Eric Bonnet

Postdoc
(Group member from 2001 until 2010)


+ 32 (0) 9 33 13 758
Personal homepage

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

Research

  • microRNAs
  • non-coding RNAs
  • Systems biology
  • Computers & grid computing

Papers

(21) Cock, M., Sterck, L., Ahmed, S., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Arun, A., Aury, J., Badger, J. H., Beszteri, B., Billiau, K., Bonnet, E., H. Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Youn Cho, G., Coelho, S.M., Collen, J., Le Corguille, G., Corre, E., Dartevelle, L., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Godfroy, O., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Luthringer, R., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Macaisne, N., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D.R., Nyvall-Collén, P., Peters, S., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Scornet, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Rouzé, P., Van de Peer, Y., Wincker, P. (2012) The Ectocarpus Genome and Brown Algal Genomics. Adv. Bot. Res. 64: 141-184.

(20) Grbic, M., Van Leeuwen, T., Clark, T. G., Rombauts, S., Rouzé, P., Grbic, V., Osborne, E., Dermauw, W., Thi Ngoc Cao, P., Ortego, F., Hernandez-Crespo, P., Diaz, I., Martinez, N.J., Navajas, M., Sucena, E., Magalhaes, S., Nagy, L., Pace, N.R., Djuranovic, S., Smagghe, G., Iga, M., Christiaens, M., Veenstra, J., Ewer, J., Mancilla Villalobos, R., Hutter, J., Hudson, A., Velez, M., Yi, S., Zeng, Q., Pires-daSilva, A., Roch, F., Cazaux, M., Navarro, M., Zhurov, V., Acevedo, G., Bjelica, A., Fawcett, J., Bonnet, E., Martens, C., Baele, G., Wissler, L., Sanchez-Rodriguez, A., Tirry, L., Blais, C., Demeestere, K., Henz, SR., Gregory, R., Mathieu, J., Verdon, L., Farinelli, L., Schmutz, J., Lindquist, E., Feyereisen, R., Van de Peer, Y. (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479,487-492.

(19) Cock, M., Colle, J., Sterck, L., Rouzé, P., Scornet, D., Anthouard, V., Artiguenave, F., Aury, J., Billiau, K., Bonnet, E., H.F. Bothwell, J., Brillet, L., Carre, W., Coelho, S.M., Corre, E., Da Silva, C., Jubin, C., Martens, C., Maumus, F., Miranda-Saavedra, D., Peters, S., Porcel, B., Quesneville, H., Boyen, C., Van de Peer, Y., Wincker, P. (2011) Nature, nurture and the structure of macroalgal genomes. Eur. J. Phycol. 46,39-39.

(18) Bonnet, E. (2010) Integrating microRNA expression data and other sources in module network reconstruction. Proceedings of the 6th workshop on computation of biochemical pathways and genetic networks. Logos Verlag Berlin GmbH. Heidelberg, Germany..

(17) Bonnet, E., Michoel, T., Van de Peer, Y. (2010) Prediction of a regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinformatics 26(18):i638-44.

(16) Michoel, T., Joshi, A., Bonnet, E., Vermeirssen, V., Van de Peer, Y. (2010) Towards system level modeling of functional modules and regulatory pathways using genome-scale data. Proceedings of the Seventh International Workshop on Computational Systems Biology (WCSB 2010) 71-74. Luxembourg, Luxembourg.

(15) Cock, M., Sterck, L., Rouzé, P., Scornet, D., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J., Badger, J., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Youn Cho, G., Coelho, S.M., Colln, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Küpper, F.C., Lang, D., Le Bail, A., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D., Nyvall-Collén, P., Peters, S., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Ségurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Van de Peer, Y., Wincker, P. (2010) The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465(7298):617-21.

(14) Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26(12):1566-8.

(13) Bonnet, E., Tatari, M., Joshi, A., Michoel, T., Marchal, K., Berx, G., Van de Peer, Y. (2010) Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLoS One 5(4):e10162.

(12) Vermeirssen, V., Joshi, A., Michoel, T., Bonnet, E., Casneuf, T., Van de Peer, Y. (2009) Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. Molecular BioSystems 5(12):1817-30.

(11) Abeel, T., Saeys, Y., Bonnet, E., Rouzé, P., Van de Peer, Y. (2008) Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res. 18(2):310-23.

(10) Michoel, T., Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module network learning algorithms using simulated data. BMC Bioinformatics 8, 860-871.

(9) * Michoel, T., * Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module networks learning algorithms using simulated data. BMC Bioinformatics 8 Suppl 2:S5. *contributed equally

(8) Van Leene, J., Stals, H., Eeckhout, D., Persiau, G., Van De Slijke, E., Van Isterdael, G., De Clercq, R., Bonnet, E., Laukens, K., Remmerie, N., Hendrickx, K., De Vijlder, T., Abdelkrim, A., Pharazyn, A., Van Onckelen, H., Witters, E., Inzé, D., De Jaeger, G. (2007) A Tandem Affinity Purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. Mol. Cel. Prot. 6(7):1226-38.

(7) Faes, P., Minnaert, B., Christiaens, M., Bonnet, E., Saeys, Y., Stroobandt, D., Van de Peer, Y. (2006) A Scalable Hardware Accelerator for Comparing Protein Sequences.. Proceedings of the First International Conference on Scalable Information Systems. Hong Kong, April 2006, on CD..

(6) Bonnet, E., Van de Peer, Y., Rouzé, P. (2006) The small RNA world of plants. New Phytol. 171(3):451-68.

(5) * Bonnet, E., * Wuyts, J., Rouzé, P., Van de Peer, Y. (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20(17):2911-7. *contributed equally

(4) Bonnet, E., Wuyts, J., Rouzé, P., Van de Peer, Y. (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important new target genes. Proc. Natl. Acad. Sci. USA 101(31):11511-6.

(3) Picaud, F., Bonnet, E., Gloaguen, V., Petit, J. (2003) Decision Making for Food Choice by Grasshoppers (Orthoptera: Acrididae): Comparison Between a Specialist Species on a Shrubby Legume and Three Graminivorous Species. Environ. Entomol. 32(3):680-688.

(2) Bonnet, E., Van de Peer, Y. (2002) ZT: a software tool for simple and partial Mantel tests. J. Stat. Softw. 7:1-12.

(1) Bonnet, E., Vilks, A., Lenain, J.F., Petit, J. (1995) Temporal and structural analysis of the relationships between orthoptera and vegetation. Ecologie 28, 209-216.











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VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
BELGIUM
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