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Items: 1 to 50 of 146

1.

Identification of novel genes involved in acetic acid tolerance of Saccharomyces cerevisiae using pooled-segregant RNA sequencing.

Fernández-Niño M, Pulido S, Stefanoska D, Pérez C, González-Ramos D, van Maris AJA, Marchal K, Nevoigt E, Swinnen S.

FEMS Yeast Res. 2018 Dec 1;18(8). doi: 10.1093/femsyr/foy100.

PMID:
30219856
2.

1-((2,4-Dichlorophenethyl)Amino)-3-Phenoxypropan-2-ol Kills Pseudomonas aeruginosa through Extensive Membrane Damage.

Defraine V, Liebens V, Loos E, Swings T, Weytjens B, Fierro C, Marchal K, Sharkey L, O'Neill AJ, Corbau R, Marchand A, Chaltin P, Fauvart M, Michiels J.

Front Microbiol. 2018 Feb 8;9:129. doi: 10.3389/fmicb.2018.00129. eCollection 2018.

3.

Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:.

Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ.

PLoS One. 2018 Feb 6;13(2):e0192504. doi: 10.1371/journal.pone.0192504. eCollection 2018.

4.

Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics.

Albers P, Weytjens B, De Mot R, Marchal K, Springael D.

Microbiologyopen. 2018 Apr;7(2):e00559. doi: 10.1002/mbo3.559. Epub 2018 Jan 3.

5.

Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium: consequences for the interspecies consortium metabolic model.

Albers P, Lood C, Özturk B, Horemans B, Lavigne R, van Noort V, De Mot R, Marchal K, Sanchez-Rodriguez A, Springael D.

Environ Microbiol. 2018 Jan;20(1):85-96. doi: 10.1111/1462-2920.13994. Epub 2017 Dec 15.

PMID:
29124862
6.

Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations.

Swings T, Weytjens B, Schalck T, Bonte C, Verstraeten N, Michiels J, Marchal K.

Mol Biol Evol. 2017 Nov 1;34(11):2927-2943. doi: 10.1093/molbev/msx228.

7.

Molecular Subtyping of Salmonella Typhimurium with Multiplex Oligonucleotide Ligation-PCR (MOL-PCR).

Wuyts V, Mattheus W, Roosens NHC, Marchal K, Bertrand S, De Keersmaecker SCJ.

Methods Mol Biol. 2017;1616:39-69. doi: 10.1007/978-1-4939-7037-7_3.

PMID:
28600761
8.

The evolutionary significance of polyploidy.

Van de Peer Y, Mizrachi E, Marchal K.

Nat Rev Genet. 2017 Jul;18(7):411-424. doi: 10.1038/nrg.2017.26. Epub 2017 May 15. Review.

PMID:
28502977
9.

Effect of genomic distance on coexpression of coregulated genes in E. coli.

Pannier L, Merino E, Marchal K, Collado-Vides J.

PLoS One. 2017 Apr 18;12(4):e0174887. doi: 10.1371/journal.pone.0174887. eCollection 2017.

10.

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing.

Mizrachi E, Verbeke L, Christie N, Fierro AC, Mansfield SD, Davis MF, Gjersing E, Tuskan GA, Van Montagu M, Van de Peer Y, Marchal K, Myburg AA.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1195-1200. doi: 10.1073/pnas.1620119114. Epub 2017 Jan 17.

11.

Early differences in islets from prediabetic NOD mice: combined microarray and proteomic analysis.

Crèvecoeur I, Gudmundsdottir V, Vig S, Marques Câmara Sodré F, D'Hertog W, Fierro AC, Van Lommel L, Gysemans C, Marchal K, Waelkens E, Schuit F, Brunak S, Overbergh L, Mathieu C.

Diabetologia. 2017 Mar;60(3):475-489. doi: 10.1007/s00125-016-4191-1. Epub 2017 Jan 12.

PMID:
28078386
12.

Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment.

Yao Y, Storme V, Marchal K, Van de Peer Y.

PeerJ. 2016 Dec 21;4:e2812. doi: 10.7717/peerj.2812. eCollection 2016.

13.

Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains.

Crauwels S, Van Opstaele F, Jaskula-Goiris B, Steensels J, Verreth C, Bosmans L, Paulussen C, Herrera-Malaver B, de Jonge R, De Clippeleer J, Marchal K, De Samblanx G, Willems KA, Verstrepen KJ, Aerts G, Lievens B.

FEMS Yeast Res. 2017 Jan;17(1). pii: fow105. doi: 10.1093/femsyr/fow105. Epub 2016 Dec 11.

PMID:
27956491
14.

SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis.

Pulido-Tamayo S, Weytjens B, De Maeyer D, Marchal K.

Sci Rep. 2016 Nov 3;6:36257. doi: 10.1038/srep36257.

15.

Simultaneous discovery of cancer subtypes and subtype features by molecular data integration.

Le Van T, van Leeuwen M, Carolina Fierro A, De Maeyer D, Van den Eynden J, Verbeke L, De Raedt L, Marchal K, Nijssen S.

Bioinformatics. 2016 Sep 1;32(17):i445-i454. doi: 10.1093/bioinformatics/btw434.

PMID:
27587661
16.

Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa.

Gerits E, Blommaert E, Lippell A, O'Neill AJ, Weytjens B, De Maeyer D, Fierro AC, Marchal K, Marchand A, Chaltin P, Spincemaille P, De Brucker K, Thevissen K, Cammue BP, Swings T, Liebens V, Fauvart M, Verstraeten N, Michiels J.

PLoS One. 2016 May 11;11(5):e0155139. doi: 10.1371/journal.pone.0155139. eCollection 2016.

17.

EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis.

Pulido-Tamayo S, Duitama J, Marchal K.

Nucleic Acids Res. 2016 Jul 8;44(W1):W142-6. doi: 10.1093/nar/gkw298. Epub 2016 Apr 21.

18.

FabR regulates Salmonella biofilm formation via its direct target FabB.

Hermans K, Roberfroid S, Thijs IM, Kint G, De Coster D, Marchal K, Vanderleyden J, De Keersmaecker SC, Steenackers HP.

BMC Genomics. 2016 Mar 22;17:253. doi: 10.1186/s12864-016-2387-x.

19.

Network-Based Analysis of eQTL Data to Prioritize Driver Mutations.

De Maeyer D, Weytjens B, De Raedt L, Marchal K.

Genome Biol Evol. 2016 Jan 23;8(3):481-94. doi: 10.1093/gbe/evw010.

20.

Optimized MOL-PCR for Characterization of Microbial Pathogens.

Wuyts V, Roosens NH, Bertrand S, Marchal K, De Keersmaecker SC.

Curr Protoc Cytom. 2016 Jan 6;75:13.15.1-13.15.15. doi: 10.1002/0471142956.cy1315s75.

PMID:
26742655
21.

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.

Voordeckers K, Kominek J, Das A, Espinosa-Cantú A, De Maeyer D, Arslan A, Van Pee M, van der Zande E, Meert W, Yang Y, Zhu B, Marchal K, DeLuna A, Van Noort V, Jelier R, Verstrepen KJ.

PLoS Genet. 2015 Nov 6;11(11):e1005635. doi: 10.1371/journal.pgen.1005635. eCollection 2015 Nov.

22.

Whole Genome Sequence Analysis of Salmonella Enteritidis PT4 Outbreaks from a National Reference Laboratory's Viewpoint.

Wuyts V, Denayer S, Roosens NH, Mattheus W, Bertrand S, Marchal K, Dierick K, De Keersmaecker SC.

PLoS Curr. 2015 Sep 11;7. pii: ecurrents.outbreaks.aa5372d90826e6cb0136ff66bb7a62fc. doi: 10.1371/currents.outbreaks.aa5372d90826e6cb0136ff66bb7a62fc.

23.

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration.

Verbeke LP, Van den Eynden J, Fierro AC, Demeester P, Fostier J, Marchal K.

PLoS One. 2015 Jul 28;10(7):e0133503. doi: 10.1371/journal.pone.0133503. eCollection 2015.

24.

A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium.

Wuyts V, Mattheus W, Roosens NH, Marchal K, Bertrand S, De Keersmaecker SC.

Appl Microbiol Biotechnol. 2015 Oct;99(19):8137-49. doi: 10.1007/s00253-015-6831-7. Epub 2015 Jul 25.

25.

Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains.

Crauwels S, Van Assche A, de Jonge R, Borneman AR, Verreth C, Troels P, De Samblanx G, Marchal K, Van de Peer Y, Willems KA, Verstrepen KJ, Curtin CD, Lievens B.

Appl Microbiol Biotechnol. 2015 Nov;99(21):9123-34. doi: 10.1007/s00253-015-6769-9. Epub 2015 Jul 2.

PMID:
26135985
26.

Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance.

Verstraeten N, Knapen WJ, Kint CI, Liebens V, Van den Bergh B, Dewachter L, Michiels JE, Fu Q, David CC, Fierro AC, Marchal K, Beirlant J, Versées W, Hofkens J, Jansen M, Fauvart M, Michiels J.

Mol Cell. 2015 Jul 2;59(1):9-21. doi: 10.1016/j.molcel.2015.05.011. Epub 2015 Jun 4.

27.

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations.

Pulido-Tamayo S, Sánchez-Rodríguez A, Swings T, Van den Bergh B, Dubey A, Steenackers H, Michiels J, Fostier J, Marchal K.

Nucleic Acids Res. 2015 Sep 18;43(16):e105. doi: 10.1093/nar/gkv478. Epub 2015 May 18.

28.

SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering.

Van den Eynden J, Fierro AC, Verbeke LP, Marchal K.

BMC Bioinformatics. 2015 Apr 23;16:125. doi: 10.1186/s12859-015-0555-7.

29.

PheNetic: network-based interpretation of molecular profiling data.

De Maeyer D, Weytjens B, Renkens J, De Raedt L, Marchal K.

Nucleic Acids Res. 2015 Jul 1;43(W1):W244-50. doi: 10.1093/nar/gkv347. Epub 2015 Apr 15.

30.

Guidelines for optimisation of a multiplex oligonucleotide ligation-PCR for characterisation of microbial pathogens in a microsphere suspension array.

Wuyts V, Roosens NH, Bertrand S, Marchal K, De Keersmaecker SC.

Biomed Res Int. 2015;2015:790170. doi: 10.1155/2015/790170. Epub 2015 Feb 3.

31.

Vitamin D3 Induces Tolerance in Human Dendritic Cells by Activation of Intracellular Metabolic Pathways.

Ferreira GB, Vanherwegen AS, Eelen G, Gutiérrez AC, Van Lommel L, Marchal K, Verlinden L, Verstuyf A, Nogueira T, Georgiadou M, Schuit F, Eizirik DL, Gysemans C, Carmeliet P, Overbergh L, Mathieu C.

Cell Rep. 2015 Feb 4. pii: S2211-1247(15)00026-1. doi: 10.1016/j.celrep.2015.01.013. [Epub ahead of print]

32.

Ultraviolet-B radiation stimulates downward leaf curling in Arabidopsis thaliana.

Fierro AC, Leroux O, De Coninck B, Cammue BP, Marchal K, Prinsen E, Van Der Straeten D, Vandenbussche F.

Plant Physiol Biochem. 2015 Aug;93:9-17. doi: 10.1016/j.plaphy.2014.12.012. Epub 2014 Dec 17.

PMID:
25542780
33.

Genome-scale co-expression network comparison across Escherichia coli and Salmonella enterica serovar Typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles.

Zarrineh P, Sánchez-Rodríguez A, Hosseinkhan N, Narimani Z, Marchal K, Masoudi-Nejad A.

PLoS One. 2014 Aug 7;9(8):e102871. doi: 10.1371/journal.pone.0102871. eCollection 2014.

34.

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks.

Mushthofa M, Torres G, Van de Peer Y, Marchal K, De Cock M.

Bioinformatics. 2014 Nov 1;30(21):3086-92. doi: 10.1093/bioinformatics/btu481. Epub 2014 Jul 15.

35.

A network-based approach to identify substrate classes of bacterial glycosyltransferases.

Sánchez-Rodríguez A, Tytgat HL, Winderickx J, Vanderleyden J, Lebeer S, Marchal K.

BMC Genomics. 2014 May 8;15:349. doi: 10.1186/1471-2164-15-349.

36.

Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing.

Crauwels S, Zhu B, Steensels J, Busschaert P, De Samblanx G, Marchal K, Willems KA, Verstrepen KJ, Lievens B.

Appl Environ Microbiol. 2014 Jul;80(14):4398-413. doi: 10.1128/AEM.00601-14. Epub 2014 May 9.

37.

Photoreceptor-mediated bending towards UV-B in Arabidopsis.

Vandenbussche F, Tilbrook K, Fierro AC, Marchal K, Poelman D, Van Der Straeten D, Ulm R.

Mol Plant. 2014 Jun;7(6):1041-1052. doi: 10.1093/mp/ssu039. Epub 2014 Apr 7.

38.

A putative de-N-acetylase of the PIG-L superfamily affects fluoroquinolone tolerance in Pseudomonas aeruginosa.

Liebens V, Defraine V, Van der Leyden A, De Groote VN, Fierro C, Beullens S, Verstraeten N, Kint C, Jans A, Frangipani E, Visca P, Marchal K, Versées W, Fauvart M, Michiels J.

Pathog Dis. 2014 Jun;71(1):39-54. doi: 10.1111/2049-632X.12174. Epub 2014 Apr 24.

PMID:
24692291
39.

Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast.

Duitama J, Sánchez-Rodríguez A, Goovaerts A, Pulido-Tamayo S, Hubmann G, Foulquié-Moreno MR, Thevelein JM, Verstrepen KJ, Marchal K.

BMC Genomics. 2014 Mar 19;15:207. doi: 10.1186/1471-2164-15-207.

40.

Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments.

Yao Y, Marchal K, Van de Peer Y.

PLoS One. 2014 Mar 5;9(3):e90695. doi: 10.1371/journal.pone.0090695. eCollection 2014.

41.

Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia.

Ishchukov I, Wu Y, Van Puyvelde S, Vanderleyden J, Marchal K.

BMC Microbiol. 2014 Jan 27;14:14. doi: 10.1186/1471-2180-14-14.

42.

MAGIC: access portal to a cross-platform gene expression compendium for maize.

Fu Q, Fierro AC, Meysman P, Sanchez-Rodriguez A, Vandepoele K, Marchal K, Engelen K.

Bioinformatics. 2014 May 1;30(9):1316-8. doi: 10.1093/bioinformatics/btt739. Epub 2014 Jan 8.

PMID:
24407224
43.

MLVA as a tool for public health surveillance of human Salmonella Typhimurium: prospective study in Belgium and evaluation of MLVA loci stability.

Wuyts V, Mattheus W, De Laminne de Bex G, Wildemauwe C, Roosens NH, Marchal K, De Keersmaecker SC, Bertrand S.

PLoS One. 2013 Dec 31;8(12):e84055. doi: 10.1371/journal.pone.0084055. eCollection 2013.

44.

Phenotypical and molecular responses of Arabidopsis thaliana roots as a result of inoculation with the auxin-producing bacterium Azospirillum brasilense.

Spaepen S, Bossuyt S, Engelen K, Marchal K, Vanderleyden J.

New Phytol. 2014 Feb;201(3):850-61. doi: 10.1111/nph.12590. Epub 2013 Nov 13.

45.

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia.

Meysman P, Sonego P, Bianco L, Fu Q, Ledezma-Tejeida D, Gama-Castro S, Liebens V, Michiels J, Laukens K, Marchal K, Collado-Vides J, Engelen K.

Nucleic Acids Res. 2014 Jan;42(Database issue):D649-53. doi: 10.1093/nar/gkt1086. Epub 2013 Nov 8.

46.

Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation.

Aslankoohi E, Zhu B, Rezaei MN, Voordeckers K, De Maeyer D, Marchal K, Dornez E, Courtin CM, Verstrepen KJ.

Appl Environ Microbiol. 2013 Dec;79(23):7325-33. doi: 10.1128/AEM.02649-13. Epub 2013 Sep 20.

47.

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks.

Verbeke LP, Cloots L, Demeester P, Fostier J, Marchal K.

Bioinformatics. 2013 May 15;29(10):1308-16. doi: 10.1093/bioinformatics/btt142. Epub 2013 Apr 16.

PMID:
23595663
48.

PheNetic: network-based interpretation of unstructured gene lists in E. coli.

De Maeyer D, Renkens J, Cloots L, De Raedt L, Marchal K.

Mol Biosyst. 2013 Jul;9(7):1594-603. doi: 10.1039/c3mb25551d. Epub 2013 Apr 16. Review.

PMID:
23591551
49.

Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles.

Meysman P, Sánchez-Rodríguez A, Fu Q, Marchal K, Engelen K.

Mol Biol Evol. 2013 Jun;30(6):1302-14. doi: 10.1093/molbev/mst029. Epub 2013 Feb 20.

50.

Identifying differentially expressed genes in the absence of replication.

Thilakarathne PJ, Verbeke G, Engelen K, Marchal K, Lin D.

Int J Bioinform Res Appl. 2013;9(1):71-90. doi: 10.1504/IJBRA.2013.050654.

PMID:
23207999

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