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Items: 1 to 50 of 65

1.

Introducing SPeDE: High-Throughput Dereplication and Accurate Determination of Microbial Diversity from Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry Data.

Dumolin C, Aerts M, Verheyde B, Schellaert S, Vandamme T, Van der Jeugt F, De Canck E, Cnockaert M, Wieme AD, Cleenwerck I, Peiren J, Dawyndt P, Vandamme P, Carlier A.

mSystems. 2019 Sep 10;4(5). pii: e00437-19. doi: 10.1128/mSystems.00437-19.

2.

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome.

De Tender C, Mesuere B, Van der Jeugt F, Haegeman A, Ruttink T, Vandecasteele B, Dawyndt P, Debode J, Kuramae EE.

Sci Rep. 2019 Jul 9;9(1):9890. doi: 10.1038/s41598-019-46106-x.

3.

A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis.

Debyser G, Aerts M, Van Hecke P, Mesuere B, Duytschaever G, Dawyndt P, De Boeck K, Vandamme P, Devreese B.

Adv Exp Med Biol. 2019;1073:137-160. doi: 10.1007/978-3-030-12298-0_6.

PMID:
31236842
4.

Unipept 4.0: Functional Analysis of Metaproteome Data.

Gurdeep Singh R, Tanca A, Palomba A, Van der Jeugt F, Verschaffelt P, Uzzau S, Martens L, Dawyndt P, Mesuere B.

J Proteome Res. 2019 Feb 1;18(2):606-615. doi: 10.1021/acs.jproteome.8b00716. Epub 2018 Dec 4.

PMID:
30465426
5.

Multifunctional sequence-defined macromolecules for chemical data storage.

Martens S, Landuyt A, Espeel P, Devreese B, Dawyndt P, Du Prez F.

Nat Commun. 2018 Oct 26;9(1):4451. doi: 10.1038/s41467-018-06926-3.

6.

Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea.

De Tender C, Devriese LI, Haegeman A, Maes S, Vangeyte J, Cattrijsse A, Dawyndt P, Ruttink T.

Environ Sci Technol. 2017 Jul 5;51(13):7350-7360. doi: 10.1021/acs.est.7b00697. Epub 2017 Jun 19.

PMID:
28562015
7.

High-throughput metaproteomics data analysis with Unipept: A tutorial.

Mesuere B, Van der Jeugt F, Willems T, Naessens T, Devreese B, Martens L, Dawyndt P.

J Proteomics. 2018 Jan 16;171:11-22. doi: 10.1016/j.jprot.2017.05.022. Epub 2017 May 24.

PMID:
28552653
8.

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection.

De Tender C, Haegeman A, Vandecasteele B, Clement L, Cremelie P, Dawyndt P, Maes M, Debode J.

Front Microbiol. 2016 Dec 22;7:2062. doi: 10.3389/fmicb.2016.02062. eCollection 2016.

9.

Global alternans instability and its effect on non-linear wave propagation: dynamical Wenckebach block and self terminating spiral waves.

Vandersickel N, Defauw A, Dawyndt P, Panfilov AV.

Sci Rep. 2016 Jul 7;6:29397. doi: 10.1038/srep29397.

10.

The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics.

Mesuere B, Van der Jeugt F, Devreese B, Vandamme P, Dawyndt P.

Proteomics. 2016 Sep;16(17):2313-8. doi: 10.1002/pmic.201600023. Epub 2016 Aug 16.

PMID:
27380722
11.

Unipept web services for metaproteomics analysis.

Mesuere B, Willems T, Van der Jeugt F, Devreese B, Vandamme P, Dawyndt P.

Bioinformatics. 2016 Jun 1;32(11):1746-8. doi: 10.1093/bioinformatics/btw039. Epub 2016 Jan 27.

PMID:
26819472
12.

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis.

Debyser G, Mesuere B, Clement L, Van de Weygaert J, Van Hecke P, Duytschaever G, Aerts M, Dawyndt P, De Boeck K, Vandamme P, Devreese B.

J Cyst Fibros. 2016 Mar;15(2):242-50. doi: 10.1016/j.jcf.2015.08.003. Epub 2015 Aug 30.

13.

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea.

De Tender CA, Devriese LI, Haegeman A, Maes S, Ruttink T, Dawyndt P.

Environ Sci Technol. 2015 Aug 18;49(16):9629-38. doi: 10.1021/acs.est.5b01093. Epub 2015 Aug 6.

PMID:
26204244
14.

A Long Fragment Aligner called ALFALFA.

Vyverman M, Baets BD, Fack V, Dawyndt P.

BMC Bioinformatics. 2015 May 15;16:159. doi: 10.1186/s12859-015-0533-0.

15.

The Unipept metaproteomics analysis pipeline.

Mesuere B, Debyser G, Aerts M, Devreese B, Vandamme P, Dawyndt P.

Proteomics. 2015 Apr;15(8):1437-42. doi: 10.1002/pmic.201400361. Epub 2015 Feb 11.

PMID:
25477242
16.

Small size ionic heterogeneities in the human heart can attract rotors.

Defauw A, Vandersickel N, Dawyndt P, Panfilov AV.

Am J Physiol Heart Circ Physiol. 2014 Nov 15;307(10):H1456-68. doi: 10.1152/ajpheart.00410.2014. Epub 2014 Sep 12.

17.

Genomic standards consortium projects.

Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.

Stand Genomic Sci. 2014 Feb 15;9(3):599-601. doi: 10.4056/sigs.5559680. eCollection 2014 Jun 15.

18.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP.

PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014 Aug.

19.

Initiation and dynamics of a spiral wave around an ionic heterogeneity in a model for human cardiac tissue.

Defauw A, Dawyndt P, Panfilov AV.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec;88(6):062703. Epub 2013 Dec 3.

PMID:
24483482
20.

StrainInfo introduces electronic passports for microorganisms.

Verslyppe B, De Smet W, De Baets B, De Vos P, Dawyndt P.

Syst Appl Microbiol. 2014 Feb;37(1):42-50. doi: 10.1016/j.syapm.2013.11.002. Epub 2013 Dec 8.

PMID:
24321274
21.

Action potential duration heterogeneity of cardiac tissue can be evaluated from cell properties using Gaussian Green's function approach.

Defauw A, Kazbanov IV, Dierckx H, Dawyndt P, Panfilov AV.

PLoS One. 2013 Nov 18;8(11):e79607. doi: 10.1371/journal.pone.0079607. eCollection 2013.

22.

Filtering and ranking techniques for automated selection of high-quality 16S rRNA gene sequences.

De Smet W, De Loof K, De Vos P, Dawyndt P, De Baets B.

Syst Appl Microbiol. 2013 Dec;36(8):549-59. doi: 10.1016/j.syapm.2013.09.001. Epub 2013 Oct 22.

PMID:
24161830
23.

RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011.

Robbins RJ, Cochrane G, Davies N, Dawyndt P, Kottmann R, Krishtalka LK, Morrison N, Tuama EÓ, San Gil I, Wooley J.

Stand Genomic Sci. 2012 Oct 10;7(1):153-8. doi: 10.4056/sigs.3146509. Epub 2012 Sep 24.

24.

RCN4GSC Meeting Report: Initiating a Testbed for Managing Data at the Interface of Biodiversity and Genomics/Metagenomics, May 2011.

Robbins RJ, Beach J, Blum S, Dawyndt P, Deck J, Kottmann R, Morrison N, Tuama EÓ, San Gil I, Vieglas D, Wieczorek J, Wooley J.

Stand Genomic Sci. 2012 Oct 10;7(1):171-4. doi: 10.4056/sigs.3176515. Epub 2012 Sep 28.

25.

essaMEM: finding maximal exact matches using enhanced sparse suffix arrays.

Vyverman M, De Baets B, Fack V, Dawyndt P.

Bioinformatics. 2013 Mar 15;29(6):802-4. doi: 10.1093/bioinformatics/btt042. Epub 2013 Jan 24.

PMID:
23349213
26.

Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples.

Mesuere B, Devreese B, Debyser G, Aerts M, Vandamme P, Dawyndt P.

J Proteome Res. 2012 Dec 7;11(12):5773-80. doi: 10.1021/pr300576s. Epub 2012 Nov 26.

PMID:
23153116
27.

Prospects and limitations of full-text index structures in genome analysis.

Vyverman M, De Baets B, Fack V, Dawyndt P.

Nucleic Acids Res. 2012 Aug;40(15):6993-7015. doi: 10.1093/nar/gks408. Epub 2012 May 13. Review.

28.

The Genomic Standards Consortium.

Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J.

PLoS Biol. 2011 Jun;9(6):e1001088. doi: 10.1371/journal.pbio.1001088. Epub 2011 Jun 21.

29.

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

Morrison N, Hancock D, Hirschman L, Dawyndt P, Verslyppe B, Kyrpides N, Kottmann R, Yilmaz P, Glöckner FO, Grethe J, Booth T, Sterk P, Nenadic G, Field D.

Stand Genomic Sci. 2011 Apr 29;4(2):286-92. doi: 10.4056/sigs.1344279.

30.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

31.

Make Histri: reconstructing the exchange history of bacterial and archaeal type strains.

Verslyppe B, De Smet W, De Baets B, De Vos P, Dawyndt P.

Syst Appl Microbiol. 2011 Jul;34(5):328-36. doi: 10.1016/j.syapm.2011.01.004. Epub 2011 Apr 22.

PMID:
21514082
32.

Classification and identification of the Burkholderia cepacia complex: Past, present and future.

Vandamme P, Dawyndt P.

Syst Appl Microbiol. 2011 Apr;34(2):87-95. doi: 10.1016/j.syapm.2010.10.002. Epub 2011 Jan 22. Review.

PMID:
21257278
33.

Microbiological Common Language (MCL): a standard for electronic information exchange in the Microbial Commons.

Verslyppe B, Kottmann R, De Smet W, De Baets B, De Vos P, Dawyndt P.

Res Microbiol. 2010 Jul-Aug;161(6):439-45. doi: 10.1016/j.resmic.2010.02.005. Epub 2010 Mar 6.

PMID:
20211251
34.

From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification.

Slabbinck B, Waegeman W, Dawyndt P, De Vos P, De Baets B.

BMC Bioinformatics. 2010 Jan 30;11:69. doi: 10.1186/1471-2105-11-69.

35.

Towards large-scale FAME-based bacterial species identification using machine learning techniques.

Slabbinck B, De Baets B, Dawyndt P, De Vos P.

Syst Appl Microbiol. 2009 May;32(3):163-76. doi: 10.1016/j.syapm.2009.01.003. Epub 2009 Feb 23.

PMID:
19237256
36.

Bayesian clustering of fuzzy feature vectors using a quasi-likelihood approach.

Marttinen P, Tang J, De Baets B, Dawyndt P, Corander J.

IEEE Trans Pattern Anal Mach Intell. 2009 Jan;31(1):74-85. doi: 10.1109/TPAMI.2008.53.

PMID:
19029547
37.

Matrix-assisted laser desorption ionisation-time-of of-flight mass spectrometry of intact cells allows rapid identification of Burkholderia cepacia complex.

Vanlaere E, Sergeant K, Dawyndt P, Kallow W, Erhard M, Sutton H, Dare D, Devreese B, Samyn B, Vandamme P.

J Microbiol Methods. 2008 Oct;75(2):279-86. doi: 10.1016/j.mimet.2008.06.016. Epub 2008 Jun 25.

PMID:
18627778
38.

Meeting report: the fifth Genomic Standards Consortium (GSC) workshop.

Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L; Genomic Standards Consortium.

OMICS. 2008 Jun;12(2):109-13. doi: 10.1089/omi.2008.A3B3.

PMID:
18564915
39.

Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.

Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T.

OMICS. 2008 Jun;12(2):101-8. doi: 10.1089/omi.2008.0014.

PMID:
18564914
40.

Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers.

Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P; Genomic Standards Consortium.

OMICS. 2008 Jun;12(2):123-7. doi: 10.1089/omi.2008.0020.

PMID:
18479205
41.

The minimum information about a genome sequence (MIGS) specification.

Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.

Nat Biotechnol. 2008 May;26(5):541-7. doi: 10.1038/nbt1360.

42.

Genus-wide Bacillus species identification through proper artificial neural network experiments on fatty acid profiles.

Slabbinck B, De Baets B, Dawyndt P, De Vos P.

Antonie Van Leeuwenhoek. 2008 Aug;94(2):187-98. doi: 10.1007/s10482-008-9229-z. Epub 2008 Mar 6.

PMID:
18322819
43.

TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers.

Slabbinck B, Dawyndt P, Martens M, De Vos P, De Baets B.

Bioinformatics. 2008 Mar 15;24(6):866-7. doi: 10.1093/bioinformatics/btn031. Epub 2008 Jan 28.

PMID:
18227116
44.

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium).

Martens M, Dawyndt P, Coopman R, Gillis M, De Vos P, Willems A.

Int J Syst Evol Microbiol. 2008 Jan;58(Pt 1):200-14. doi: 10.1099/ijs.0.65392-0.

PMID:
18175710
45.

Identification of lactobacilli by pheS and rpoA gene sequence analyses.

Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I, Vancanneyt M, Swings J.

Int J Syst Evol Microbiol. 2007 Dec;57(Pt 12):2777-89.

PMID:
18048724
46.

Ecological diversification in the Bacillus cereus Group.

Guinebretière MH, Thompson FL, Sorokin A, Normand P, Dawyndt P, Ehling-Schulz M, Svensson B, Sanchis V, Nguyen-The C, Heyndrickx M, De Vos P.

Environ Microbiol. 2008 Apr;10(4):851-65. Epub 2007 Nov 25.

PMID:
18036180
47.

Fame-based Bacillus species identification using artificial neural networks.

Slabbinck B, Dawyndt P, De Baets B, De Vos P.

Commun Agric Appl Biol Sci. 2006;71(1):259-62. No abstract available.

PMID:
17191518
48.

Stepping stones towards a new prokaryotic taxonomy.

Gevers D, Dawyndt P, Vandamme P, Willems A, Vancanneyt M, Swings J, De Vos P.

Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1911-6. Review.

49.

Raman microspectroscopy as an identification tool within the phylogenetically homogeneous 'Bacillus subtilis' group.

Hutsebaut D, Vandroemme J, Heyrman J, Dawyndt P, Vandenabeele P, Moens L, de Vos P.

Syst Appl Microbiol. 2006 Dec;29(8):650-60. Epub 2006 Mar 24.

PMID:
16564151
50.

Mining fatty acid databases for detection of novel compounds in aerobic bacteria.

Dawyndt P, Vancanneyt M, Snauwaert C, De Baets B, De Meyer H, Swings J.

J Microbiol Methods. 2006 Sep;66(3):410-33. Epub 2006 Mar 7.

PMID:
16522336

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