search
English Bewerken
search EN

Dr. B.E. (Bas) Dutilh

Universitair hoofddocent 
Bètawetenschappen
Biologie
Biodynamics and Biocomplexity
Bioinformatics
Bioinformatics

Dr. B.E. (Bas) Dutilh

Universitair hoofddocent
Bioinformatics
Profiel Publicaties Prijzen Onderzoek Onderwijs Nevenwerkzaamheden Contact
Profiel Publicaties Prijzen Onderzoek Onderwijs Nevenwerkzaamheden Contact
Expertises
Onderzoeksthema's

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. https://doi.org/10.1038/s41559-023-02027-7
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. https://doi.org/10.1038/s41564-018-0124-8
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. https://doi.org/10.1186/s13059-019-1817-x
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. https://doi.org/10.1038/s41564-019-0494-6
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. https://doi.org/10.1038/ncomms5498

Publicaties

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. https://doi.org/10.1007/s00705-023-05880-w
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. https://doi.org/10.1038/s43705-023-00294-w
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. https://doi.org/10.1007/s00705-022-05694-2
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. https://doi.org/10.3390/v15020519
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. https://doi.org/10.1093/ecco-jcc/jjad092
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. https://doi.org/10.1007/s00705-023-05797-4
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. https://doi.org/10.1371/journal.pbio.3002083
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. https://doi.org/10.1038/s41587-023-01844-2
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. https://doi.org/10.1038/s41587-023-01952-z
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. https://doi.org/10.1038/s41559-023-02027-7
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. https://doi.org/10.1099/jgv.0.001840
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. https://doi.org/10.1371/journal.pbio.3001922
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. https://doi.org/10.1038/s41396-023-01453-6

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. https://doi.org/10.1101/2022.11.24.517860
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. https://doi.org/10.1007/s00705-021-05323-4
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. https://doi.org/10.1038/s41467-022-31390-5
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. https://doi.org/10.1186/s12862-022-02052-3
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. https://doi.org/10.1007/s00705-022-05516-5
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. https://doi.org/10.1099/jgv.0.001800
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. https://doi.org/10.1016/j.watres.2022.118767
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. https://doi.org/10.1016/j.cub.2021.10.038

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. https://doi.org/10.1186/s12915-021-01204-z
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. https://doi.org/10.1007/s00705-021-05205-9
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. https://doi.org/10.1016/j.coviro.2021.10.011
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. https://doi.org/10.1038/s41396-021-00900-6
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. https://doi.org/10.1016/j.mimet.2021.106208
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. https://doi.org/10.3390/v13050766
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. https://doi.org/10.1016/j.celrep.2021.109132
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. https://doi.org/10.1073/pnas.2017947118
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. https://doi.org/10.1016/j.patter.2021.100274
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. https://doi.org/10.1002/mbo3.1191
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. https://doi.org/10.1007/s00705-021-05156-1
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. https://doi.org/10.1128/mSphere.00614-21
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. https://doi.org/10.1186/s12859-021-04343-w
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. https://doi.org/10.1128/mSphere.00476-21
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. https://doi.org/10.7554/eLife.62719
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. https://doi.org/10.1111/1462-2920.15265
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. https://doi.org/10.1016/j.scitotenv.2020.142758
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. https://doi.org/10.1093/bioinformatics/btaa760
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. https://doi.org/10.1038/s41396-020-00772-2

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. https://doi.org/10.1016/b978-0-12-814515-9.00034-5
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. https://doi.org/10.1016/j.watres.2020.116416
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. https://doi.org/10.3390/v12091035
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. https://doi.org/10.1080/19490976.2020.1799733
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. https://doi.org/10.1016/j.isci.2020.101439
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 . https://doi.org/10.1007/s00705-020-04752-x
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. https://doi.org/10.1371/journal.pone.0225808
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. https://doi.org/10.1128/JVI.01559-20
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. https://doi.org/10.1007/s00705-020-04555-0
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. https://doi.org/10.1186/s40170-020-0208-9
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. https://doi.org/10.1186/s12864-020-6555-7
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. https://doi.org/10.3389/fgene.2019.01344
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. https://doi.org/10.1007/s00705-019-04477-6
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. https://doi.org/10.1186/s13059-020-1926-6
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. https://doi.org/10.1007/s00248-019-01480-x
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. https://doi.org/10.1016/j.watres.2020.115586
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. https://doi.org/10.1007/s00705-020-04577-8
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. https://doi.org/10.1038/s41431-019-0538-7
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. https://doi.org/10.1093/sysbio/syz036

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. https://doi.org/10.1186/s13059-019-1817-x
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. https://doi.org/10.1093/bioinformatics/btz369
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. https://doi.org/10.1016/j.chom.2019.08.019
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. https://doi.org/10.3389/fcimb.2019.00364
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. https://doi.org/10.3390/v11121085
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. https://doi.org/10.1007/s00705-018-04136-2
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. https://doi.org/10.1038/s41467-018-08286-4
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. https://doi.org/10.1016/j.scitotenv.2019.04.009
Tara Oceans Coordinators (2019). Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell, 177(5), 1109-1123.e14. https://doi.org/10.1016/j.cell.2019.03.040
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. https://doi.org/10.3390/v11050420
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. https://doi.org/10.1007/s00705-019-04306-w
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. https://doi.org/10.1038/s41564-019-0494-6
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. https://doi.org/10.1016/j.tim.2018.08.006
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. https://doi.org/10.1016/j.jgar.2018.08.018

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. https://doi.org/10.1101/448035
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. https://doi.org/10.1371/journal.pone.0200437
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. https://doi.org/10.1038/nbt.4306
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. https://doi.org/10.1038/s41579-018-0070-8
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. https://doi.org/10.1038/s41598-018-29763-2
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. https://doi.org/10.1007/s00705-018-3847-1
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. https://doi.org/10.1038/s41564-018-0124-8
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. https://doi.org/10.3390/v10050256
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. https://doi.org/10.1007/978-1-4939-7343-9_17
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. https://doi.org/10.1186/s12864-018-4498-z
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. https://doi.org/10.1007/s00705-018-3723-z
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. https://doi.org/10.3389/fcimb.2018.00025
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. https://doi.org/10.1038/ismej.2017.157
Computational Pan-Genomics Consortium, & Dutilh, B. E. (2018). Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19(1), 118–135. https://doi.org/10.1093/bib/bbw089

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. https://doi.org/10.3389/fmicb.2017.02132
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. https://doi.org/10.3389/fmicb.2017.01710
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. https://doi.org/10.1038/ncomms15955
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. https://doi.org/10.1136/jclinpath-2017-204592
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. https://doi.org/10.3389/fmicb.2017.00352
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. https://doi.org/10.3390/v9060134
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. https://doi.org/10.1007/s00705-016-3173-4
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. https://doi.org/10.1007/s00248-017-0929-7

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. https://doi.org/10.1201/9781315381909
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. https://doi.org/10.3389/fmicb.2016.01740
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. https://doi.org/10.1038/nature19366
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. https://doi.org/10.1007/s00203-016-1256-y
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. https://doi.org/10.3389/fmicb.2015.01481
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. https://doi.org/10.1007/s00705-015-2728-0
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. https://doi.org/10.1038/ncomms11172
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. https://doi.org/10.1093/femsre/fuv048
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. https://doi.org/10.1093/bioinformatics/btv584
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. https://doi.org/10.1111/1462-2920.13019

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. https://doi.org/10.1371/journal.pmed.1001898
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. https://doi.org/10.1186/s12859-015-0758-y
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. https://doi.org/10.1371/journal.pone.0126883
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. https://doi.org/10.1007/s10646-015-1460-6
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. https://doi.org/10.1111/his.12714
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. https://doi.org/10.1007/s00018-015-2004-1
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. https://doi.org/10.7717/peerj.1008
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. https://doi.org/10.3389/fmicb.2015.00224
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, Article 359–370. https://doi.org/10.1007/s00203-014-1071-2
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. https://doi.org/10.1128/genomeA.01415-14

2014

Wetenschappelijke publicaties

Dutilh, B. E. (2014). Metagenomic ventures into outer sequence space. Bacteriophage, 4(4), Article e979664. https://doi.org/10.4161/21597081.2014.979664
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. https://doi.org/10.1007/s00203-014-1035-6
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. https://doi.org/10.1089/omi.2014.0018
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. https://doi.org/10.7717/peerj.425
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. https://doi.org/10.1371/journal.pone.0100290
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. https://doi.org/10.1038/ncomms5498
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 . https://doi.org/10.1186/1471-2164-15-654
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. https://doi.org/10.7717/peerj.520

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. https://doi.org/10.1016/j.bpg.2013.03.008
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. https://doi.org/10.1371/journal.pone.0058404
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. https://doi.org/10.1111/j.1462-2920.2012.02774.x
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. https://doi.org/10.1093/bfgp/elt008
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. https://doi.org/10.1186/1751-0473-8-23

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. https://doi.org/10.1371/journal.pone.0037283
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. https://doi.org/10.1128/JB.00446-12
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. https://doi.org/10.1371/journal.pone.0039905
Mokili, J. L., Rohwer, F., & Dutilh, B. E. (2012). Metagenomics and future perspectives in virus discovery. Current Opinion in Virology, 2(1), 63-77. https://doi.org/10.1016/j.coviro.2011.12.004
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. https://doi.org/10.1038/nrmicro2819
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. https://doi.org/10.1074/mcp.M112.019315
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. https://doi.org/10.1111/j.1462-2920.2012.02891.x
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. https://doi.org/10.1093/bioinformatics/bts613
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. https://doi.org/10.1371/journal.pone.0050034

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 . https://doi.org/10.1186/2191-0855-1-41
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. https://doi.org/10.1093/molbev/msr059
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. https://doi.org/10.1371/journal.pone.0020447
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. https://doi.org/10.1530/JOE-10-0219
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. https://doi.org/10.1371/journal.pone.0016762
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. https://doi.org/10.1128/JB.05643-11
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. https://doi.org/10.1111/j.1758-2229.2011.00260.x

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. https://doi.org/10.1038/nature08883
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). https://doi.org/10.1371/journal.pgen.1001065

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. https://doi.org/10.1186/1471-2164-10-514
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. https://doi.org/10.1186/gb-2009-10-2-r19
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. https://doi.org/10.1093/bioinformatics/btp377

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. https://doi.org/10.1093/nar/gkn277
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. https://doi.org/10.1098/rsif.2007.1047
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. https://doi.org/10.1016/j.tig.2008.02.003
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. https://doi.org/10.1186/1471-2164-9-587
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 . https://doi.org/10.1186/1471-2164-8-190
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. https://doi.org/10.1186/1471-2164-7-22
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. https://doi.org/10.1146/annurev.micro.59.030804.121233

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. https://doi.org/10.1007/s00239-003-2575-6

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.

Direct naar

Diensten

Over de UU