Stephane Rombauts

Senior Staff Scientist
(Group member since 1996)


+ 32 (0) 9 33 13 821
Personal homepage

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

CV

  • Birthdate:  05 February 1969, Gent, Belgium.
  • Since October 1997: Staff member in the Bioinformatics and Evolutionary Genomics at the University of Ghent, VIB, Belgium
  • October 1991 - June 1996: M.Sc. Biotechnology, Ghent University, Belgium.
  • Service as reviewer: Journal of experimental Botany, Bioinformatics

Research

As a bioinformatician with a molecular biologists background, my first project was to set up from scratch what was going to become the PlantCARE database and brought me to focus my interest on gene expression. I then have been working on the annotation of the genomic sequences that contributed to the ESSA projects for the sequencing of Arabidopsis were the first genome duplications in Arabidopsis were shown. This involved next to some dataming, a lot of manual annotation of raw genomic sequences and genes, correcting faulty annotation done by automated systems that reported poor results at that time. I since then collaborated and still now provide an input in the development and enhancement of the Eugene gene prediction platform that performs now among the best. Over the years I have kept both interest. I'm still maintaining the PlantCARE database, that became part of the PlaNet project aiming at interconnecting databases on different aspects of plant genomics, while, on the other hand, I'm involved in the annotation of new upcoming plant genomes, which brough us to adapt the Eugene platform to other plant genomes than Arabidopsis thaliana. Now I try to combine both, as more plant genomes become available and comparative methods enable more reliable in silico promoter analyses. This means that from a raw genomic sequences I follow the whole pipe line from genome annotation, to the extraction of the data necessary to study promoter sequences and find clues to decifer potential co-expressed genes in networks.

Papers

(64) Orr, R., Rombauts, S., Van de Peer, Y., Shalchian-Tabrizi, K. (2017) Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples. Genome Announc. 5(33). pii: e00787-17.
(63) Miclotte, G., Plaisance, S., Rombauts, S., Van de Peer, Y., Audenaert, P., Fostier, J. (2017) OMSim: a simulator for optical map data. Bioinformatics (In Press).
(62) Thi Ngoc Cao, P., Greenhalgh, R., Dermauw, W., Rombauts, S., Bajda, S., Zhurov, V., Grbić, M., Van de Peer, Y., Van Leeuwen, T., Rouzé, P., M. Clark, R. (2016) Complex evolutionary dynamics of massively expanded chemosensory receptor families in an extreme generalist chelicerate herbivore. Genome Biol. Evol. 8(11):3323-3339.
(61) Miclotte, G., Heydari, M., Demeester, P., Rombauts, S., Van de Peer, Y., Audenaert, P., Fostier, J. (2016) Jabba: Hybrid Error Correction for Long Sequencing Reads. Algorithms for Molecular Biology 11:10.
(60) Blanc-Mathieu, R., Verhelst, B., Derelle, E., Rombauts, S., Bouget, F.-Y., Carre, W., Château, A., Eyre-Walker, A., Grimsley, N., Moreau, H., Piegu, B., Rivals, E., Schackwitz, W., Van de Peer, Y., Piganeau, G. (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics 15:1103.
(59) Zimmer, A., Lang, D., Buchta, K., Rombauts, S., Nishiyama, T., Hasebe, M., Van de Peer, Y., Rensing, S.A., Reski, R. (2013) Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics 14:498.
(58) Andolfo, G., Sanseverino, W., Rombauts, S., Van de Peer, Y., Bradeen, J. M., Carputo, D., Frusciante, L., Ercolano, M. (2012) Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. New Phytol. 197(1):223-37.
(57) Moreau, H., Verhelst, B., Couloux, A., Derelle, E., Rombauts, S., Grimsley, N., Van Bel, M., Poulain, J., Katinka, M., Hohmann-Marriott, M., Piganeau, G., Rouzé, P., Da Silva, C., Wincker, P., Van de Peer, Y., Vandepoele, K. (2012) Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage . Genome Biol. 13, R74.
(56) Tomato Genome Consortium (TGC): ..., ..., Rombauts, S., Fawcett, J., Van de Peer, Y., ..., ... (2012) The tomato genome sequence provides insights intofleshy fruit evolution. Nature 485(7400):635-41.
(55) 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.
(54) Young, N.D., Debelle, F., Oldroyd, G.E., Geurts, P., Cannon, S.B., Udvardi, M., Benedito, V., Mayer, K., Gouzy, J.P., Schoof, H., Van de Peer, Y., Proost, S., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, K., Mudge, J., Bharti, A., Murray, J.A.H., Naoumkina, M., Rosen, B., Silverstein, K., Tang, H., Rombauts, S., Zhao, Q., Zhou, K., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, J., Bidwell, S.L., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, Y., Doyle, J., Dudez, A., Farmer, E.E., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., Gonzalez, A., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S., Jeong, D., Jing, Y., Jöcker, A., Kenton, S., Kim, J.R., Klee, K., Lai, M.-H., Lang, D., Lin, S., Macmil, S., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E., Mun, J., Najar, F., Nicholson, C., Noirot, C., OBleness, M., Paule, C., Poulain, J., Prion, F., Qin, B., Qu, D., Retzel, E., Riddle, C., Sallet, E., Samain, S., Samson, G., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Ségurens, B., Severin, A., Sherrier, J., Shi, J., Sims, S., Singer, S., Sinharoy, S., Sterck, L., Viollet, A., Wang, X., Wang, X., Wang, X., Wang, X., Warfsmann, J., Weissenbach, J., White, O., White, O., Wiley, G., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, K., Zuber, A., Denarie, J., Dixon, R., May, G., Schwartz, D., Rogers, J., Quetier, F., Town, C.D., Roe, B. (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378):520-4.
(53) Mortier, V., Fenta, B.A., Martens, C., Rombauts, S., Holsters, M. & Ver, Kunert, K., Goormachtig, S. (2011) Search for nodulation-related CLE genes in the genome of Glycine max. J. Exp. Bot. 62(8):2571-83.
(52) Boruc, J., Van Den Daele, H., Hollunder, J., Rombauts, S., Mylle, E., Hilson, P., Inzé, D., De Veylder, L., Russinova, E. (2010) Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. The Plant Cell 22(4):1264-80.
(51) Mortier, V., Den Herder, G., Whitford, R., Van De Velde, S., Rombauts, S., D'haeseleer, K., Holsters, M. & Ver, Goormachtig, S. (2010) CLE peptides control Medicago truncatula nodulation locally and systemically. Plant Physiol. 153(1):222-37.
(50) Rehrauer, H., Aquino, C., Gruissem, W., Henz, SR., Hilson, P., Laubinger, S., Naouar, N., Patrignani, A., Rombauts, S., Shu, C.-L., Van de Peer, Y., Vuylsteke, M., Weigel, D., Zeller, G., Hennig, L. (2010) AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol. 152(2):487-99.
(49) Boruc, J., Engler, G., Mylle, E., De Veylder, L., De Groodt, R., Duda, M., De Clercq, R., Rombauts, S., Boudolf, V., Duda, M., Geelen, D., Geelen, D., Hilson, P., Inzé, D., Ferreira, P.C.P., Van Damme, D., Beeckman, T., Russinova, E., Karimi, M., Hilson, P., Inzé, D., Engler, G. (2010) Systematic localization of the Arabidopsis core cell cycle proteins reveals novel cell division complexes. Plant Physiol. 152(2):553-65.
(48) Mueller, L., Lankhorst, R., Tanksley, S., Giovannoni, J., White, O., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A., Menda, N., Tecle, I., Bombarely, A., Stack, S., Royer, S., Chang, Y., Shearer, L., Kim, J.R., Jo, S., Hur, C., Choi, D., Li, C., Zhao, Q., Jiang, H., Geng, Y., Dai, Y., Fan, M.-J., Chen, J., Lu, F., Shi, J., Sun, S., Chen, J., Yang, X., Lu, C., Chen, M., Cheng, Y.-Y., Li, C., Ling, H., Xue, Y., Wang, X., Seymour, G., Bishop, G., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., McLaren, K., Mathur, S., Vyas, S., Solanke, A., Kumar, R., Gupta, A., Sharma, A., Khurana, J., Khurana, J., Tyagi, A., Sarita, ., Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, N., Kumar, A., Dixit, R., Singh, N., Praveen, S., Dalal, V., Yadav, M., Ghazi, I., Gaikwad, K., Raj Sharma, T., Mohapatra, T., Singh, N., Szinay, D., de Jong, P.J., Peters, S., van Staveren, M., Datema, E., Fiers, M., van Ham, R., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, M., Botella, M., Perez-Alonso, M., Fernandez-Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, J., He, Y., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, X., Ye, Z., Yang, W., Wang, X., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D?Agostino, N., Chiusano, M., Ercolano, M., Barone, A., Frusciante, L., Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K., Guigó, R., Camara, F., Rombauts, S., Fawcett, J., Van de Peer, Y., Knapp, S., Zamir, D., Stiekema, W. (2009) A Snapshot of the Emerging Tomato Genome Sequence: The Tomato Genome Sequencing Consortium. The Plant Genome 2:78-92.
(47) Engler, G., De Veylder, L., De Groodt, R., Rombauts, S., Boudolf, V., De Meyer, B., Hemerly, A., Ferreira, P.C.P., Beeckman, T., Karimi, M., Hilson, P., Inzé, D., Engler, G. (2009) Systematic analysis of cell-cycle gene expression during Arabidopsis development. Plant J. 59(4):645-60.
(46) Worden, A.Z., J-Lee, H., Mock, T., Rouzé, P., Simmons, M.P., Aerts, A., Allen, A., Cuvelier, M.L., Derelle, E., Everett, M.V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S.M., Parker, M.S., Rombauts, S., Salamov, A., Von, P. Dasso, Badger, J., Coutinho, P.M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J.E., John, U., Lanier, W., Lindquist, E., Lucas, S., Mayer, K., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, V., Bhattacharya, D., Goodenough, U.W., Van de Peer, Y., Grigoriev, I. (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324(5924):268-72.
(45) Benhamed, M., Martin-Magniette, ML., Taconnat, L., Bitton, F., Servet, C., De Clercq, R., De Meyer, B., Buysschaert, C., Rombauts, S., Villarroel, R., Aubourg, S., Beynon, J., Bhalerao, R.P., Coupland, G., Gruissem, W., Menke, FL., Weisshaar, B., Renou, JP., Zhou, K., Hilson, P. (2008) Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J. 56(3):493-504.
(44) Den Herder, G., De Keyser, A., De Rycke, R., Rombauts, S., Van De Velde, S., Clemente, MR., Verplancke, C., Mergaert, P., Kondorosi, E., Holsters, M. & Ver, Goormachtig, S. (2008) Seven in absentia proteins affect plant growth and nodulation in Medicago truncatula. Plant Physiol. 148(1):369-82.
(43) Foissac, S., Gouzy, J.P., Rombauts, S., Mathé, C., Amselem, J., Sterck, L., Van de Peer, Y., Rouzé, P., Schiex, T. (2008) Genome Annotation in Plants and Fungi: EuGene as a model platform. Curr. Bioinform. 3(2):87-97.
(42) Rensing, S.A., Lang, D., Zimmer, A., Terry, A., Salamov, A., H,Shapiro, , Nishiyama, T., P.-Perroud, F., Lindquist, E., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K., Shin-I, T., Kuroki, Y., Toyoda, A., Suzuki, Y., S.-Hashimoto, I., Yamaguchi, K., Sugano, S., Kohara, Y., Fujiyama, A., Ashton, N., Anterola, A., Aoki, S., Barbazuk, W.B., Barker, E., Bennetzen, J., Blankenship, R., Cho, S.H., Dutcher, S., Estelle, M., Fawcett, J., Gundlach, H., Hanada, K., Heyl, A., Hicks, K. A., Hughes, J., Lohr, M., Mayer, K., Melkozernov, A., Murata, T., Nelson, D.R., Pils, B., Prigge, M., Reiss, B., Renner, T., Rombauts, S., Rushton, P., Sanderfoot, A., Schween, G., S.-Shiu, H., Stueber, K., Theodoulou, F.L., Tu, H., Van de Peer, Y., Verrier, P.J., Waters, E., Wood, A., Yang, G., Cove, D., Cuming, A.C., Hasebe, M., Lucas, S., Mishler, B.D., Reski, R., Grigoriev, I., Quatrano, R.S., Boore, J.L. (2008) The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319(5859):64-9.
(41) Ruttink, T., Arend, M., Morreel, K., Storme, V., Rombauts, S., Fromm, J., Bhalerao, R.P., Boerjan, W., Rohde, A. (2007) A molecular timetable for apical bud formation and dormancy induction in poplar. The Plant Cell 19(8):2370-90.
(40) Capoen, W. ., Den Herder, G., Rombauts, S., De Gussem, J. ., De Keyser, A., Holsters, M. & Ver, Goormachtig, S. (2007) Comparative transcriptome analysis reveals common and specific tags for root hair and crack-entry invasion in Sesbania rostrata. Plant Physiol. 144(4):1878-89.
(39) Palenik, B., Grimwood, J., Aerts, A., Rouzé, P., Salamov, A., Putnam, N., Zhou, K., Jorgensen, R., Derelle, E., Rombauts, S., Otillar, R., Merchant, S., Podell, S., Gaasterland, T., Manuell, A., Napoli, C., Gendler, K., Vallon, O., Peyretaillade, E., Jancek, S., Piganeau, G., Heijde, M., Jabbari, K., Bowler, C., Werner, G., Robbens, S., Pazour, G., Dubchak, I., Ren, Q., Delwiche, C., Paulsen, I., De Boever, P., Schmutz, J., Rokhsar, D., Van de Peer, Y., Moreau, H., Grigoriev, I. (2007) The Tiny Eukaryote Ostreococcus Provides Genomic Insights Into The Paradox Of Plankton Speciation. Proc. Natl. Acad. Sci. USA 104(18):7705-10.
(38) Den Herder, G., Lievens, S. ., Rombauts, S., Holsters, M. & Ver, Goormachtig, S. (2007) A symbiotic plant peroxidase involved in bacterial invasion of the tropical legume Sesbania rostrata. Plant Physiol. 144(2):717-27.
(37) Sterck, L., Rombauts, S., Vandepoele, K., Rouzé, P., Van de Peer, Y. (2007) How many genes are there in plants (... and why are they there)?. Curr. Opin. Plant Biol. 10(2):199-203.
(36) * Cannon, S.B., * Sterck, L., * Rombauts, S., Sato, S., Wang, X., Mudge, J., Vasdewani, J., Cheung, F., Gouzy, J.P., Schiex, T., Spanngl, M., Schoof, H., Nicholson, C., Humphrays, S., Mayer, K., Rogers, J., Quetier, F., Oldroyd, G.E., Debelle, F., Cook, D.R., Town, C.D., Roe, B.A., Tabata, S., Van de Peer, Y., Young, N.D. (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl. Acad. Sci. USA 103(40):14959-64. *contributed equally
(35) Tuskan, G., * DiFazio, S., * Jansson, S., * Bohlmann, J., * Grigoriev, I., * Hellsten, U., * Putnam, N., * Ralph, S., * Rombauts, S., * Salamov, A., * Schein, J., * Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.-L., Cooper, D., Coutinho, P., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J., Locascio, P., Luo, Y., Lucas, S., Martin, F., Montanini, B., Nelson, D.R., Nelson, C., Nieminen, K., Nilsson, O., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouzé, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de Peer, Y., Rokhsar, D. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw). Science 313(5793):1596-604. *contributed equally
(34) * Derelle, E., * Ferraz, C., * Rombauts, S., * Rouzé, P., Worden, A.Z., Robbens, S., Partensky, F., Degroeve, S., Echeynie, S., Cooke, R., Saeys, Y., Wuyts, J., Panaud, O., Piegu, B., Ball, S., Ral, J.P., Bouget, F.-Y., Piganeau, G., De Baets, B., Picard, A., Delseny, M., Demaille, J., Van de Peer, Y., Moreau, H. (2006) Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl. Acad. Sci. USA 103(31):11647-52. *contributed equally
(33) Van De Velde, S., Guerra, JC. ., De Keyser, A., De Rycke, R., Rombauts, S., Maunoury, N. ., Mergaert, P., Kondorosi, E., Holsters, M. & Ver, Goormachtig, S. (2006) Aging in legume symbiosis. A molecular view on nodule senescence in Medicago truncatula. Plant Physiol. 141(2):711-20.
(32) Vanderauwera, S., Zimmermann, P. ., Rombauts, S., Vandenabeele, S., Langebartels, C., Gruissem, W., Inzé, D., Van Breusegem, F. (2005) Genome-wide analysis of hydrogen peroxide-regulated gene expression in Arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol. 139(2):806-21.
(31) Aubourg, S., Brunaud, V., Bruyere, C., Cooke, R., Cottet, A., Couloux, A., Dehais, P., Deleage, G., Duclert, A., Echeverria, M., Eschbach, A., Falconet, D., Filippi, G., Gaspin, C., Geourjon, C., Grienenberger, J.M., Houlne, G., Jamet, E., Lechauve, F., Leleu, O. L., Leroy, P., Mache, R., Meyer, C., Nedjari, H., Negrutiu, I., Orsini, V., Peyretaillade, E., Raes, J., Risler, J.L., Riviere, S., Rombauts, S., Rouzé, P., Schneider, M., Schwob, P., Small, I., Soumayet-Kampetenga, G., Stankovski, D., Toffano, C., Tognolli, M., Caboche, M., Lecharny, A. (2005) GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Res. 33(Database issue):D641-6.
(30) Sterck, L., Rombauts, S., Jansson, S., Sterky, F., Rouzé, P., Van de Peer, Y. (2005) EST data suggest that poplar is an ancient polyploid. New Phytol. 167(1):165-70.
(29) Vandenabeele, S., Vuylsteke, M., Vanderauwera, S., Rombauts, S., Langebartels, C., Zabeau, M., Van Montagu, M., Inzé, D., Van Breusegem, F. (2004) Catalase deficiency drastically affects gene expression induced byhigh light in Arabidopsis thaliana. Plant J. 39(1):45-58.
(28) Rombauts, S., Lescot, M., Zhang, J., Aubourg, S., Mathé, C., Jansson, S., Rouzé, P., Boerjan, W. (2004) Annotation of a 95-kb Populus deltoides genomic sequence reveals a disease resistance gene cluster and novel class I and class II transposable elements. Theor. Appl. Genet. 109(1):10-22.
(27) Ral, J.P., Derelle, E., Ferraz, C., Wattebled, F., Farinas, B., Corellou, F., Buleon, A., Slomianny, M.C., Delvalle, D., D'Hulst, C., Rombauts, S., Moreau, H., Ball, S. (2004) Starch Division and Partitioning. A Mechanism for Granule Propagation and Maintenance in the Picophytoplanktonic Green Alga Ostreococcus tauri. Plant Physiol. 136(2):3333-40.
(26) Ral, J.P., Derelle, E., Ferraz, C., Wattebled, F., Farinas, B., Corellou, F., Buleon, A., Slomianny, M.C., Delvalle, D., D'Hulst, C., Rombauts, S., Moreau, H., Ball, S. (2004) Starch division and partitioning. A mechanism for granulepropagation and maintenance in the picophytoplanktonic green alga Ostreococcus tauri. Plant Physiol. 136(2):3333-40.
(25) Vlieghe, K., Florquin, K., Vuylsteke, M., Rombauts, S., Van Hummelen, P., Van de Peer, Y., Inzé, D., De Veylder, L. (2003) Microarray analysis of E2Fa-DPa-overexpressingplants uncovers a cross-talking genetic networkbetween DNA replication and nitrogen assimilation. J. Cell Sci. 116(Pt 20):4249-59.
(24) Rombauts, S., Van de Peer, Y., Rouzé, P. (2003) AFLPInsilico, simulating AFLP fingerprints. Bioinformatics 19(6):776-7.
(23) * Rombauts, S., * Florquin, K., Lescot, M., Marchal, K., Rouzé, P., Van de Peer, Y. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 132(3):1162-76. *contributed equally
(22) Breyne, P., Dreesen, R., Cannoot, B., Rombaut, D., Vandepoele, K., Rombauts, S., Vanderhaeghen, R., Inzé, D., Zabeau, M. (2003) Quantitative cDNA-AFLP analysis for genome-wide expression studies. Mol. Genet. Genom. 269(2):173-9.
(21) De Bodt, S., Raes, J., Florquin, K., Rombauts, S., Rouzé, P., Theissen, G., Van de Peer, Y. (2003) Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J. Mol. Evol. 56(5):573-86.
(20) Breyne, P., Dreesen, R., Vandepoele, K., De Veylder, L., Van Breusegem, F., Callewaert, L., Rombauts, S., Raes, J., Cannoot, B., Engler, G., Inzé, D., Zabeau, M. (2002) Analysis of the transcriptome during cell division in plants. Proc. Natl. Acad. Sci. USA 99(23):14825-30.
(19) Thijs, G., Moreau, Y., De Smet, F., Mathys, J., Lescot, M., Rombauts, S., Rouzé, P., De Moor, B., Marchal, K. (2002) INCLUSive: INtegrated clustering, upstream of sequence retrieval and motif sampling. Bioinformatics 18, 331-332.
(18) Lescot, M., Dehais, P., Moreau, Y., Van de Peer, Y., Rouzé, P., Rombauts, S. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30(1):325-7.
(17) Rensing, S.A., Rombauts, S., Van de Peer, Y., Reski, R. (2002) Moss transcriptome and beyond. Trends Plant Science 7(12):535-8.
(16) Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J. Comput. Biol. 9(2):447-64.
(15) Vandepoele, K., Raes, J., De Veylder, L., Rouzé, P., Rombauts, S., Inzé, D. (2002) Genome-wide analysis of core cell cycle genes in Arabidopsis. The Plant Cell 14(4):903-16.
(14) Thijs, G., Moreau, Y., De Smet, F., Mathys, J., Lescot, M., Rombauts, S., Rouzé, P., De Moor, B., Marchal, K. (2002) INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics 18(2):331-2.
(13) Thijs, G., Lescot, M., Marchal, K., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 17, 1113-1122.
(12) Thijs, G., Lescot, M., Rombauts, S., Marchal, K., De Moor, B., Moreau, Y., Rouzé, P. (2001) A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences. Bioinformatics 17(12):1113-22.
(11) Boudolf, V., Rombauts, S., Naudts, M., Inzé, D., De Veylder, L. (2001) Identification of novel cyclin-dependent kinases interacting with the CKS1protein of Arabidopsis. J. Exp. Bot. 52(359):1381-2.
(10) Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2001) A Gibbs Sampling method to detect over-represented motifs in upstream regions of co-expressed genes. In : 5th Annual International Conference on Computational Biology (RECOMB 2001). 5th Annual International Conference on Computational Biology (RECOMB 2001), Montreal, Canada, Apr. 2001 pp. 296-302.
(9) Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2001) A Gibbs Sampling method to detect over-represented motifs in upstream regions of co-expressed genes. In : Proc. of the 5th Annual International Conference on Computational Biology (RECOMB’2001). 5th Annual International Conference on Computational Biology (RECOMB 2001), Montreal, Canada, Apr. 2001 pp. 305-312.
(8) Magyar, Z., Atanassova, A., De Veylder, L., Rombauts, S., Inzé, D. (2000) Characterization of two distinct DP-related genes from Arabidopsis thaliana. FEBS Lett. 486(1):79-87.
(7) Mathé, C., Dehais, P., Pavy, N., Rombauts, S., Van Montagu, M., Rouzé, P. (2000) Gene prediction and gene classes in Arabidopsis thaliana. J. Biotechnol. 78(3):293-9.
(6) Thijs, G., Rombauts, S., Lescot, M., Marchal, K., De Moor, B., Moreau, Y., Rouzé, P. (2000) Detection of cis-acting regulatory elements in plants: a Gibbs sampling approach. In : Proc. of Bioinformatics of Gene regularisation and structure (BGRS’2000). The second international conference on bioinformatics, genome regulation and structure, Novosibirsk, Russia, Aug. 2000 pp. 119-123.
(5) Terryn, N., Heijnen, L., De Keyser, A., Van Asseldonck, M., De Clercq, R., Verbakel, H., Gielen, J., Zabeau, M., Villarroel, R., Jesse, T., Neyt, P., Hogers, R., Van Den Daele, H., Ardiles, W., Schueller, C., Mayer, K., Dehais, P., Rombauts, S., Van Montagu, M., Rouzé, P., De Vos, P. (1999) Evidence for an ancient chromosomal duplication in Arabidopsis thaliana bysequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett. 445(2-3):237-45.
(4) Rombauts, S., D?hais, P., Van Montagu, M., Rouzé, P. (1999) PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res. 27, 295-6.
(3) Pavy, N., Rombauts, S., D?hais, P., Mathé, C., Ramana, D.V., Leroy, P., Rouzé, P. (1999) Evaluation of gene prediction software using a genomic data set: application of Arabidopsis thaliana sequences. Bioinformatics 15(11):887-99.
(2) Rouzé, P., Pavy, N., Rombauts, S. (1999) Genome annotation: which tools do we have for it?. Curr. Opin. Plant Biol. 2(2):90-5.
(1) Pavy, N., Mathé, C., Rombauts, S., Rouzé, P. (1999) Genomics and bio-computing (in French). OCL-OLEAGINEUX CORPS GRAS LIPIDES 6,148-154.








Contact:
VIB / UGent
Bioinformatics & Evolutionary Genomics
Technologiepark 927
B-9052 Gent
BELGIUM
+32 (0) 9 33 13807 (phone)
+32 (0) 9 33 13809 (fax)
Don't hesitate to contact the in case of problems with the website!

You are visiting an outdated page of the BEG/Van de Peer Lab site.

Not all pages have been ported, so these archived pages are still available.

Redirect to the new website?