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Items: 1 to 50 of 90

1.

Reply to: Caution in inferring viral strategies from abundance correlations in marine metagenomes.

Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL.

Nat Commun. 2019 Jan 30;10(1):502. doi: 10.1038/s41467-018-08286-4. No abstract available.

2.

Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018).

Siddell SG, Walker PJ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert M, Rubino L, Sabanadzovic S, Sanfaçon H, Simmonds P, Varsani A, Zerbini FM, Davison AJ.

Arch Virol. 2019 Mar;164(3):943-946. doi: 10.1007/s00705-018-04136-2.

PMID:
30663020
3.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2018 Dec 17. doi: 10.1038/nbt.4306. [Epub ahead of print]

PMID:
30556814
4.

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei.

Brito TL, Campos AB, Bastiaan von Meijenfeldt FA, Daniel JP, Ribeiro GB, Silva GGZ, Wilke DV, de Moraes DT, Dutilh BE, Meirelles PM, Trindade-Silva AE.

PLoS One. 2018 Nov 14;13(11):e0200437. doi: 10.1371/journal.pone.0200437. eCollection 2018.

5.

Molecular and Evolutionary Determinants of Bacteriophage Host Range.

de Jonge PA, Nobrega FL, Brouns SJJ, Dutilh BE.

Trends Microbiol. 2019 Jan;27(1):51-63. doi: 10.1016/j.tim.2018.08.006. Epub 2018 Sep 1. Review.

PMID:
30181062
6.

Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia.

Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A, Apriani L, Huynen MA, Ruslami R, Hill PC, van Crevel R, Alisjahbana B.

J Glob Antimicrob Resist. 2018 Aug 29;16:170-177. doi: 10.1016/j.jgar.2018.08.018. [Epub ahead of print]

PMID:
30172045
7.

Targeting mechanisms of tailed bacteriophages.

Nobrega FL, Vlot M, de Jonge PA, Dreesens LL, Beaumont HJE, Lavigne R, Dutilh BE, Brouns SJJ.

Nat Rev Microbiol. 2018 Dec;16(12):760-773. doi: 10.1038/s41579-018-0070-8. Review.

PMID:
30104690
8.

Establishing normal metabolism and differentiation in hepatocellular carcinoma cells by culturing in adult human serum.

Steenbergen R, Oti M, Ter Horst R, Tat W, Neufeldt C, Belovodskiy A, Chua TT, Cho WJ, Joyce M, Dutilh BE, Tyrrell DL.

Sci Rep. 2018 Aug 3;8(1):11685. doi: 10.1038/s41598-018-29763-2.

9.

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M.

Viruses. 2018 May 14;10(5). pii: E256. doi: 10.3390/v10050256.

10.

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

King AMQ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Davison AJ.

Arch Virol. 2018 Sep;163(9):2601-2631. doi: 10.1007/s00705-018-3847-1. Epub 2018 May 12.

PMID:
29754305
11.

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

Garza DR, van Verk MC, Huynen MA, Dutilh BE.

Nat Microbiol. 2018 Apr;3(4):456-460. doi: 10.1038/s41564-018-0124-8. Epub 2018 Mar 12.

PMID:
29531366
12.

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

Gigliucci F, von Meijenfeldt FAB, Knijn A, Michelacci V, Scavia G, Minelli F, Dutilh BE, Ahmad HM, Raangs GC, Friedrich AW, Rossen JWA, Morabito S.

Front Cell Infect Microbiol. 2018 Feb 6;8:25. doi: 10.3389/fcimb.2018.00025. eCollection 2018.

13.

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

Ruesen C, Chaidir L, van Laarhoven A, Dian S, Ganiem AR, Nebenzahl-Guimaraes H, Huynen MA, Alisjahbana B, Dutilh BE, van Crevel R.

BMC Genomics. 2018 Feb 5;19(1):122. doi: 10.1186/s12864-018-4498-z.

14.

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

Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB, Dutilh BE, Jang HB, van Zyl LJ, Klumpp J, Lobocka M, Moreno Switt AI, Rumnieks J, Edwards RA, Uchiyama J, Alfenas-Zerbini P, Petty NK, Kropinski AM, Barylski J, Gillis A, Clokie MRC, Prangishvili D, Lavigne R, Aziz RK, Duffy S, Krupovic M, Poranen MM, Knezevic P, Enault F, Tong Y, Oksanen HM, Rodney Brister J.

Arch Virol. 2018 Apr;163(4):1125-1129. doi: 10.1007/s00705-018-3723-z. Epub 2018 Jan 22. No abstract available.

PMID:
29356990
15.

Ecogenomics and Taxonomy of Cyanobacteria Phylum.

Walter JM, Coutinho FH, Dutilh BE, Swings J, Thompson FL, Thompson CC.

Front Microbiol. 2017 Nov 14;8:2132. doi: 10.3389/fmicb.2017.02132. eCollection 2017.

16.

Phage Genome Annotation Using the RAST Pipeline.

McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R.

Methods Mol Biol. 2018;1681:231-238. doi: 10.1007/978-1-4939-7343-9_17.

PMID:
29134599
17.

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

Arkhipova K, Skvortsov T, Quinn JP, McGrath JW, Allen CC, Dutilh BE, McElarney Y, Kulakov LA.

ISME J. 2018 Jan;12(1):199-211. doi: 10.1038/ismej.2017.157. Epub 2017 Oct 13.

18.

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

Dutilh BE, Reyes A, Hall RJ, Whiteson KL.

Front Microbiol. 2017 Sep 8;8:1710. doi: 10.3389/fmicb.2017.01710. eCollection 2017. No abstract available.

19.

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

Couto Furtado Albuquerque M, van Herwaarden Y, Kortman GAM, Dutilh BE, Bisseling T, Boleij A.

J Clin Pathol. 2017 Nov;70(11):994-996. doi: 10.1136/jclinpath-2017-204592. Epub 2017 Aug 22. No abstract available.

20.

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

Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL.

Nat Commun. 2017 Jul 5;8:15955. doi: 10.1038/ncomms15955.

21.

Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses.

Maat DS, Biggs T, Evans C, van Bleijswijk JDL, van der Wel NN, Dutilh BE, Brussaard CPD.

Viruses. 2017 Jun 2;9(6). pii: E134. doi: 10.3390/v9060134.

22.

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

Motlagh AM, Bhattacharjee AS, Coutinho FH, Dutilh BE, Casjens SR, Goel RK.

Front Microbiol. 2017 Mar 3;8:352. doi: 10.3389/fmicb.2017.00352. eCollection 2017.

23.

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.

Speth DR, Lagkouvardos I, Wang Y, Qian PY, Dutilh BE, Jetten MSM.

Microb Ecol. 2017 Jul;74(1):1-5. doi: 10.1007/s00248-017-0929-7. Epub 2017 Jan 10.

24.

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

Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MR, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH.

Arch Virol. 2017 Apr;162(4):1153-1157. doi: 10.1007/s00705-016-3173-4. Epub 2016 Dec 31. No abstract available.

PMID:
28040838
25.

Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture.

Gambelli L, Cremers G, Mesman R, Guerrero S, Dutilh BE, Jetten MS, Op den Camp HJ, van Niftrik L.

Front Microbiol. 2016 Nov 8;7:1740. eCollection 2016.

26.

Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features.

Coutinho FH, Dutilh BE, Thompson CC, Thompson FL.

Arch Microbiol. 2016 Dec;198(10):973-986. Epub 2016 Jun 23.

PMID:
27339259
27.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D; Tara Oceans Coordinators, Bork P, Acinas SG, Wincker P, Sullivan MB.

Nature. 2016 Sep 29;537(7622):689-693. doi: 10.1038/nature19366. Epub 2016 Sep 21.

28.

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

Speth DR, In 't Zandt MH, Guerrero-Cruz S, Dutilh BE, Jetten MS.

Nat Commun. 2016 Mar 31;7:11172. doi: 10.1038/ncomms11172.

29.

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

Kortman GA, Dutilh BE, Maathuis AJ, Engelke UF, Boekhorst J, Keegan KP, Nielsen FG, Betley J, Weir JC, Kingsbury Z, Kluijtmans LA, Swinkels DW, Venema K, Tjalsma H.

Front Microbiol. 2016 Jan 6;6:1481. doi: 10.3389/fmicb.2015.01481. eCollection 2015.

30.

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

Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK, Sullivan MB, Rumnieks J, Prangishvili D, Lavigne R, Kropinski AM, Klumpp J, Gillis A, Enault F, Edwards RA, Duffy S, Clokie MR, Barylski J, Ackermann HW, Kuhn JH.

Arch Virol. 2016 Apr;161(4):1095-9. doi: 10.1007/s00705-015-2728-0. Epub 2016 Jan 5. No abstract available.

PMID:
26733293
31.

Computational approaches to predict bacteriophage-host relationships.

Edwards RA, McNair K, Faust K, Raes J, Dutilh BE.

FEMS Microbiol Rev. 2016 Mar;40(2):258-72. doi: 10.1093/femsre/fuv048. Epub 2015 Dec 9. Review.

32.

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

Bezemer D, Cori A, Ratmann O, van Sighem A, Hermanides HS, Dutilh BE, Gras L, Rodrigues Faria N, van den Hengel R, Duits AJ, Reiss P, de Wolf F, Fraser C; ATHENA observational cohort.

PLoS Med. 2015 Nov 3;12(11):e1001898; discussion e1001898. doi: 10.1371/journal.pmed.1001898. eCollection 2015 Nov.

33.

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

Silva GG, Green KT, Dutilh BE, Edwards RA.

Bioinformatics. 2016 Feb 1;32(3):354-61. doi: 10.1093/bioinformatics/btv584. Epub 2015 Oct 9.

34.

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

Hou Q, Dutilh BE, Huynen MA, Heringa J, Feenstra KA.

BMC Bioinformatics. 2015 Oct 8;16:325. doi: 10.1186/s12859-015-0758-y.

35.

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

Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL.

Environ Microbiol. 2016 Jan;18(1):273-87. doi: 10.1111/1462-2920.13019. Epub 2015 Oct 21.

PMID:
26279094
36.

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

Garza DR, Dutilh BE.

Cell Mol Life Sci. 2015 Nov;72(22):4287-308. doi: 10.1007/s00018-015-2004-1. Epub 2015 Aug 9. Review.

37.

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

Coutinho FH, Meirelles PM, Moreira AP, Paranhos RP, Dutilh BE, Thompson FL.

PeerJ. 2015 Jun 16;3:e1008. doi: 10.7717/peerj.1008. eCollection 2015.

38.

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

Matthews TD, Schmieder R, Silva GG, Busch J, Cassman N, Dutilh BE, Green D, Matlock B, Heffernan B, Olsen GJ, Farris Hanna L, Schifferli DM, Maloy S, Dinsdale EA, Edwards RA.

PLoS One. 2015 Jun 3;10(6):e0126883. doi: 10.1371/journal.pone.0126883. eCollection 2015.

39.

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

Busch J, Nascimento JR, Magalhães AC, Dutilh BE, Dinsdale E.

Ecotoxicology. 2015 Jul;24(5):1131-40. doi: 10.1007/s10646-015-1460-6. Epub 2015 Apr 18.

40.

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

Appenzeller S, Gilissen C, Rijntjes J, Tops BB, Kastner-van Raaij A, Hebeda KM, Nissen L, Dutilh BE, van Krieken JH, Groenen PJ.

Histopathology. 2015 Dec;67(6):843-58. doi: 10.1111/his.12714. Epub 2015 Jun 26.

PMID:
25891511
41.

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

Hall RJ, Draper JL, Nielsen FG, Dutilh BE.

Front Microbiol. 2015 Mar 25;6:224. doi: 10.3389/fmicb.2015.00224. eCollection 2015.

42.

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

Speth DR, Russ L, Kartal B, Op den Camp HJ, Dutilh BE, Jetten MS.

Genome Announc. 2015 Jan 8;3(1). pii: e01415-14. doi: 10.1128/genomeA.01415-14.

43.

Microbial taxonomy in the post-genomic era: rebuilding from scratch?

Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL.

Arch Microbiol. 2015 Apr;197(3):359-70. doi: 10.1007/s00203-014-1071-2. Epub 2014 Dec 23.

PMID:
25533848
44.

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

Lim YW, Cuevas DA, Silva GG, Aguinaldo K, Dinsdale EA, Haas AF, Hatay M, Sanchez SE, Wegley-Kelly L, Dutilh BE, Harkins TT, Lee CC, Tom W, Sandin SA, Smith JE, Zgliczynski B, Vermeij MJ, Rohwer F, Edwards RA.

PeerJ. 2014 Aug 19;2:e520. doi: 10.7717/peerj.520. eCollection 2014.

45.

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

Dutilh BE, Thompson CC, Vicente AC, Marin MA, Lee C, Silva GG, Schmieder R, Andrade BG, Chimetto L, Cuevas D, Garza DR, Okeke IN, Aboderin AO, Spangler J, Ross T, Dinsdale EA, Thompson FL, Harkins TT, Edwards RA.

BMC Genomics. 2014 Aug 5;15:654. doi: 10.1186/1471-2164-15-654.

46.

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

Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA.

Nat Commun. 2014 Jul 24;5:4498. doi: 10.1038/ncomms5498.

47.

Cell wall modifications during conidial maturation of the human pathogenic fungus Pseudallescheria boydii.

Ghamrawi S, Rénier G, Saulnier P, Cuenot S, Zykwinska A, Dutilh BE, Thornton C, Faure S, Bouchara JP.

PLoS One. 2014 Jun 20;9(6):e100290. doi: 10.1371/journal.pone.0100290. eCollection 2014.

48.

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

Silva GG, Cuevas DA, Dutilh BE, Edwards RA.

PeerJ. 2014 Jun 5;2:e425. doi: 10.7717/peerj.425. eCollection 2014.

49.

Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.

ElRakaiby M, Dutilh BE, Rizkallah MR, Boleij A, Cole JN, Aziz RK.

OMICS. 2014 Jul;18(7):402-14. doi: 10.1089/omi.2014.0018. Epub 2014 May 2. Review.

50.

Metagenomic ventures into outer sequence space.

Dutilh BE.

Bacteriophage. 2014 Dec 15;4(4):e979664. eCollection 2014.

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