Dr. B.E. (Bas) Dutilh
Universitair hoofddocent
Sleutelpublicaties
von Meijenfeldt, F. A. B., Hogeweg, P., & Dutilh, B. E. (2023). A social niche breadth score reveals niche range strategies of generalists and specialists. Nature Ecology & Evolution, 7(5), 768-781. [DOI] [Repository]
Garza, D. R., van Verk, M. C., Huynen, M. A., & Dutilh, B. E. (2018). Towards predicting the environmental metabolome from metagenomics with a mechanistic model. Nature Microbiology, 3(4), 456-460. [DOI] [Repository]
von Meijenfeldt, F. A. B., Arkhipova, K., Cambuy, D. D., Coutinho, F. H., & Dutilh, B. E. (2019). Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biology, 20, Article 217. [DOI] [Repository]
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., Bibby, K., Brouns, S. J. J., Cazares, A., de Jonge, P. A., Desnues, C., Díaz Muñoz, S. L., Fineran, P. C., Kurilshikov, A., Lavigne, R., ... Dutilh, B. E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nature Microbiology, 4, 1727-1736. [DOI] [Repository]
Dutilh, B. E., Cassman, N., McNair, K., Sanchez, S. E., Silva, G. G. Z., Boling, L., Barr, J. J., Speth, D. R., Seguritan, V., Aziz, R. K., Felts, B., Dinsdale, E. A., Mokili, J. L., & Edwards, R. A. (2014). A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nature Communications [E], 5, Article 4498. [DOI] [Repository]
Publicaties
2026
Wetenschappelijke publicaties
Escobar Doncel, Á., Patinios, C., Campos, A., Walter Costa, M. B., Turkina, M. V., Murace, M., Staals, R. H. J., Vignolini, S., Dutilh, B. E., & Ingham, C. J. (2026). Deletion of the
moeA gene in
Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism. eLife, 14. [DOI]
2025
Wetenschappelijke publicaties
Saghaei, S., Siemers, M., Ossetek, K. L., Richter, S., Edwards, R. A., Roux, S., Zielezinski, A., Dutilh, B. E., Marz, M., & Cassman, N. A. (2025). VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses. Nucleic Acids Research. Advance online publication. [DOI]
Bolduc, B., Zablocki, O., Turner, D., Bin Jang, H., Guo, J., Adriaenssens, E. M., Dutilh, B. E., & Sullivan, M. B. (2025). Machine learning enables scalable and systematic hierarchical virus taxonomy. Nature Biotechnology. Advance online publication. [DOI]
Zhong, Y., Zhang, Y., Luis López Arcondo, J., Xu, R., Radosevich, M., Dangl, J. L., Dutilh, B. E., & Liang, X. (2025). Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development. ISME Communications, 5(1), Article ycaf203. [DOI] [Portal]
Wang, S., López Arcondo, J. L., Xie, N., Wang, Y., Zhang, Y., Radosevich, M., Dutilh, B. E., & Liang, X. (2025). Exogenous carbon-to-nitrogen imbalance drives soil viral roles in microbial carbon mineralization and necromass accrual. Soil Biology and Biochemistry, 210, Article 109952. [DOI]
Grigson, S. R., Bouras, G., Dutilh, B. E., Olson, R. D., & Edwards, R. A. (2025). Computational function prediction of bacteria and phage proteins. Microbiology and Molecular Biology Reviews, 89(3), Article e0002225. [DOI]
van Eijnatten, A. L., van Zon, L., Manousou, E., Bikineeva, M., Wubs, E. R. J., van der Putten, W. H., Morriën, E., Dutilh, B. E., & Snoek, L. B. (2025). SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks. ISME Communications, 5(1), Article ycaf036. [DOI] [Portal]
Turner, D., Adriaenssens, E. M., Amann, R. I., Bardy, P., Bartlau, N., Barylski, J., Błażejak, S., Bouzari, M., Briegel, A., Briers, Y., Carrillo, D., Chen, X., Claessen, D., Cook, R., Crisci, M. A., Dechesne, A., Deptula, P., Dutilh, B. E., Ely, B., ... Ictv Taxonomy Summary Consortium (2025). Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025. Journal of General Virology, 106(7), Article 002111. [DOI] [Portal]
Human Microbiome Action Consortium, Joos, R., Boucher, K., Lavelle, A., Arumugam, M., Blaser, M. J., Claesson, M. J., Clarke, G., Cotter, P. D., De Sordi, L., Dominguez-Bello, M. G., Dutilh, B. E., Ehrlich, S. D., Ghosh, T. S., Hill, C., Junot, C., Lahti, L., Lawley, T. D., Licht, T. R., ... Pinto, F. (2025). Correction to: Examining the healthy human microbiome concept (Nature Reviews Microbiology, (2024), 10.1038/s41579-024-01107-0). Nature Reviews Microbiology, 23(3), Article 206. [DOI] [Portal]
Human Microbiome Action Consortium, Joos, R., Boucher, K., Lavelle, A., Arumugam, M., Blaser, M. J., Claesson, M. J., Clarke, G., Cotter, P. D., De Sordi, L., Dominguez-Bello, M. G., Dutilh, B. E., Ehrlich, S. D., Ghosh, T. S., Hill, C., Junot, C., Lahti, L., Lawley, T. D., Licht, T. R., ... Pinto, F. (2025). Examining the healthy human microbiome concept. Nature Reviews Microbiology, 23(3), 192–205. Article 103. [DOI] [Portal]
2024
Wetenschappelijke publicaties
de Jonge, P. A., van den Born, B. J. H., Zwinderman, A. H., Nieuwdorp, M., Dutilh, B. E., & Herrema, H. (2024). Erratum: Author Correction: Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage (Nature communications (2024) 15 1 DOI: 10.1038/s41467-024-50777-0). Nature Communications, 15(1), Article 9734. [DOI] [Portal]
Simmonds, P., Adriaenssens, E. M., Lefkowitz, E. J., Oksanen, H. M., Siddell, S. G., Zerbini, F. M., Alfenas-Zerbini, P., Aylward, F. O., Dempsey, D. M., Dutilh, B. E., Freitas-Astúa, J., García, M. L., Hendrickson, R. C., Hughes, H. R., Junglen, S., Krupovic, M., Kuhn, J. H., Lambert, A. J., Łobocka, M., ... Varsani, A. (2024). Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024). Archives of Virology, 169(11), Article 236. [DOI] [Portal]
Piedade, G. J., Schön, M. E., Lood, C., Fofanov, M. V., Wesdorp, E. M., Biggs, T. E. G., Wu, L., Bolhuis, H., Fischer, M. G., Yutin, N., Dutilh, B. E., & Brussaard, C. P. D. (2024). Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape. Nature Communications, 15(1), Article 9192. [DOI] [Portal]
Zomer, A., Ingham, C. J., von Meijenfeldt, F. A. B., Escobar Doncel, Á., van de Kerkhof, G. T., Hamidjaja, R., Schouten, S., Schertel, L., Müller, K. H., Catón, L., Hahnke, R. L., Bolhuis, H., Vignolini, S., & Dutilh, B. E. (2024). Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype. Proceedings of the National Academy of Sciences of the United States of America, 121(29), Article e2309757121. [DOI] [Portal]
Hauptfeld, E., Pappas, N., van Iwaarden, S., Snoek, B. L., Aldas-Vargas, A., Dutilh, B. E., & von Meijenfeldt, F. A. B. (2024). Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes. Nature Communications, 15(1), Article 3373. [DOI] [Repository]
Hrovat, K., Dutilh, BE., Medema, MH., & Melkonian, C. (2024). Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria. ISME Communications, 4(1), Article ycae034. [DOI] [Repository]
Loos, D., Filho, A. P. D. C., Dutilh, B. E., Barber, A. E., & Panagiotou, G. (2024). A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists. Cell Reports, 43(4), Article 114046. [DOI] [Repository]
Rozwalak, P., Barylski, J., Wijesekara, Y., Dutilh, B. E., & Zielezinski, A. (2024). Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces. Nature Communications, 15(1), Article 495. [DOI] [Repository]
Wu, L. Y., Wijesekara, Y., Piedade, G. J., Pappas, N., Brussaard, C. P. D., & Dutilh, B. E. (2024). Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes. Genome Biology, 25(1), Article 97. [DOI] [Repository]
2023
Wetenschappelijke publicaties
Zerbini, F. M., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Adriaenssens, E. M., Alfenas-Zerbini, P., Dempsey, D. M., Dutilh, B. E., García, M. L., Hendrickson, R. C., Junglen, S., Krupovic, M., Kuhn, J. H., Lambert, A. J., Łobocka, M., Oksanen, H. M., Robertson, D. L., Rubino, L., Sabanadzovic, S., ... Varsani, A. (2023). Erratum: Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023) (Archives of virology (2023) 168 7 (175)). Archives of Virology, 168(11), Article 269. [DOI] [Repository]
van Dijk, B., Buffard, P., Farr, A. D., Giersdorf, F., Meijer, J., Dutilh, B. E., & Rainey, P. B. (2023). Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME Communications, 3(1), 1-13. Article 90. [DOI] [Repository]
Turner, D., Shkoporov, A. N., Lood, C., Millard, A. D., Dutilh, B. E., Alfenas-Zerbini, P., van Zyl, L. J., Aziz, R. K., Oksanen, H. M., Poranen, M. M., Kropinski, A. M., Barylski, J., Brister, J. R., Chanisvili, N., Edwards, R. A., Enault, F., Gillis, A., Knezevic, P., Krupovic, M., ... Adriaenssens, E. M. (2023). Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Archives of Virology, 168(2), Article 74. [DOI] [Repository]
Oliveira, L. S., Reyes, A., Dutilh, B. E., & Gruber, A. (2023). Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons. Viruses, 15(2), Article 519. [DOI] [Repository]
Bruggeling, C. E., Te Groen, M., Garza, D. R., van Heeckeren Tot Overlaer, F., Krekels, J. P. M., Sulaiman, B.-C., Karel, D., Rulof, A., Schaaphok, A. R., Hornikx, D. L. A. H., Nagtegaal, I. D., Dutilh, B. E., Hoentjen, F., & Boleij, A. (2023). Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis. Journal of Crohn's & Colitis, 17(11), 1870-1881. [DOI] [Repository]
Zerbini, F. M., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Adriaenssens, E. M., Alfenas-Zerbini, P., Dempsey, D. M., Dutilh, B. E., García, M. L., Hendrickson, R. C., Junglen, S., Krupovic, M., Kuhn, J. H., Lambert, A. J., Łobocka, M., Oksanen, H. M., Robertson, D. L., Rubino, L., Sabanadzovic, S., ... Varsani, A. (2023). Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023). Archives of Virology, 168(7), Article 175. [DOI] [Repository]
Roux, S., Camargo, A. P., Coutinho, F. H., Dabdoub, S. M., Dutilh, B. E., Nayfach, S., & Tritt, A. (2023). iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria. PLoS Biology, 21(4), Article e3002083. [DOI] [Repository]
Adriaenssens, E. M., Roux, S., Brister, J. R., Karsch-Mizrachi, I., Kuhn, J. H., Varsani, A., Yigang, T., Reyes, A., Lood, C., Lefkowitz, E. J., Sullivan, M. B., Edwards, R. A., Simmonds, P., Rubino, L., Sabanadzovic, S., Krupovic, M., & Dutilh, B. E. (2023). Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification. Nature Biotechnology, 41(7), 898-902. [DOI] [Repository]
Adriaenssens, E. M., Roux, S., Brister, J. R., Karsch-Mizrachi, I., Kuhn, J. H., Varsani, A., Yigang, T., Reyes, A., Lood, C., Lefkowitz, E. J., Sullivan, M. B., Edwards, R. A., Simmonds, P., Rubino, L., Sabanadzovic, S., Krupovic, M., & Dutilh, B. E. (2023). Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification (Nature Biotechnology, (2023), 41, 7, (898-902), 10.1038/s41587-023-01844-2). Nature Biotechnology, 41(9), 1346. Article 1346. [DOI] [Repository]
von Meijenfeldt, F. A. B., Hogeweg, P., & Dutilh, B. E. (2023). A social niche breadth score reveals niche range strategies of generalists and specialists. Nature Ecology & Evolution, 7(5), 768-781. [DOI] [Repository]
Siddell, S. G., Smith, D. B., Adriaenssens, E., Alfenas-Zerbini, P., Dutilh, B. E., Garcia, M. L., Junglen, S., Krupovic, M., Kuhn, J. H., Lambert, A. J., Lefkowitz, E. J., Łobocka, M., Mushegian, A. R., Oksanen, H. M., Robertson, D. L., Rubino, L., Sabanadzovic, S., Simmonds, P., Suzuki, N., ... Zerbini, F. M. (2023). Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). Journal of General Virology, 104(5), Article 001840. [DOI] [Repository]
Simmonds, P., Adriaenssens, E. M., Zerbini, F. M., Abrescia, N. G. A., Aiewsakun, P., Alfenas-Zerbini, P., Bao, Y., Barylski, J., Drosten, C., Duffy, S., Duprex, W. P., Dutilh, B. E., Elena, S. F., García, M. L., Junglen, S., Katzourakis, A., Koonin, E. V., Krupovic, M., Kuhn, J. H., ... Vasilakis, N. (2023). Four principles to establish a universal virus taxonomy. PLoS Biology, 21(2), Article e3001922. [DOI] [Repository]
López, J. L., Fourie, A., Poppeliers, S. W. M., Pappas, N., Sánchez-Gil, J. J., de Jonge, R., & Dutilh, B. E. (2023). Growth rate is a dominant factor predicting the rhizosphere effect. ISME Journal, 17, 1396–1405. [DOI] [Repository]
2022
Wetenschappelijke publicaties
López, J. L., Pappas, N., Poppeliers, S. WM., Sanchez-Gil, J. J., Fourie-Fouche, A., Jonge, R. D., & Dutilh, B. E. (2022). Copiotrophs dominate rhizosphere microbiomes and growth rate potential is a major factor explaining the rhizosphere effect. (pp. 1-23). bioRxiv. [DOI] [Repository]
Zerbini, F. M., Siddell, S. G., Mushegian, A. R., Walker, P. J., Lefkowitz, E. J., Adriaenssens, E. M., Alfenas-Zerbini, P., Dutilh, B. E., García, M. L., Junglen, S., Krupovic, M., Kuhn, J. H., Lambert, A. J., Łobocka, M., Oksanen, H. M., Robertson, D. L., Rubino, L., Sabanadzovic, S., Simmonds, P., ... Varsani, A. (2022). Differentiating between viruses and virus species by writing their names correctly. Archives of Virology, 167(4), 1231-1234. [DOI] [Repository]
de Jonge, P. A., Wortelboer, K., Scheithauer, T. P. M., van den Born, B.-J. H., Zwinderman, A. H., Nobrega, F. L., Dutilh, B. E., Nieuwdorp, M., & Herrema, H. (2022). Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome. Nature Communications, 13(1), 1-15. Article 3594. [DOI] [Repository]
Garza, D. R., von Meijenfeldt, F. A. B., van Dijk, B., Boleij, A., Huynen, M. A., & Dutilh, B. E. (2022). Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes. BMC Ecology and Evolution, 22(1), 1-16. Article 101. [DOI] [Repository]
Walker, P. J., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Adriaenssens, E. M., Alfenas-Zerbini, P., Dempsey, D. M., Dutilh, B. E., García, M. L., Curtis Hendrickson, R., Junglen, S., Krupovic, M., Kuhn, J. H., Lambert, A. J., Łobocka, M., Oksanen, H. M., Orton, R. J., Robertson, D. L., Rubino, L., ... Zerbini, F. M. (2022). Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Archives of Virology, 167(11), 2429-2440. [DOI] [Repository]
Postler, T. S., Rubino, L., Adriaenssens, E. M., Dutilh, B. E., Harrach, B., Junglen, S., Kropinski, A. M., Krupovic, M., Wada, J., Crane, A., Kuhn, J. H., Mushegian, A., Rūmnieks, J., Sabanadzovic, S., Simmonds, P., Varsani, A., Zerbini, F. M., Callanan, J., Draper, L. A., ... Stockdale, S. R. (2022). Guidance for creating individual and batch latinized binomial virus species names. Journal of General Virology, 103(12), 1-9. [DOI] [Repository]
Hauptfeld, E., Pelkmans, J., Huisman, T. T., Anocic, A., Snoek, B. L., von Meijenfeldt, F. A. B., Gerritse, J., van Leeuwen, J., Leurink, G., van Lit, A., van Uffelen, R., Koster, M. C., & Dutilh, B. E. (2022). A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater. Water Research, 221, 1-10. Article 118767. [DOI] [Repository]
Meaden, S., Biswas, A., Arkhipova, K., Morales, S. E., Dutilh, B. E., Westra, E. R., & Fineran, P. C. (2022). High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. Current Biology, 32(1), 220-227.e5. [DOI] [Repository]
2021
Wetenschappelijke publicaties
Andralojc, K. M., Molina, M. A., Qiu, M., Spruijtenburg, B., Rasing, M., Pater, B., Huynen, M. A., Dutilh, B. E., Ederveen, T. H. A., Elmelik, D., Siebers, A. G., Loopik, D., Bekkers, R. L. M., Leenders, W. P. J., & Melchers, W. J. G. (2021). Novel high-resolution targeted sequencing of the cervicovaginal microbiome. BMC Biology, 19(1), Article 267. [DOI] [Repository]
Krupovic, M., Turner, D., Morozova, V., Dyall-Smith, M., Oksanen, H. M., Edwards, R., Dutilh, B. E., Lehman, S. M., Reyes, A., Baquero, D. P., Sullivan, M. B., Uchiyama, J., Nakavuma, J., Barylski, J., Young, M. J., Du, S., Alfenas-Zerbini, P., Kushkina, A., Kropinski, A. M., ... Adriaenssens, E. M. (2021). Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Archives of Virology, 166(11), 3239-3244. [DOI] [Repository]
Dutilh, B. E., Varsani, A., Tong, Y., Simmonds, P., Sabanadzovic, S., Rubino, L., Roux, S., Muñoz, A. R., Lood, C., Lefkowitz, E. J., Kuhn, J. H., Krupovic, M., Edwards, R. A., Brister, J. R., Adriaenssens, E. M., & Sullivan, M. B. (2021). Perspective on taxonomic classification of uncultivated viruses. Current Opinion in Virology, 51, 207-215. [DOI] [Repository]
Jahn, M. T., Lachnit, T., Markert, S. M., Stigloher, C., Pita, L., Ribes, M., Dutilh, B. E., & Hentschel, U. (2021). Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. The ISME Journal, 15(7), 2001-2011. [DOI] [Repository]
Taddese, R., Belzer, C., Aalvink, S., de Jonge, M. I., Nagtegaal, I. D., Dutilh, B. E., & Boleij, A. (2021). Production of inactivated gram-positive and gram-negative species with preserved cellular morphology and integrity. Journal of Microbiological Methods, 184, 1-10. Article 106208. [DOI] [Repository]
Goettsch, W., Beerenwinkel, N., Deng, L., Dölken, L., Dutilh, B. E., Erhard, F., Kaderali, L., von Kleist, M., Marquet, R., Matthijnssens, J., McCallin, S., McMahon, D., Rattei, T., Van Rij, R. P., Robertson, D. L., Schwemmle, M., Stern-Ginossar, N., & Marz, M. (2021). ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses, 13(5), 1-20. Article 766. [DOI] [Repository]
Garmaeva, S., Gulyaeva, A., Sinha, T., Shkoporov, A. N., Clooney, A. G., Stockdale, S. R., Spreckels, J. E., Sutton, T. D. S., Draper, L. A., Dutilh, B. E., Wijmenga, C., Kurilshikov, A., Fu, J., Hill, C., & Zhernakova, A. (2021). Stability of the human gut virome and effect of gluten-free diet. Cell Reports, 35(7), 1-21. Article 109132. [DOI] [Repository]
Amato, K. R., Arrieta, M.-C., Azad, M. B., Bailey, M. T., Broussard, J. L., Bruggeling, C. E., Claud, E. C., Costello, E. K., Davenport, E. R., Dutilh, B. E., Swain Ewald, H. A., Ewald, P., Hanlon, E. C., Julion, W., Keshavarzian, A., Maurice, C. F., Miller, G. E., Preidis, G. A., Segurel, L., ... Kuzawa, C. W. (2021). The human gut microbiome and health inequities. Proceedings of the National Academy of Sciences of the United States of America, 118(25), 1-10. Article e2017947118. [DOI] [Repository]
Coutinho, F. H., Zaragoza-Solas, A., López-Pérez, M., Barylski, J., Zielezinski, A., Dutilh, B. E., Edwards, R., & Rodriguez-Valera, F. (2021). RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content. Patterns (New York, N.Y.), 2(7), 1-9. Article 100274. [DOI] [Repository]
Bruggeling, C. E., Garza, D. R., Achouiti, S., Mes, W., Dutilh, B. E., & Boleij, A. (2021). Optimized bacterial DNA isolation method for microbiome analysis of human tissues. MicrobiologyOpen, 10(3), 1-22. Article e1191. [DOI] [Repository]
Walker, P. J., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Adriaenssens, E. M., Alfenas-Zerbini, P., Davison, A. J., Dempsey, D. M., Dutilh, B. E., García, M. L., Harrach, B., Harrison, R. L., Hendrickson, R. C., Junglen, S., Knowles, N. J., Krupovic, M., Kuhn, J. H., Lambert, A. J., Łobocka, M., ... Zerbini, F. M. (2021). Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Archives of Virology, 166(9), 2633-2648. [DOI] [Repository]
van Esveld, S. L., Meerstein-Kessel, L., Boshoven, C., Baaij, J. F., Barylyuk, K., Coolen, J. P. M., van Strien, J., Duim, R. A. J., Dutilh, B. E., Garza, D. R., Letterie, M., Proellochs, N. I., de Ridder, M. N., Venkatasubramanian, P. B., de Vries, L. E., Waller, R. F., Kooij, T. W. A., & Huynen, M. A. (2021). A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. mSphere, 6(5), 1-17. Article e00614-21. [DOI] [Repository]
Pappas, N., & Dutilh, B. E. (2021). Finding functional associations between prokaryotic virus orthologous groups: a proof of concept. BMC Bioinformatics, 22(1), 1-11. Article 438. [DOI] [Repository]
Andeweg, S. P., Kesmir, C., & Dutilh, B. E. (2021). Quantifying The Impact Of Human Leukocyte Antigen On The Human Gut Microbiota. mSphere, 6(4), 1-12. [DOI] [Repository]
Sheinman, M., Arkhipova, K., Arndt, P. F., Dutilh, B. E., Hermsen, R., & Massip, F. (2021). Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife, 10, Article e62719. [DOI] [Repository]
van Vliet, D. M., von Meijenfeldt, F. A. B., Dutilh, B. E., Villanueva, L., Sinninghe Damsté, J. S., Stams, A. J. M., & Sánchez-Andrea, I. (2021). The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environmental Microbiology, 23(6), 2834-2857. [DOI] [Repository]
Coutinho, F. H., von Meijenfeldt, F. A. B., Walter, J. M., Haro-Moreno, J. M., Lopéz-Pérez, M., van Verk, M. C., Thompson, C. C., Cosenza, C. A. N., Appolinario, L., Paranhos, R., Cabral, A., Dutilh, B. E., & Thompson, F. L. (2021). Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome. Science of the Total Environment, 765, 1-20. Article 142758. [DOI] [Repository]
Balvert, M., Luo, X., Hauptfeld, E., Schönhuth, A., & Dutilh, B. E. (2021). OGRE: Overlap Graph-based metagenomic Read clustEring. Bioinformatics, 37(7), 905–912. Article btaa760. [DOI] [Repository]
Villanueva, L., von Meijenfeldt, F. A. B., Westbye, A. B., Yadav, S., Hopmans, E. C., Dutilh, B. E., & Damsté, J. S. S. (2021). Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids. ISME Journal, 15(1), 168-182. [DOI] [Repository]
2020
Wetenschappelijke publicaties
Pappas, N., Roux, S., Hölzer, M., Lamkiewicz, K., Mock, F., Marz, M., & Dutilh, B. E. (2020). Virus Bioinformatics. In Elsevier Reference Collection in: Life Sciences (Elsevier Reference Collection). Elsevier. [DOI] [Repository]
Douterelo, I., Dutilh, B. E., Calero, C., Rosales, E., Martin, K., & Husband, S. (2020). Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks. Water Research, 187, Article 116416. [DOI] [Repository]
Rossi, A., Treu, L., Toppo, S., Zschach, H., Campanaro, S., & Dutilh, B. E. (2020). Evolutionary Study of the Crassphage Virus at Gene Level. Viruses, 12(9), Article 1035. [DOI] [Repository]
Taddese, R., Garza, D. R., Ruiter, L. N., de Jonge, M. I., Belzer, C., Aalvink, S., Nagtegaal, I. D., Dutilh, B. E., & Boleij, A. (2020). Growth rate alterations of human colorectal cancer cells by 157 gut bacteria. Beneficial microbes, 12(1), 1-20. [DOI] [Repository]
de Jonge, P. A., von Meijenfeldt, F. A. B., Costa, A. R., Nobrega, F. L., Brouns, S. J. J., & Dutilh, B. E. (2020). Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts. iScience, 23(9), Article 101439. [DOI] [Repository]
Walker, P. J., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Adriaenssens, E. M., Dempsey, D. M., Dutilh, B. E., Harrach, B., Harrison, R. L., Hendrickson, R. C., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M., Orton, R. J., Rubino, L., Sabanadzovic, S., ... Davison, A. J. (2020). Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020). Archives of Virology, 165, 2737–2748 . [DOI] [Repository]
Klein, J., Neilen, M., van Verk, M., Dutilh, B. E., & Van den Ackerveken, G. (2020). Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering. PLoS One, 15(5), Article e0225808. [DOI] [Repository]
de Jonge, P. A., Smit Sibinga, D. J. C., Boright, O. A., Costa, A. R., Nobrega, F. L., Brouns, S. J. J., & Dutilh, B. E. (2020). Development of styrene maleic acid lipid particles (SMALPs) as a tool for studies of phage-host interactions. Journal of Virology, 94(23), Article e01559-20. [DOI] [Repository]
Siddell, S. G., Walker, P. J., Lefkowitz, E. J., Mushegian, A. R., Dutilh, B. E., Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M. L., Rubino, L., Sabanadzovic, S., Simmonds, P., Varsani, A., Zerbini, F. M., & Davison, A. J. (2020). Correction to: Binomial nomenclature for virus species: a consultation. Archives of Virology, 165, 1263–1264. [DOI] [Repository]
Garza, D. R., Taddese, R., Wirbel, J., Zeller, G., Boleij, A., Huynen, M. A., & Dutilh, B. E. (2020). Metabolic models predict bacterial passengers in colorectal cancer. Cancer & metabolism, 8, Article 3. [DOI] [Repository]
IBESS group (2020). Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity. BMC Genomics, 21(1), Article 138. [DOI] [Repository]
Mascarenhas, R., Ruziska, F. M., Moreira, E. F., Campos, A. B., Loiola, M., Reis, K., Trindade-Silva, A. E., Barbosa, F. A. S., Salles, L., Menezes, R., Veiga, R., Coutinho, F. H., Dutilh, B. E., Guimarães, P. R., Assis, A. P. A., Ara, A., Miranda, J. G. V., Andrade, R. F. S., Vilela, B., & Meirelles, P. M. (2020). Integrating Computational Methods to Investigate the Macroecology of Microbiomes. Frontiers in Genetics, 10, Article 1344. [DOI] [Repository]
Siddell, S. G., Walker, P. J., Lefkowitz, E. J., Mushegian, A. R., Dutilh, B. E., Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M. L., Rubino, L., Sabanadzovic, S., Simmonds, P., Varsani, A., Zerbini, F. M., & Davison, A. J. (2020). Binomial nomenclature for virus species: a consultation. Archives of Virology, 165(2), 519-525. [DOI] [Repository]
Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., Pinello, L., Skums, P., Stamatakis, A., Attolini, C. S.-O., Aparicio, S., Baaijens, J., Balvert, M., Barbanson, B. D., Cappuccio, A., ... Schönhuth, A. (2020). Eleven grand challenges in single-cell data science. Genome Biology, 21(1), Article 31. [DOI] [Repository]
Walter, J. M., Coutinho, F. H., Leomil, L., Hargreaves, P. I., Campeão, M. E., Vieira, V. V., Silva, B. S., Fistarol, G. O., Salomon, P. S., Sawabe, T., Mino, S., Hosokawa, M., Miyashita, H., Maruyama, F., van Verk, M. C., Dutilh, B. E., Thompson, C. C., & Thompson, F. L. (2020). Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia. Microbial Ecology, 80, 249–265. [DOI] [Repository]
Douterelo, I., Dutilh, B. E., Arkhipova, K., Calero, C., & Husband, S. (2020). Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems. Water Research, 173, Article 115586. [DOI] [Repository]
Adriaenssens, E. M., Sullivan, M. B., Knezevic, P., van Zyl, L. J., Sarkar, B. L., Dutilh, B. E., Alfenas-Zerbini, P., Łobocka, M., Tong, Y., Brister, J. R., Moreno Switt, A. I., Klumpp, J., Aziz, R. K., Barylski, J., Uchiyama, J., Kropinski, A. M., Petty, N. K., Clokie, M. R. J., Kushkina, A. I., ... Krupovic, M. (2020). Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology, 165, 1253–1260. [DOI] [Repository]
Dabir, P. D., Bruggeling, C. E., van der Post, R. S., Dutilh, B. E., Hoogerbrugge, N., Ligtenberg, M. J. L., Boleij, A., & Nagtegaal, I. D. (2020). Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients? A systematic review and meta-analysis. European Journal of Human Genetics, 28, 277–286. [DOI] [Repository]
Barylski, J., Enault, F., Dutilh, B. E., Schuller, M. B. P., Edwards, R. A., Gillis, A., Klumpp, J., Knezevic, P., Krupovic, M., Kuhn, J. H., Lavigne, R., Oksanen, H. M., Sullivan, M. B., Jang, H. B., Simmonds, P., Aiewsakun, P., Wittmann, J., Tolstoy, I., Brister, J. R., ... Adriaenssens, E. M. (2020). Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages. Systems and Synthetic Biology, 69(1), 110–123. [DOI] [Repository]
2019
Wetenschappelijke publicaties
von Meijenfeldt, F. A. B., Arkhipova, K., Cambuy, D. D., Coutinho, F. H., & Dutilh, B. E. (2019). Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome Biology, 20, Article 217. [DOI] [Repository]
Yin, B., Balvert, M., van der Spek, R. A. A., Dutilh, B. E., Bohté, S., Veldink, J., & Schönhuth, A. (2019). Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype. Bioinformatics, 35(14), i538-i547. [DOI] [Repository]
Jahn, M. T., Arkhipova, K., Markert, S. M., Stigloher, C., Lachnit, T., Pita, L., Kupczok, A., Ribes, M., Stengel, S. T., Rosenstiel, P., Dutilh, B. E., & Hentschel, U. (2019). A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion. Cell Host & Microbe, 26(4), 542-550.e5. [DOI] [Repository]
Metz, P., Tjan, M. J. H., Wu, S., Pervaiz, M., Hermans, S., Shettigar, A., Sears, C. L., Ritschel, T., Dutilh, B. E., & Boleij, A. (2019). Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin. Frontiers in cellular and infection microbiology, 9, Article 364. [DOI] [Repository]
Jonge, P. A. D., Meijenfeldt, F. A. B. V., Rooijen, L. E. V., Brouns, S. J. J., & Dutilh, B. E. (2019). Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages. Viruses, 11(12), Article 1085. [DOI] [Repository]
Siddell, S. G., Walker, P. J., Lefkowitz, E. J., Mushegian, A. R., Adams, M. J., Dutilh, B. E., Gorbalenya, A. E., Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M., Rubino, L., Sabanadzovic, S., Sanfaçon, H., Simmonds, P., ... Davison, A. J. (2019). Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018). Archives of Virology, 164(3), 943-946. [DOI] [Repository]
Coutinho, F. H., Silveira, C. B., Gregoracci, G. B., Thompson, C. C., Edwards, R. A., Brussaard, C. P. D., Dutilh, B. E., & Thompson, F. L. (2019). Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes. Nature Communications, 10(1), Article 502. [DOI] [Repository]
Coutinho, F. H., Thompson, C. C., Cabral, A. S., Paranhos, R., Dutilh, B. E., & Thompson, F. L. (2019). Modelling the influence of environmental parameters over marine planktonic microbial communities using artificial neural networks. Science of the Total Environment, 677, 205-214. [DOI] [Repository]
Tara Oceans Coordinators (2019). Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell, 177(5), 1109-1123.e14. [DOI] [Repository]
Hufsky, F., Ibrahim, B., Modha, S., Clokie, M. R. J., Deinhardt-Emmer, S., Dutilh, B. E., Lycett, S., Simmonds, P., Thiel, V., Abroi, A., Adriaenssens, E. M., Escalera-Zamudio, M., Kelly, J. N., Lamkiewicz, K., Lu, L., Susat, J., Sicheritz, T., Robertson, D. L., & Marz, M. (2019). The Third Annual Meeting of the European Virus Bioinformatics Center. Viruses, 11(5), Article 420. [DOI] [Repository]
Walker, P. J., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Dempsey, D. M., Dutilh, B. E., Harrach, B., Harrison, R. L., Hendrickson, R. C., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M., Rubino, L., Sabanadzovic, S., Simmonds, P., Varsani, A., ... Davison, A. J. (2019). Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019). Archives of Virology, 164(9), 2417-2429. [DOI] [Repository]
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., Bibby, K., Brouns, S. J. J., Cazares, A., de Jonge, P. A., Desnues, C., Díaz Muñoz, S. L., Fineran, P. C., Kurilshikov, A., Lavigne, R., ... Dutilh, B. E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nature Microbiology, 4, 1727-1736. [DOI] [Repository]
de Jonge, P. A., Nobrega, F. L., Brouns, S. J. J., & Dutilh, B. E. (2019). Molecular and Evolutionary Determinants of Bacteriophage Host Range. Trends in Microbiology, 27(1), 51-63. [DOI] [Repository]
Chaidir, L., Ruesen, C., Dutilh, B. E., Ganiem, A. R., Andryani, A., Apriani, L., Huynen, M. A., Ruslami, R., Hill, P. C., Crevel, R. V., & Alisjahbana, B. (2019). Use of whole genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. Journal of Global Antimicrobial Resistance, 16, 170-177. [DOI]
2018
Wetenschappelijke publicaties
Villanueva, L., von Meijenfeldt, F. A. B., Westbye, A. B., Hopmans, E. C., Dutilh, B. E., & Sinninghe Damsté, J. S. (2018). Bridging the divide: bacteria synthesizing archaeal membrane lipids. bioRxiv. [DOI]
Brito, T. L., Campos, A. B., Bastiaan Von Meijenfeldt, F. A., Daniel, J. P., Ribeiro, G. B., Silva, G. G. Z., Wilke, D. V., De Moraes, D. T., Dutilh, B. E., Meirelles, P. M., Trindade-silva, A. E., & Cullen, D. (Ed.) (2018). The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei. PLoS One, 13(11), Article e0200437. [DOI] [Repository]
Roux, S., Adriaenssens, E. M., Dutilh, B. E., Koonin, E. V., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Lavigne, R., Brister, J. R., Varsani, A., Amid, C., Aziz, R. K., Bordenstein, S. R., Bork, P., Breitbart, M., Cochrane, G. R., Daly, R. A., Desnues, C., Duhaime, M. B., ... Eloe-fadrosh, E. A. (2018). Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology, 37(1), 29-37. [DOI] [Repository]
Nobrega, F. L., Vlot, M., de Jonge, P. A., Dreesens, L. L., Beaumont, H. J. E., Lavigne, R., Dutilh, B. E., & Brouns, S. J. J. (2018). Targeting mechanisms of tailed bacteriophages. Nature Reviews. Microbiology, 16, 760–773. [DOI] [Repository]
Steenbergen, R., Oti, M., Ter Horst, R., Tat, W., Neufeldt, C., Belovodskiy, A., Chua, T. T., Cho, W. J., Joyce, M., Dutilh, B. E., & Tyrrell, D. L. (2018). Establishing normal metabolism and differentiation in hepatocellular carcinoma cells by culturing in adult human serum. Scientific Reports, 8(1), Article 11685. [DOI] [Repository]
King, A. M. Q., Lefkowitz, E. J., Mushegian, A. R., Adams, M. J., Dutilh, B. E., Gorbalenya, A. E., Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Nibert, M. L., Rubino, L., Sabanadzovic, S., Sanfaçon, H., Siddell, S. G., Simmonds, P., ... Davison, A. J. (2018). Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018). Archives of Virology, 163(9), 2601–2631. [DOI] [Repository]
Garza, D. R., van Verk, M. C., Huynen, M. A., & Dutilh, B. E. (2018). Towards predicting the environmental metabolome from metagenomics with a mechanistic model. Nature Microbiology, 3(4), 456-460. [DOI] [Repository]
Ibrahim, B., Arkhipova, K., Andeweg, A. C., Posada-Céspedes, S., Enault, F., Gruber, A., Koonin, E. V., Kupczok, A., Lemey, P., McHardy, A. C., McMahon, D. P., Pickett, B. E., Robertson, D. L., Scheuermann, R. H., Zhernakova, A., Zwart, M. P., Schönhuth, A., Dutilh, B. E., & Marz, M. (2018). Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses, 10(5), Article 256. [DOI] [Repository]
McNair, K., Aziz, R. K., Pusch, G. D., Overbeek, R., Dutilh, B. E., & Edwards, R. A. (2018). Phage Genome Annotation Using the RAST Pipeline. In M. R. J. Clokie, A. M. Kropinski, & R. Lavigne (Eds.), Bacteriophages: Methods and Protocols (Vol. 3, pp. 231-238). (Methods in Molecular Biology; Vol. 1681). Springer. [DOI] [Repository]
Ruesen, C., Chaidir, L., van Laarhoven, A., Dian, S., Ganiem, A. R., Nebenzahl-Guimaraes, H., Huynen, M. A., Alisjahbana, B., Dutilh, B. E., & van Crevel, R. (2018). Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis. BMC Genomics, 19(1), Article 122. [DOI] [Repository]
Adriaenssens, E. M., Wittmann, J., Kuhn, J. H., Turner, D., Sullivan, M. B., Dutilh, B. E., Jang, H. B., van Zyl, L. J., Klumpp, J., Lobocka, M., Moreno Switt, A. I., Rumnieks, J., Edwards, R. A., Uchiyama, J., Alfenas-Zerbini, P., Petty, N. K., Kropinski, A. M., Barylski, J., Gillis, A., ... Rodney Brister, J. (2018). Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Archives of Virology, 163(4), 1125–1129. [DOI] [Repository]
Gigliucci, F., von Meijenfeldt, F. A. B., Knijn, A., Michelacci, V., Scavia, G., Minelli, F., Dutilh, B. E., Ahmad, H. M., Raangs, G. C., Friedrich, A. W., Rossen, J. W. A., & Morabito, S. (2018). Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients. Frontiers in cellular and infection microbiology, 8. [DOI] [Repository]
Arkhipova, K., Skvortsov, T., Quinn, J. P., McGrath, J. W., Allen, C. C., Dutilh, B. E., McElarney, Y., & Kulakov, L. A. (2018). Temporal dynamics of uncultured viruses: a new dimension in viral diversity. ISME Journal, 12, 199–211. [DOI] [Repository]
Computational Pan-Genomics Consortium, & Dutilh, B. E. (2018). Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19(1), 118–135. [DOI] [Repository]
2017
Wetenschappelijke publicaties
Walter, J. M., Coutinho, F. H., Dutilh, B. E., Swings, J., Thompson, F. L., & Thompson, C. C. (2017). Ecogenomics and Taxonomy of Cyanobacteria Phylum. Frontiers in Microbiology, 8, Article 2132. [DOI] [Repository]
Dutilh, B. E., Reyes, A., Hall, R. J., & Whiteson, K. L. (2017). Virus Discovery by Metagenomics: The (Im)possibilities. Frontiers in Microbiology, 8, Article 1710. [DOI] [Repository]
Coutinho, F. H., Silveira, C. B., Gregoracci, G. B., Thompson, C. C., Edwards, R. A., Brussaard, C. P. D., Dutilh, B. E., & Thompson, F. L. (2017). Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans. Nature Communications, 8, Article 15955. [DOI] [Repository]
Couto Furtado Albuquerque, M., van Herwaarden, Y., Kortman, G. A. M., Dutilh, B. E., Bisseling, T., & Boleij, A. (2017). Preservation of bacterial DNA in 10-year-old guaiac FOBT cards and FIT tubes. Journal of Clinical Pathology - Clinical Molecular Pathology, 70(11), 994-996. [DOI] [Repository]
Motlagh, A. M., Bhattacharjee, A. S., Coutinho, F. H., Dutilh, B. E., Casjens, S. R., & Goel, R. K. (2017). Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses. Frontiers in Microbiology, 8, Article 352. [DOI] [Repository]
Maat, D. S., Biggs, T., Evans, C., van Bleijswijk, J. D. L., van der Wel, N. N., Dutilh, B., & Brussaard, C. P. D. (2017). Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses. Viruses, 9(6), Article 134. [DOI] [Repository]
Adriaenssens, E. M., Krupovic, M., Knezevic, P., Ackermann, H. W., Barylski, J., Brister, J. R., Clokie, M. R. C., Duffy, S., Dutilh, B. E., Edwards, R. A., Enault, F., Jang, H. B., Klumpp, J., Kropinski, A. M., Lavigne, R., Poranen, M. M., Prangishvili, D., Rumnieks, J., Sullivan, M. B., ... Kuhn, J. H. (2017). Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology, 162(4), 1153–1157. [DOI] [Repository]
Speth, D. R., Lagkouvardos, I., Wang, Y., Qian, P. Y., Dutilh, B. E., & Jetten, M. S. M. (2017). 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. Microbial Ecology, 74(1), 1-5. [DOI] [Repository]
2016
Wetenschappelijke publicaties
Fróes, A. M., & Dutilh, B. E. (2016). Bioinformatics for studying environmental microorganisms. In T. B. Rodrigues, & A. E. Trindade Silva (Eds.), Molecular Diversity of Environmental Prokaryotes (pp. 263-284). CRC Press. [DOI] [Repository]
Gambelli, L., Cremers, G., Mesman, R., Guerrero, S., Dutilh, B. E., Jetten, M. S. M., den Camp, H. J. M. O., & van Niftrik, L. (2016). Ultrastructure and viral metagenome of bacteriophages from an anaerobic methane oxidizing methylomirabilis bioreactor enrichment culture. Frontiers in Microbiology, 7, Article 1740. [DOI] [Repository]
Roux, S., Brum, J. R., Dutilh, B. E., Sunagawa, S., Duhaime, M. B., Loy, A., Poulos, B. T., Solonenko, N., Lara, E., Poulain, J., Pesant, S., Kandels-Lewis, S., Dimier, C., Picheral, M., Searson, S., Cruaud, C., Alberti, A., Duarte, C. M., Gasol, J. M., ... Tara Oceans Coordinators (2016). Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature, 537, 689–693. [DOI] [Repository]
Coutinho, F. H., Dutilh, B. E., Thompson, C. C., & Thompson, F. L. (2016). Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features. Archives of Microbiology, 198(10), 973-986. [DOI] [Repository]
Kortman, G. A. M., Dutilh, B. E., Maathuis, A. J. H., Engelke, U. F., Boekhorst, J., Keegan, K. P., Nielsen, F. G. G., Betley, J., Weir, J. C., Kingsbury, Z., Kluijtmans, L. A. J., Swinkels, D. W., Venema, K., & Tjalsma, H. (2016). Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon. Frontiers in Microbiology, 6, Article 1481. [DOI] [Repository]
Krupovic, M., Dutilh, B. E., Adriaenssens, E. M., Wittmann, J., Vogensen, F. K., Sullivan, M. B., Rumnieks, J., Prangishvili, D., Lavigne, R., Kropinski, A. M., Klumpp, J., Gillis, A., Enault, F., Edwards, R. A., Duffy, S., Clokie, M. R. C., Barylski, J., Ackermann, H.-W., & Kuhn, J. H. (2016). Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Archives of Virology, 161(4), 1095-9. [DOI] [Repository]
Speth, D. R., In 't Zandt, M. H., Guerrero-Cruz, S., Dutilh, B. E., & Jetten, M. S. M. (2016). Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system. Nature Communications [E], 7, Article 11172. [DOI] [Repository]
Edwards, R. A., McNair, K., Faust, K., Raes, J., & Dutilh, B. E. (2016). Computational approaches to predict bacteriophage-host relationships. FEMS Microbiology Reviews, 40(2), 258-272. [DOI] [Repository]
Silva, G. G. Z., Green, K. T., Dutilh, B. E., & Edwards, R. A. (2016). SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data. Bioinformatics, 32(3), 354–361. [DOI] [Repository]
Barr, J. J., Dutilh, B. E., Skennerton, C. T., Fukushima, T., Hastie, M. L., Gorman, J. J., Tyson, G. W., & Bond, P. L. (2016). Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm. Environmental Microbiology, 18(1), 273–287. [DOI] [Repository]
2015
Wetenschappelijke publicaties
Bezemer, D., Cori, A., Ratmann, O., van Sighem, A., Hermanides, H. S., Dutilh, B. E., Gras, L., Rodrigues Faria, N., van den Hengel, R., Duits, A. J., Reiss, P., de Wolf, F., Fraser, C., & ATHENA observational cohort (2015). Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis. PLoS Medicine, 12(11), Article e1001898. [DOI] [Repository]
Hou, Q., Dutilh, B. E., Huynen, M. A., Heringa, J., & Feenstra, K. A. (2015). Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. BMC Bioinformatics, 16(1), Article 325. [DOI] [Repository]
Matthews, T. D., Schmieder, R., Silva, G. G. Z., Busch, J., Cassman, N., Dutilh, B. E., Green, D., Matlock, B., Heffernan, B., Olsen, G. J., Farris Hanna, L., Schifferli, D. M., Maloy, S., Dinsdale, E. A., & Edwards, R. A. (2015). Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum. PLoS One, 10(6), Article e0126883. [DOI] [Repository]
Busch, J., Nascimento, J. R., Magalhães, A. C. R., Dutilh, B. E., & Dinsdale, E. (2015). Copper tolerance and distribution of epibiotic bacteria associated with giant kelp Macrocystis pyrifera in southern California. Ecotoxicology, 24(5), 1131–1140. [DOI] [Repository]
Appenzeller, S., Gilissen, C., Rijntjes, J., Tops, B. B. J., Kastner-van Raaij, A., Hebeda, K. M., Nissen, L., Dutilh, B. E., van Krieken, J. H. J. M., & Groenen, P. J. T. A. (2015). Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next-generation sequencing. Histopathology, 67(6), 843-858. [DOI]
Garza, D. R., & Dutilh, B. E. (2015). From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cellular and Molecular Life Sciences, 72, 4287–4308. [DOI] [Repository]
Coutinho, F. H., Meirelles, P. M., Moreira, A. P. B., Paranhos, R. P., Dutilh, B. E., & Thompson, F. L. (2015). Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review. PeerJ [E], 3, Article e1008. [DOI] [Repository]
Hall, R. J., Draper, J. L., Nielsen, F. G. G., & Dutilh, B. E. (2015). Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. Frontiers in Microbiology, 6, Article 224. [DOI] [Repository]
Thompson, C. C., Amaral, G. R., Edwards, R. A., Polz, M. F., Dutilh, B. E., Ussery, D. W., Swings, J., & Thompson, F. L. (2015). Microbial taxonomy in the post-genomic era: Rebuilding from scratch? Archives of Microbiology, 197, 359–370. [DOI]
Speth, D. R., Russ, L., Kartal, B., Op den Camp, H. J. M., Dutilh, B. E., & Jetten, M. S. M. (2015). Draft Genome Sequence of Anammox Bacterium "Candidatus Scalindua brodae," Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments. Genome Announcements, 3(1), Article e01415-14. [DOI] [Repository]
2014
Wetenschappelijke publicaties
Dutilh, B. E. (2014). Metagenomic ventures into outer sequence space. Bacteriophage, 4(4), Article e979664. [DOI] [Repository]
Alves Junior, N., Meirelles, P. M., de Oliveira Santos, E., Dutilh, B., Silva, G. G. Z., Paranhos, R., Cabral, A. S., Rezende, C., Iida, T., de Moura, R. L., Kruger, R. H., Pereira, R. C., Valle, R., Sawabe, T., Thompson, C., & Thompson, F. (2014). Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean. Archives of Microbiology, 197, 165–179. [DOI]
ElRakaiby, M., Dutilh, B. E., Rizkallah, M. R., Boleij, A., Cole, J. N., & Aziz, R. K. (2014). Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics. OMICS-A Journal of Integrative Biology, 18(7), 402-414. [DOI] [Repository]
Silva, G. G. Z., Cuevas, D. A., Dutilh, B. E., & Edwards, R. A. (2014). FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ [E], 2, Article 2:e425. [DOI] [Repository]
Ghamrawi, S., Rénier, G., Saulnier, P., Cuenot, S., Zykwinska, A., Dutilh, B. E., Thornton, C., Faure, S., & Bouchara, J.-P. (2014). Cell wall modifications during conidial maturation of the human pathogenic fungus Pseudallescheria boydii. PLoS One, 9(6), Article e100290. [DOI] [Repository]
Dutilh, B. E., Cassman, N., McNair, K., Sanchez, S. E., Silva, G. G. Z., Boling, L., Barr, J. J., Speth, D. R., Seguritan, V., Aziz, R. K., Felts, B., Dinsdale, E. A., Mokili, J. L., & Edwards, R. A. (2014). A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nature Communications [E], 5, Article 4498. [DOI] [Repository]
Dutilh, B. E., Thompson, C. C., Vicente, A. C. P., Marin, M. A., Lee, C., Silva, G. G. Z., Schmieder, R., Andrade, B. G. N., Chimetto, L., Cuevas, D., Garza, D. R., Okeke, I. N., Aboderin, A. O., Spangler, J., Ross, T., Dinsdale, E. A., Thompson, F. L., Harkins, T. T., & Edwards, R. A. (2014). Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions. BMC Genomics, 15, Article 15:654 . [DOI] [Repository]
Lim, Y. W., Cuevas, D. A., Silva, G. G. Z., Aguinaldo, K., Dinsdale, E. A., Haas, A. F., Hatay, M., Sanchez, S. E., Wegley-Kelly, L., Dutilh, B. E., Harkins, T. T., Lee, C. C., Tom, W., Sandin, S. A., Smith, J. E., Zgliczynski, B., Vermeij, M. J. A., Rohwer, F., & Edwards, R. A. (2014). Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ [E], 2, Article e520. [DOI] [Repository]
2013
Wetenschappelijke publicaties
Dutilh, B. E., Backus, L., Van Hijum, S. A. F. T., & Tjalsma, H. (2013). Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer. Best Practice & Research in Clinical Gastroenterology, 27(1), 85-99. [DOI]
Mokili, J. L., Dutilh, B. E., Lim, Y. W., Schneider, B. S., Taylor, T., Haynes, M. R., Metzgar, D., Myers, C. A., Blair, P. J., Nosrat, B., Wolfe, N. D., & Rohwer, F. (2013). Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness. PLoS One, 8(3), Article e58404. [DOI]
Van de Vossenberg, J., Woebken, D., Maalcke, W. J., Wessels, H. J. C. T., Dutilh, B. E., Kartal, B., Janssen-Megens, E. M., Roeselers, G., Yan, J., Speth, D., Gloerich, J., Geerts, W., Van der Biezen, E., Pluk, W., Francoijs, K.-J., Russ, L., Lam, P., Malfatti, S. A., Tringe, S. G., ... Jetten, M. S. M. (2013). The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. Environmental Microbiology, 15(5), 1275-1289. [DOI]
Dutilh, B. E., Backus, L., Edwards, R. A., Wels, M., Bayjanov, J. R., & Van Hijum, S. A. F. T. (2013). Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Briefings in Functional Genomics, 12(4), 366-380. Article elt008. [DOI]
Silva, G. G., Dutilh, B. E., Matthews, T. D., Elkins, K., Schmieder, R., Dinsdale, E. A., & Edwards, R. A. (2013). Combining de novo and reference-guided assembly with scaffold_builder. Source Code for Biology and Medicine, 8(1), 23. [DOI]
2012
Wetenschappelijke publicaties
Garza, D. R., Thompson, C. C., Loureiro, E. C. B., Dutilh, B. E., Inada, D. T., Junior, E. C. S., Cardoso, J. F., Nunes, M. R. T., de Lima, C. P. S., Silvestre, R. V. D., Nunes, K. N. B., Santos, E. C. O., Edwards, R. A., Vicente, A. C. P., & de Sá Morais, L. L. C. (2012). Genome-wide study of the defective sucrose fermenter strain of vibrio cholerae from the Latin American cholera epidemic. PLoS One, 7(5), Article e37283. [DOI]
de Lucena, B. T. L., Silva, G. G. Z., dos Santos, B. M., Dias, G. M., Amaral, G. R. S., Moreira, A. P. B., Júnior, M. A. D. M., Dutilh, B. E., Edwards, R. A., Balbino, V., Thompson, C. C., & Thompson, F. L. (2012). Genome sequences of the ethanol-tolerant lactobacillus vini strains LMG 23202Tand JP7.8.9. Journal of Bacteriology, 194(11), 3018. [DOI]
Trindade-Silva, A. E., Rua, C., Silva, G. G. Z., Dutilh, B. E., Moreira, A. P. B., Edwards, R. A., Hajdu, E., Lobo-Hajdu, G., Vasconcelos, A. T., Berlinck, R. G. S., & Thompson, F. L. (2012). Taxonomic and functional microbial signatures of the endemic marine sponge arenosclera brasiliensis. PLoS One, 7(7), Article e39905. [DOI]
Mokili, J. L., Rohwer, F., & Dutilh, B. E. (2012). Metagenomics and future perspectives in virus discovery. Current Opinion in Virology, 2(1), 63-77. [DOI]
Tjalsma, H., Boleij, A., Marchesi, J. R., & Dutilh, B. E. (2012). A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects. Nature Reviews. Microbiology, 10(8), 575-82. [DOI]
Boleij, A., Dutilh, B. E., Kortman, G. A. M., Roelofs, R., Laarakkers, C. M., Engelke, U. F., & Tjalsma, H. (2012). Bacterial responses to a simulated colon tumor microenvironment. Molecular & Cellular Proteomics, 11(10), 851-62. [DOI]
Cassman, N., Prieto-Davó, A., Walsh, K., Silva, G. G. Z., Angly, F., Akhter, S., Barott, K., Busch, J., McDole, T., Haggerty, J. M., Willner, D., Alarcón, G., Ulloa, O., DeLong, E. F., Dutilh, B. E., Rohwer, F., & Dinsdale, E. A. (2012). Oxygen minimum zones harbour novel viral communities with low diversity. Environmental Microbiology, 14(11), 3043-65. [DOI]
Dutilh, B. E., Schmieder, R., Nulton, J., Felts, B., Salamon, P., Edwards, R. A., & Mokili, J. L. (2012). Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics, 28(24), 3225-31. [DOI]
Camps, S. M. T., Dutilh, B. E., Arendrup, M. C., Rijs, A. J. M. M., Snelders, E., Huynen, M. A., Verweij, P. E., & Melchers, W. J. G. (2012). Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing. PLoS One, 7(11), e50034. [DOI]
2011
Wetenschappelijke publicaties
van Kessel, M. A. H. J., Dutilh, B. E., Neveling, K., Kwint, M. P., Veltman, J. A., Flik, G., Jetten, M. S. M., Klaren, P. H. M., & Op den Camp, H. J. M. (2011). Pyrosequencing of 16s rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). Optics Express [E], 1, Article 1:41 . [DOI]
De Graaf, R. M., Ricard, G., Van Alen, T. A., Duarte, I., Dutilh, B. E., Burgtorf, C., Kuiper, J. W. P., Van Der Staay, G. W. M., Tielens, A. G. M., Huynen, M. A., & Hackstein, J. H. P. (2011). The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of nyctotherus ovalis. Molecular Biology and Evolution, 28(8), 2379-2391. [DOI]
Marchesi, J. R., Dutilh, B. E., Hall, N., Peters, W. H. M., Roelofs, R., Boleij, A., & Tjalsma, H. (2011). Towards the human colorectal cancer microbiome. PLoS One, 6(5), Article e20447. [DOI]
Emons, J., Dutilh, B. E., Decker, E., Pirzer, H., Sticht, C., Gretz, N., Rappold, G., Cameron, E. R., Neil, J. C., Stein, G. S., van Wijnen, A. J., Wit, J. M., Post, J. N., & Karperien, M. (2011). Genome-wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation. Journal of Endocrinology, 209(2), 245-254. [DOI]
Dutilh, B. E., Jurgelenaite, R., Szklarczyk, R., van Hijum, S. A. F. T., Harhangi, H. R., Schmid, M., de Wild, B., Françoijs, K.-J., Stunnenberg, H. G., Strous, M., Jetten, M. S. M., Op den Camp, H. J. M., & Huynen, M. A. (2011). FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics, 27(14), 1929-1933.
Tjalsma, H., Laarakkers, C. M. M., van Swelm, R. P. L., Theurl, M., Theurl, I., Kemna, E. H., van der Burgt, Y. E. M., Venselaar, H., Dutilh, B. E., Russel, F. G. M., Weiss, G., Masereeuw, R., Fleming, R. E., & Swinkels, D. W. (2011). Mass Spectrometry Analysis of Hepcidin Peptides in Experimental Mouse Models. PLoS One, 6(3), Article e16762. [DOI]
Thompson, C. C., Marin, M. A., Dias, G. M., Dutilh, B. E., Edwards, R. A., Iida, T., Thompson, F. L., & Vicente, A. C. P. (2011). Genome sequence of the human pathogen Vibrio cholerae Amazonia. Journal of Bacteriology, 193(20), 5877-8. [DOI]
Kip, N., Dutilh, B. E., Pan, Y., Bodrossy, L., Neveling, K., Kwint, M. P., Jetten, M. S. M., & Op den Camp, H. J. M. (2011). Ultra-deep pyrosequencing of pmoA amplicons confirms the prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog. Environmental Microbiology Reports, 3(6), 667-73. [DOI]
2010
Wetenschappelijke publicaties
Ettwig, K. F., Butler, M. K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M. M. M., Schreiber, F., Dutilh, B. E., Zedelius, J., De Beer, D., Gloerich, J., Wessels, H. J. C. T., Van Alen, T., Luesken, F., Wu, M. L., Van De Pas-Schoonen, K. T., Op Den Camp, H. J. M., Janssen-Megens, E. M., Francoijs, K.-J., ... Strous, M. (2010). Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature, 464(7288), 543-548. [DOI]
Kouwenhoven, E. N., va Heeringen, S. J., Tena, J. J., Oti, M., Dutilh, B. E., Alonso, M. E., de la Elisa, C.-M., Smeenk, L., Rinne, T., Parsaulian, L., Bolat, E., Jurgelenaite, R., Huynen, M. A., Hoischen, A., Veltman, J. A., Brunner, H. G., Roscioli, T., Oates, E., Wilson, M., ... Zhou, H. (2010). Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 shfm1 locus. PLoS Genetics, 6(8). [DOI]
2009
Wetenschappelijke publicaties
de Graaf, R. M., van Alen, T. A., Dutilh, B. E., Kuiper, J. W. P., van Zoggel, H. J. A. A., Huynh, M. B., Görtz, H.-D., Huynen, M. A., & Hackstein, J. H. P. (2009). The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus. BMC Genomics, 10, 514. Article 1471. [DOI]
Notebaart, R. A., Kensche, P. R., Huynen, M. A., & Dutilh, B. E. (2009). Asymmetric relationships between proteins shape genome evolution. Genome Biology, 10(2), R19. [DOI]
Dutilh, B. E., Huynen, M. A., & Strous, M. (2009). Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics, 25(21), 2878-81. [DOI]
2008
Wetenschappelijke publicaties
Dutilh, B. E., He, Y., Hekkelman, M. L., & Huynen, M. A. (2008). Signature, a web server for taxonomic characterization of sequence samples using signature genes. Nucleic Acids Research, 36(Suppl. 2), W470-474. [DOI]
Kensche, P. R., van Noort, V., Dutilh, B. E., & Huynen, M. A. (2008). Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. Journal of the Royal Society Interface, 5(19), 151-70. [DOI]
Kensche, P. R., Oti, M., Dutilh, B. E., & Huynen, M. A. (2008). Conservation of divergent transcription in fungi. Trends in Genetics, 24(5), 207-11. [DOI]
Ricard, G., de Graaf, R. M., Dutilh, B. E., Duarte, I., van Alen, T. A., van Hoek, A. H., Boxma, B., van der Staay, G. W. M., Moon-van der Staay, S. Y., Chang, W.-J., Landweber, L. F., Hackstein, J. H. P., & Huynen, M. A. (2008). Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics, 9, 587. [DOI]
Dutilh, B. E., Snel, B., Ettema, T. J., & Huynen, M. A. (2008). Signature genes as a phylogenomic tool. Molecular Biology and Evolution, 25, 1659-1667.
2007
Wetenschappelijke publicaties
Datson, N. A., Morsink, M. C., Atanasova, S., Armstrong, V. W., Zischler, H., Schlumbohm, C., Dutilh, B. E., Huynen, M. A., Waegele, B., Ruepp, A., de Kloet, E. R., & Fuchs, E. (2007). Development of the first marmoset-specific DNA microarray (EUMAMA): A new genetic tool for large-scale expression profiling in a non-human primate. BMC Genomics, 8, Article 8:190 . [DOI]
Dutilh, B. E., van Noort, V., van der Heijden, R. T., Boekhout, T., Snel, B., & Huynen, M. A. (2007). Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics, 23(7), 815-824.
2006
Wetenschappelijke publicaties
Ricard, G., McEwan, N. R., Dutilh, B. E., Jouany, J.-P., Macheboeuf, D., Mitsumori, M., McIntosh, F. M., Michalowski, T., Nagamine, T., Nelson, N., Newbold, C. J., Nsabimana, E., Takenaka, A., Thomas, N. A., Ushida, K., Hackstein, J. H. P., & Huynen, M. A. (2006). Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics, 7, 22. [DOI]
Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M. W., Horn, H., Daims, H., Bartol-Malvel, D., Wincker, P., Barbe, V., Fonknechten, N., Vallenet, D., Segurens, B., Schenowitz-Truong, C., Medigue, C., Collingro, A., Snel, B., Dutilh, B. E., ... Le Paslier, D. (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature, 440, 790-794.
Dutilh, B. E., Huynen, M. A., & Snel, B. (2006). A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. BMC Genomics, 7, 1-10.
2005
Wetenschappelijke publicaties
Snel, B., Huynen, M. A., & Dutilh, B. E. (2005). Genome trees and the nature of genome evolution. Annual Review of Microbiology, 59, 191-209. [DOI]
2004
Wetenschappelijke publicaties
Dutilh, B. E., Huynen, M. A., Bruno, W. J., & Snel, B. (2004). The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. Journal of Molecular Evolution, 58(5), 527-539. [DOI]
2003
Wetenschappelijke publicaties
Dutilh, B. E., & de Boer, R. J. (2003). Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells. Journal of Theoretical Biology, 224(3), 351-8.
Dutilh, B. E., & de Boer, R. J. (2003). Decline in excision circles is no evidence for homeostatic renewal of naive T cells. Journal of Theoretical Biology, 224, 351-358.