    Article • November 2008, Faculty of 1000, Ltd.

    Prof. Dr. Bas E. Dutilh

  81. Signature, a web server for taxonomic characterization of sequence samples using signature genes

    Article • Nucleic Acids Research, May 2008, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh

  82. Conservation of divergent transcription in fungi

    Article • Trends in Genetics, May 2008, Elsevier

    Prof. Dr. Bas E. Dutilh

  83. Signature Genes as a Phylogenomic Tool

    Article • Molecular Biology and Evolution, April 2008, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh

  84. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution

    Article • Journal of The Royal Society Interface, February 2008, Royal Society Publishing

    Prof. Dr. Bas E. Dutilh

  85. Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

    Article • BMC Genomics, January 2008, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  86. Assessment of phylogenomic and orthology approaches for phylogenetic inference

    Article • Bioinformatics, January 2007, Oxford University Press (OUP)

    Prof. Dr. Bas E. Dutilh

  87. Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate

    Article • BMC Genomics, January 2007, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  88. Deciphering the evolution and metabolism of an anammox bacterium from a community genome

    Article • April 2006, Nature

    Prof. Dr. Bas E. Dutilh, Dr. Huub JM Op den Camp, Professor Mike Jetten, Prof. Dr. Dr. h.c. Michael Wagner

  89. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

    Article • BMC Genomics, February 2006, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  90. A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation

    Article • BMC Genomics, January 2006, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  91. GENOME TREES AND THE NATURE OF GENOME EVOLUTION

    Article • Annual Review of Microbiology, October 2005, Annual Reviews

    Prof. Dr. Bas E. Dutilh

  92. The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise

    Article • Journal of Molecular Evolution, May 2004, Springer Science + Business Media

    Prof. Dr. Bas E. Dutilh

  93. Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells

    Article • Journal of Theoretical Biology, October 2003, Elsevier

    Prof. Dr. Bas E. Dutilh, Professor Rob J de Boer