Publications

Publications resulting from the project:

De Maeyer, D., Cloots, L., Renkens, J., De Raedt, L., Marchal, K. (2013). PheNetic: Network-based interpretation of unstructured gene lists in E. coli. Molecular Biosystems.

Selected publications demonstrating the track record in the field of the project:

CMPG

Van Puyvelde, S., Steenackers, H.P., Vanderleyden, J. (2013). Small RNAs regulating biofilm formation and outer membrane homeostasis. RNA Biology, 10(2), 185-191.

Robijns S.C., De Pauw B., Loosen B., Marchand A., Chaltin P., De Keersmaecker S.C., Vanderleyden J., Steenackers H.P. (2012). Identification and characterization of 4-[4-(3-phenyl-2-propen-1-yl)-1-piperazinyl]-5H-pyrimido[5,4-b]indole derivatives as Salmonella biofilm inhibitors. FEMS Immunol Med Microbiol, 65(2), 390-394.

Steenackers H.#, Hermans K.#, Vanderleyden J., De Keersmaecker S. (2012). Salmonella Biofilms: an Overview on Occurrence, Regulation and Eradication. Food Research International, 45(2).

Steenackers H., Ermolat’ev D., Savaliya B., De Weerdt A., De Coster D., Shah A., De Vos D., Vanderleyden J., De Keersmaecker S. (2011). Structure-Activity Relationship of 2-Hydroxy-2-aryl-2,3-dihydro-imidazo[1,2-a]pyrimidinium Salts and 2N-Substituted 4(5)-Aryl-2-Amino-1H-imidazoles as Inhibitors of Biofilm Formation by Salmonella Typhimurium and Pseudomonas aeruginosa. Bioorganic & Medicinal Chemistry, 19(11), 3462-73.

Steenackers H., Ermolat’ev D., Savaliya B., De Weerdt A., De Coster D., Shah A., De Vos D., Vanderleyden J., De Keersmaecker S. (2010). Structure-Activity Relationship of 4(5)-Aryl-2-amino-1H-imidazoles, N1-Substituted 2-Aminoimidazoles and Imidazo[1,2-a] pyrimidinium Salts as Inhibitors of Biofilm Formation by Salmonella Typhimurium and Pseudomonas aeruginosa. Journal of Medicinal Chemistry, 54(2), 472-484.

Hermans, K., Anh Nguyen, T., Roberfroid, S., Schoofs, G., Verhoeven, T., De Coster, D., Vanderleyden, J., De Keersmaecker, S. (2011). Gene expression analysis of monospecies Salmonella Typhimurium biofilms using differential fluorescence induction. Journal of Microbiological Methods, 84 (3), 467-478.

Kint, G., De Coster, D., Marchal, K., Vanderleyden, J., De Keersmaecker, S. (2010). The small regulatory RNA molecule MicA is involved in Salmonella enterica serovar Typhimurium biofilm formation. BMC Microbiology, 10, 276.

Lebeer, S., Vanderleyden, J., De Keersmaecker, S.C.J. (2010). Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nature Rev. Microbiol. 8, 171-184.

Ermolat’ev D., Bariwal B., Steenackers H., De Keersmaecker S. and Van der Eycken E. (2010). Concise and Diversity-Oriented Route toward Polysubstituted 2-Aminoimidazole Alkaloids and Their Analogues. Angewandte Chemie, 49(49), 9465-9468

Steenackers H.#, Levin J.#, Janssens J., De Weerdt A., De Vos D., Vanderleyden J., De Keersmaecker S. (2010). Structure-activity relationship of brominated 3-alkyl-5-methylene-2(5H)-furanones and alkylmaleic anhydrides as inhibitors of Salmonella biofilm formation and quorum sensing regulated bioluminescence in Vibrio harveyi. Bioorganic & Medicinal Chemistry, 18(14), 5224-5233. #equal contribution

Sonck, K.A.J., Kint, G., Schoofs, G., Vander Wauven, C., Vanderleyden J., and De Keersmaecker, S.C.J., (2009). The proteome of Salmonella Typhimurium grown under in vivo-mimicking conditions. Proteomics 9, 565-579.

Steenackers H., Robijns S., Gellens E., Levin J., Zhao H., Hermans K., De Coster D., Verhoeven T., Marchal K., Vanderleyden J., De Vos D., De Keersmaecker S. (2008). Brominated furanones inhibit biofilm formation by Salmonella enterica serovar Typhimurium. Applied and Environmental Microbiology, 74 (21), 6639-6648.

Francius, G., Lebeer, S., Alsteens, D., Wildling, L., Gruber, H.J., Hols, P., De Keersmaecker, S., Vanderleyden, J., and Dufrêne, Y.F. (2008). Detection, localization, and conformational analysis of single polysaccharide molecules on live bacteria. ACS Nano, 2(9), 1921-1929. IF Publ. year: 5.47. IF last year: 9.87; Citation: 36.

De Keersmaecker, S.C.J., Varszegi C., van Boxel N., Habel L.W., Metzger K., Daniels R., Marchal K., De Vos D., and Vanderleyden J., 2005. Chemical synthesis of (S)-4,5-Dihydroxy-2,3-pentanedione, a bacterial signal molecule precursor, and validation of its activity in Salmonella typhimurium. J. Biol. Chem. 280(20), 19563-19568.


N2N

Proost S., Fostier J., De Witte D., Dhoedt B., Demeester P., Van de Peer Y., Vandepoele K (2011).  i‑ADHoRe 3.0 - Fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res. (Epub.)

Michoel, T., De Smet, R., Joshi, A., Van de Peer, Y., Marchal, K. (2009). Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Systems Biology, 3, art.nr. 49.

Lemmens, K., De Bie, T., Dhollander, T., De Keersmaecker, S., Thijs, I., Schoofs, G., De Weerdt, A., De Moor, B., Vanderleyden, J., Collado-Vides, J., Engelen, K., Marchal, K. (2009). DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biology, 10(3), R27.

Lemmens, K., Dhollander, T., De Bie, T., Monsieurs, P., Engelen, K., Smets, B., Winderickx, J., De Moor, B., Marchal, K. (2006). Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biology, 7(5), R37.

Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouze, P., Moreau, Y. (2002). A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. Journal of computational biology, 9(3), 447-464.


DTAI

Schietgat, L., Costa, F., Ramon, J., De Raedt, L. (2011). Effective feature construction by maximum common subgraph sampling. Machine Learning, 83 (2), 137-161.

De Grave, K., Costa, F. (2010). Molecular graph augmentation with rings and functional groups. Journal of Chemical Information and Modeling, 50 (9), 1660-1668.

Costa, F.,  De Grave, K. (2010). Fast neighborhood subgraph pairwise distance kernel, Proceedings of the 27th International Conference on Machine Learning, pp 255–262, Omnipress.

Schietgat, L., Vens, C., Struyf, J., Blockeel, H., Kocev, D., Dzeroski, S. (2010). Predicting gene function using hierarchical multi-label decision tree ensembles. BMC Bioinformatics, 11 (2).

Davis, Jesse; Ray, Soumya; Page, David; Santos Costa, Vitor. An integrated approach to feature construction and model building for drug activity prediction, Proceedings of the 24th International Conference on Machine Learning, pp 217–224, ACM Press 2007.


Biomol

Venken, T., Krnavek, D., Münch, J., Kirchhoff, F., Henklein, P., De Maeyer, M., Voet, A. (2011). An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor. Proteins: Structure, Function and Genetics, 79(11), art.nr. 10.1002/prot.23158, 3221-35.

Voet, A., Callewaert, L., Ulens, T., Vanderkelen, L., Van Herreweghe, J., Michiels, C., De Maeyer, M. (2011). Structure based discovery of small molecule suppressors targeting bacterial lysozyme inhibitors. Biochemical and Biophysical Research Communications, 405(4), 527-532.

Christ, F., Voet, A., Marchand, A., Nicolet, S., Desimmie, B., Marchand, D., Bardiot, D., Van der Veken, N., Van Remoortel, B., Strelkov, S., De Maeyer, M., Chaltin, P., Debyser, Z. (2010). Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nature Chemical Biology, 6(6), 442-448.

Vandecaetsbeek, I., Trekels, M., De Maeyer, M., Ceulemans, H., Lescrinier, E., Raeymaekers, L., Wuytack, F., Vangheluwe, P. (2009). Structural basis for the high Ca2+ affinity of the ubiquitous SERCA2b Ca2+ pump. Proceedings of the National Academy of Sciences of the United States of America, 106(44), 18533-18538.

Zimmer, J., Roman, F., Lambert, C., Jonckheer, A., Vazquez, A., Plesséria, J., Servais, J., Covens, K., Weber, J., Van Laethem, K., Schmit, J., Vandamme, A., Quinones-Mateu, M., De Maeyer, M. (2008). Impact on replicative fitness of the G48E substitution in the protease of HIV-1: an in vitro and in silico evaluation. Journal of Acquired Immune Deficiency Syndromes, 48(3), 255-62.


CD3

Christ, F., Voet, A., Marchand, A., Nicolet, S., Desimmie, B., Marchand, D., Bardiot, D., Van der Veken, N., Van Remoortel, B., Strelkov, S., De Maeyer, M., Chaltin, P., Debyser, Z. (2010). Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nature Chemical Biology, 6(6), 442-448.

Thevissen, K., Marchand, A., Chaltin, P., Meert, E., Cammue, B. (2009). Antifungal carbazoles. Current Medicinal Chemistry - Anti-Infective Agents, 16(17), 2205-2211.

Hu J., Fiten P., Van den Steen P.E., Chaltin P. and Opdenakker G. (2005). Simulation of evolution-selected propeptide by high-throughput selection of a peptidomimetic inhibitor on a capillary DNA sequencer platform. Anal. Chem. 2005, 77(7), 2116-2124.

Chaltin P., Borgions F., Zhang Z., Rozenski J., Van Aerschot A. and Herdewijn P. (2003). New dsDNA binding hybrid molecules combining an unnatural peptide and an intercalating moiety. Helv. Chim. Acta, 86, 533 - 547.

Chaltin P., Borgions F., Arthur Van Aerschot A. and Herdewijn P. (2003). Comparison of library screening techniques used in the development of dsDNA ligands.  Bioorg. Med. Chem. Lett., 13, 47 - 50.