Pierre Rouzé

Group Leader
(Group member since 1994)


+ 32 (0) 9 331 36 94

Laboratoire Associ? de l'INRA / VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

CV

Birthdate: 14 July 1946, Steenwerck, France.

July 2001: part-time INRA appointment

March 1994 : joined the Department of Plant Genetics (Pr Van Montagu), Ghent University (Belgium), and launched the BioInformatics Team.

Sept.1992 - March 1994 : Sabbatical at the Plant Biology Laboratory, (Pr. B Lindberg Møller) Royal Veterinary & Agricultural University, Copenhagen. Biochemistry of cyanogen glucosides & glucosinolates biosynthesis

May 1989 appointed Research Director by INRA (France)

Sept.1981- Sept.1992 Laboratory of Cell Biology (Dr Jean-Pierre Bourgin), INRA Versailles (France). Work on T-DNA opines synthases, Nitrate assimilation

(co-team leader with Michel Caboche) Arabidopsis EST sequences analysis

July 1976–Sept.1981 Virology & Immunology Station, Parasitology Unit

(Dr Pierre Péry) INRA Thiverval-Grignon (France). Parasite immunology: search for antigenic components as vaccine against nematodes. F. hepatica diagnostic in cattle

July 1976 appointed Senior Researcher by INRA (France)

Dec 1972-July 1976 Virology & Immunology Station, Immunology Unit

(Dr Jean-Jacques Metzger) Maternal Immunity & Immune response in Piglets.

Dec.1969-Dec.1972 Molecular Biology (J.Monod) Institute, Immuno-differentiation Unit (Pr Jean-Marie Dubert), Paris-7 University (France) Biochemichal markers of in vitro cellular differentiation

Dec.1969 appointed Research Associate by INRA (France)

July 1969 appointed as contractual associate by INRA, Virology & Immunology Station (Dr Alain Paraf) INRA Thiverval-Grignon (France), in vitro cell differentiation

Background

1972 MD (DEA) in Biochemistry, Paris-7 University, Option: immunology, protein structure

1969 MD in Agronomy (INA, Paris), Speciality: Genetics

Research

I have always been drawn to biology; I am not a computer freak. Nevertheless, as soon as it turned out that it will be possible to sequence DNA routinely, and as biological sequences begun to accumulate in the early eighties, I got the strong conviction that a new way to investigate biology using computers was open and I battled in my institute to convince people to invest in this field and get the tools for it, with quite few success in the beginning, I must confess, colleagues of mine telling me that 'I should better work than play with a keyboard' or 'why are you stealing the results of others instead of producing yours?'. Life circumstances and an open-minded boss (maybe not that unprejudiced?) offered me the great opportunity to devote all my time playing with BioInformatics since 1994.

My deep interest is shared by many: from the fast accumulating raw genome data, sequences, microarrays and others, how to decipher information and build knowledge on function of genes and intermediary to end products of genes, on their interplay at the cell level, and finally on biology of the organism leaving in its environment. Wide and unfocussed, especially for someone of your age, will you say! The focus comes from history and necessity: sequences were first, sequencing Arabidopsis begun, and not many were interested in doing bioinformatics for plant genomes ten years ago, but my colleagues at bench in Ghent and in France were (elsewhere too, as a matter of fact). Gene prediction, genome sequence annotation became therefore my first topic, and is still today, as so many new organisms are going to be sequenced and as there are still so many uncertainties in simply finding (all) their genes and modeling them correctly. My second interest came later, aiming at gathering functional attributes for the genes after their finding. Database (and literature) mining provides functional information but essentially on products of genes. To get information on mechanisms governing their expression proper, one has to pay attention to promoters, and the coming of transcriptomics was making this topic timely. I would like to know not only what are the motifs and modules involved, but how their interplay control specifically a given gene expression, and to investigate ways to integrate experimental data and biological knowledge at the different molecular and cellular levels.

I am deeply convinced that, with bioinformatics, we are only making the first steps into something I would call 'dry biology', just the same way physics did more than a century ago, and that the landscape is wide open for creative and uninhibited young scientists.

Papers

(84) Olsen, J.L., Rouzé, P., Verhelst, B., Lin, Y.-C., Bayer, T., Collen, J., Dattolo, E., De Paoli, E., Dittami, S., Maumus, F., Michel, G., Kersting, A.R., Lauritano, C., Lohaus, R., T?pel, M., Tonon, T., Vanneste, K., Amirebrahimi, M., Brakel, J., Bostr?m, C., Chovatia, M., Grimwood, J., Jenkins, B., J?terbock, A., Mraz, A., Stam, W.T., Tice, H., Bornberg-Bauer, E., Green, P.J., Pearson, G.A., Procaccini, G., Duarte, C.M., Schmutz, J., Reusch, T.B.H., Van de Peer, Y. (2016) The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 530(7590):331-5.

(83) Verhelst, B., Van de Peer, Y., Rouzé, P. (2013) The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution. Genome Biol. Evol. 5(12):2393-401.

(82) * Ruttink, T., * Sterck, L., Rohde, A., Bendixen, C., Rouzé, P., Aslankoohi, E., Van de Peer, Y., Roldán-Ruiz, I. (2013) Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne. Plant Biotechnol J. 11(5):605-17. *contributed equally

(81) Read, B. A., Kegel, J., Klute, M. J., Kuo, Y.-C., Lefebvre, S. C., Maumus, F., Mayer, K., Miller, G., Monier, A., Salamov, A., Young, N.D., Aguilar, ., Aguilar, ., Claverie, J., Frickenhaus, S., Gonzalez, A., Herman, E. K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A. F., Schmutz, J., Schroeder, D., de Vargas, C., Vérret, F., von Dassow, P., Valentin, K., Van de Peer, Y., Rouzé, P., Wheeler, G., Allen, A. E., Bidle, K., Borodovsky, M., Bowler, C., Brownlee, C., Mark Cock, J., Elias, M., Gladyshev, V. N., Groth, M., Groth, M., Guda, C., Hadaegh, A., Iglesias-Rodriguez, D., Jenkins, B., Jones, B. M., Leese, F., Lobanov, A., Lawson, T., Lindquist, E., Marsh, M. E., Lomsadze, A., Mueller-Roeber, B., Lucas, S., Malik, S.-B., Pagarete, A., Mock, T., Probert, I., Parker, M.S., Quesneville, H., Raines, C., Rensing, S.A., Mauricio Riano-Pachon, D., Richier, S., Rokitta, S., Shiraiwa, Y., Soanes, D. M., van der Giezen, M., Wahlund, T. M., Williams, C., Wilson, W., Wolfe, K., Wurch, L. L., Dacks, J. B., Delwiche, C. F., Dyhrman, S. T., Glöckner, G., John, U., Richards, T., Worden, A. Z., Zhang, J., V. Grigoriev, I. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499(7457):209-13.

(80) Sterck, L., Billiau, K., Abeel, T., Rouzé, P., Van de Peer, Y. (2012) ORCAE: online resource for community annotation of eukaryotes. Nat. Methods 9(11):1041.

(79) 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.

(78) Olson, A., Aerts, A., Asiegbu, F., Belbahri, L., Bouzid, O., Broberg, A., Canbäck, B., Coutinho, P.M., Cullen, D., Dalman, K., Deflorio, G., van Diepen, L., Dunand, C., Duplessis, S., Durling, M., Gonthier, P., Grimwood, J., Gunnar Fossdal, C., Hansson, D., Henrissat, B., Hietala, A., Himmelstrand, K., Hoffmeister, D., Hogberg, N., James, T., Karlsson, J., Kohler, A., Kües, U., Lee, Y., Lin, Y.-C., Lind, M., Lindquist, E., Lombard, V., Lucas, S., Lunden, K., Morin, E., Murat, C., Park, R., Raffaello, T., Rouzé, P., Salamov, A., Schmutz, J., Solheim, H., Stahlberg, J., Velez, M., de Vries, R., Wiebenga, A., Woodward, S., Yakovlev, I., Garbelotto, M., Martin, F., Grigoriev, I., Stenlid, J. (2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol. 194, 1001-13.

(77) 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.

(76) Fawcett, J., Rouzé, P., Van de Peer, Y. (2012) Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol. Biol. Evol. 29(2):849-59.

(75) Hacquard, S., Joly, D., Lin, Y.-C., Tisserant, E., Feau, N., Delaruelle, C., Legué, V., Kohler, A., Tanguay, P., Petre, B., Frey, P., Van de Peer, Y., Rouzé, P., Martin, F., Hamelin, R., Duplessis, S. (2012) A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici- populina (poplar leaf rust). Mol. Plant Microbe In. 25(3):279-93.

(74) 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.

(73) 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.

(72) Chancerel, E., Lepoittevin, C., Le Provost, G., Lin, Y.-C., Pablo Jaramillo-Correa, J., J Eckert, A., L Wegrzyn, J., Zelenika, D., Boland, A., Frigerio, J., Chaumeil, P., Garnier-Géré, P., Boury, C., Grivet, D., C González-Martínez, S., Rouzé, P., Van de Peer, Y., B Neale, D., T Cervera, M., Kremer, A., Plomion, C. (2011) Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics 12:368.

(71) Duplessis, S., A. Cuomo, C., Lin, Y.-C., Aerts, A., Tisserant, E., Veneault-Fourrey, C., L. Joly, D., Hacquard, S., Amselem, J., L. Cantarel, B., Chiu, C.-H., Couthinho, P., Feau, N., Field, M., Frey, P., Gelhaye, E., Goldberg, J., Grabherr, M., D. Kodira, C., Kohler, A., Kües, U., A. Lindquist, E., Lucas, S., Mago, R., Mauceli, E., Morin, E., Murat, C., L. Pangilinan, J., Park, R., Pearson, M., Quesneville, H., Rouhier, N., Sakthikumar, S., A. Salamov, A., Schmutz, J., Selles, B., Shapiro, H.J., Tangay, P., Henrissat, B., Van de Peer, Y., Rouzé, P., G. Ellis, J., N. Dodds, P., E. Schein, J., Zhong, S., C. Hamelin, R., V. Grigoriev, I., J. Szabon, L., Martina, F. (2011) Obligate Biotrophy Features Unraveled by the Genomic Analysis of Rust Fungi. Proc. Natl. Acad. Sci. USA 108(22):9166-71.

(70) Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., Fontana, P., Bhatnagar, S.K., Troggio, M., Pruss, D., Salvi, S., Pindo, M., Baldi, P., Castelletti, S., Cavaiuolo, M., Coppola, G., Costa, F., Cova, V., Dal Ri, A., Goremykin, V., Komjanc, M., Longhi, S., Magnago, P., Malacarne, G., Malnoy, M., Micheletti, D., Moretto, M., Perazzolli, M., Si-Ammour, A., Vezzulli, S., Zini, E., Eldredge, G., FitzGerald, L.M., Gutin, N., Lanchbury, J., Macalma, T., Mitchell, J.T., Reid, J., Wardell, B., Kodira, C., Chen, Z., Desany, B., Niazi, F., Palmer, L., Koepke, T., Jiwan, D., Schaeffer, S., Krishnan, V., Wu, C., Chu, V.T., King, S.T., Vick, J., Tao, Q., Mraz, A., Stormo, K., Stormo, K., Bogden, R., Ederle, D., Stella, A., Vecchietti, A., Kater, M.M., Masiero, S., Lasserre, P., Lespinasse, Y., Allan, A.C., Bus, V., Chagné, D., Crowhurst, R.N., Gleave, A.P., Lavezzo, E., Fawcett, J., Proost, S., Rouzé, P., Sterck, L., Toppo, S., Lazzari, B., Hellens, R.P., Durel, C., Gutin, A., Bumgarner, R.E., Gardiner, S.E., Skolnick, M., Egholm, M., Van de Peer, Y., Salamini, F., Viola, R. (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat. Genet. 42(10):833-9.

(69) 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.

(68) Mattanovich, D., Callewaert, L., Rouzé, P., Lin, Y.-C., Graf, A., Redl, A., Tiels, P., Gasser, B., De Schutter, K. (2009) Open access to sequence: Browsing the Pichia pastoris genome. Microbial Cell Factories 8:53.

(67) De Bodt, S., Proost, S., Vandepoele, K., Rouzé, P., Van de Peer, Y. (2009) Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10:288.

(66) Dittami, S., Scornet, D., Petit, J., Ségurens, B., Da Silva, C., Corre, E., Dondrup, M., Glatting, K., Konig, R., Sterck, L., Rouzé, P., Van de Peer, Y., Cock, M., Boyen, C., Tonon, T. (2009) Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol. 10(6):R66.

(65) De Schutter, K., Lin, Y.-C., Tiels, P., Van Hecke, A., Glinka, S., Weber-Lehmann, J., Rouzé, P., Van de Peer, Y., Callewaert, L. (2009) Genome sequence of the recombinant protein production host Pichia pastoris, a methylotrophic yeast. Nature Biotechnology 27(6):561-6.

(64) 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.

(63) Abeel, T., Saeys, Y., Rouzé, P., Van de Peer, Y. (2008) ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 24(13):i24-31.

(62) 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.

(61) Martin, F., Aerts, A., Ahrén, D., Brun, A., Duchaussoy, F., Gibon, J., Kohler, A., Lindquist, E., Pereda, V., Salamov, A., Shapiro, H.J., Wuyts, J., Blaudez, D., Buée, M., Brokstein, P., Canbäck, B., Cohen, D., Courty, P.E., Coutinho, P., Danchin, E.G.J., Delaruelle, C., Detter, J., Deveau, A., DiFazio, S., Duplessis, S., Fraissinet-Tachet, L., Lucic, E., Frey-Klett, P., Fourrey, C., Feussner, I., Gay, G., Gérard, J., Grimwood, J., Hoegger, P.J., Jain, P., Kilaru, S., Labbé, J., Lin, Y.-C., Legué, V., F LeTacon, ., Marmeisse, R., Melayah, D., Montanini, B., Muratet, M., Nehls, U., Niculita-Hirzel, H., Oudot-LeSecq, M.P., Peter, G., Quesneville, H., Rajashekar, B., Reich, M., Rouhier, N., Schmutz, J., Yin, T., Chalot, M., Henrissat, B., Kües, U., Lucas, S., Van de Peer, Y., Podila, G., Polle, A., Pukkila, PJ., Richardson, P., Rouzé, P., Sanders, I., Stajich, J.E., Tunlid, A., Tuskan, G., Grigoriev, I. (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183):88-92.

(60) 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.

(59) Robbens, S., Rouzé, P., Cock, M., Spring, J., Worden, A.Z., Van de Peer, Y. (2008) The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. J. Mol. Evol. 66(1):80-4.

(58) Robbens, S., Petersen, J., Brinkmann, H., Rouzé, P., Van de Peer, Y. (2007) Unique regulation of the Calvin cycle in the ultrasmall green alga Ostreococcus. J. Mol. Evol. 64(5):601-4.

(57) 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.

(56) Saeys, Y., Rouzé, P., Van de Peer, Y. (2007) In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi, and protists. Bioinformatics 23(4):414-20.

(55) 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.

(54) 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

(53) * 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

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

(51) Degroeve, S., Saeys, Y., De Baets, B., Rouzé, P., Van de Peer, Y. (2005) Predicting splice sites from high-dimensional local context representations. Bioinformatics 21(8):1332-8.

(50) 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.

(49) 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.

(48) * 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

(47) 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.

(46) Saeys, Y., Degroeve, S., Aeyels, D., Rouzé, P., Van de Peer, Y. (2004) Feature selection for splice site prediction: A new method using EDA-based feature ranking. BMC Bioinformatics 5:64.

(45) Degroeve, S., Saeys, Y., De Baets, B., Van de Peer, Y., Rouzé, P. (2004) Splice site prediction in eukaryote genome sequences: the algorithmic issues. The New Avenues in Bioinformatics J. Seckbach (ed.) another book of the Cellular Origin and Life in Extreme Habitats Book Series. Kluwer Academic Publishers, Dordrecht, The Netherlands. (2004).

(44) Saeys, Y., Degroeve, S., Aeyels, D., Rouzé, P., Van de Peer, Y. (2004) Selecting relevant features for gene structure prediction. Proceedings of Benelearn 13:103-109.

(43) 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.

(42) Hilson, P., Hilson, P., Allemeersch, J., Altmann, T., Aubourg, S., Avon, A., Beynon, J., Bhalerao, R.P., Bitton, F., Caboche, M., Cannoot, B., Chardakov, V., Cognet-Holliger, C., Colot, V., Crowe, M.L., Darimont, C., Durinck, S., Eickhoff, H., De Longevialle, A.F., Farmer, E.E., Grant, M., Kuiper, M., Lehrach, H., Leon, C., Leyva, A., Lundeberg, J., Lurin, C., Moreau, Y., Nietfeld, W., Paz-Ares, J., Reymond, P., Rouzé, P., Sandberg, G., Segura, M.D., Serizet, C., Tabrett, A., Taconnat, L., Thareau, V., Van Hummelen, P., Vercruysse, S., Vuylsteke, M., Weingartner, M., Weisbeek, P., Wirta, V., Wittink, F.R.A., Zabeau, M., Small, I. (2004) Versatile gene-specific sequence tags for Arabidopsis functional genomics:Trancript profiling and reverse genetics applications. Genome Res. 14(10B):2176-89.

(41) Thareau, V., D?hais, P., Hilson, P., Rouzé, P., Aubourg, S. (2003) Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics 19(17):2191-8.

(40) Rombauts, S., Van de Peer, Y., Rouzé, P. (2003) AFLPInsilico, simulating AFLP fingerprints. Bioinformatics 19(6):776-7.

(39) Crowe, M.L., Serizet, C., Thareau, V., Aubourg, S., Rouzé, P., Hilson, P., Beynon, J., Weisbeek, P., Van Hummelen, P., Reymond, P., Paz-Ares, J., Nietfeld, W., Trick, M. (2003) CATMA: a complete Arabidopsis GST database. Nucleic Acids Res. 31(1):156-8.

(38) Saeys, Y., Degroeve, S., Aeyels, D., Van de Peer, Y., Rouzé, P. (2003) Selecting Relevant Features for Splice Site Prediction by estimation of Distribution Algorithms. Proceedings of the 12th Belgian-Dutch Conference on Machine Learning (Benelearn 2002) 64-70. Utrecht, The Netherlands.

(37) * 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

(36) Blayo, P., Rouzé, P., Sagot, M.F. (2003) Orphan gene finding - an exon assembly approach. Theor. Comput. Sci. 290, 1407-1431..

(35) 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.

(34) Mathé, C., Sagot, M.F., Schiex, T., Rouzé, P. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30(19):4103-17.

(33) 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.

(32) 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.

(31) Degroeve, S., De Baets, B., Van de Peer, Y., Rouzé, P. (2002) Feature subset selection for splice site prediction. Bioinformatics 18 Suppl 2:S75-83.

(30) 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.

(29) 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.

(28) 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.

(27) 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.

(26) 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.

(25) Schiex, T., Moisan, A., Rouzé, P. (2001) EuG?ne: an eukaryotic gene finder that combines several sources of evidence. Lect. Notes in Comput. Sci. 2066, 11-125.

(24) 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.

(23) 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.

(22) 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.

(21) Sahnoun, I., D?hais, P., Van Montagu, M., Rossignol, M., Rouzé, P. (2000) PPMdb: a plant plasma membrane database. J. Biotechnol. 78(3):235-46.

(20) Terryn, N., Rouzé, P. (2000) The sense of naturally transcribed antisense RNAs in plants. Trends Plant Science 5(9):394-6.

(19) 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.

(18) 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.

(17) Mathé, C., Peresetsky, A., Dehais, P., Van Montagu, M., Rouzé, P. (1999) Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction. J. Mol. Biol. 285(5):1977-91.

(16) 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.

(15) 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.

(14) Rouzé, P., Pavy, N., Rombauts, S. (1999) Genome annotation: which tools do we have for it?. Curr. Opin. Plant Biol. 2(2):90-5.

(13) Pavy, N., Mathé, C., Rombauts, S., Rouzé, P. (1999) Genomics and bio-computing (in French). OCL-OLEAGINEUX CORPS GRAS LIPIDES 6,148-154.

(12) Crochemore, M., Konopka, A.K., Risler, J.L., Rouzé, P. (1999) Information and the genome -Preface. Comput & Chem. 23, 187-189.

(11) Terryn, N., Rouzé, P., Van Montagu, M. (1999) Plant genomics. FEBS Lett. 452, 3-6.

(10) Terryn, N., Gielen, J., De Keyser, A., Van Den Daele, H., Ardiles, W., Neyt, P., De Clercq, R., Coppieters, J., Dehais, P., Villarroel, R., Rouzé, P., Van Montagu, M. (1998) Sequence analysis of a 40-kb Arabidopsis thaliana genomic region located at the top of chromosome 1. Gene 215(1):11-7.

(9) Kertbundit, S., Linacero, R., Galis, I., Macas, J., Deboeck, F., Rouzé, P., Hernalstens, J.-P., De Greve, H. (1998) Molecular analysis of T-DNA-mediated translational b-glucoronidase gene fusions. Plant Mol. Biol. 36, 205-217.

(8) Santoni, V., Rouquié, D., Doumas, P., Mansion, M., Boutry, M., Degand, H., Dupree, P., Packman, L., Sherrier, J., Prime, T., Bauw, G., Posada, E., Rouzé, P., Dehais, P., Sahnoun, I., Barlier, I., Rossignol, M. (1998) Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J. 16(5):633-41.

(7) Tolstrup, N., Rouzé, P., Brunak, S. (1997) A branch-point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res. 25(15):3159-63.

(6) Terryn, N., Neyt, P., De Clercq, R., De Keyser, A., Van Den Daele, H., Ardiles, W., Dehais, P., Rouzé, P., Gielen, J., Villarroel, R., Van Montagu, M. (1997) Sequence analysis of a 24-kb continuous genomic region at the Arabidopsis thaliana PFL locus on chromosome 1. FEBS Lett. 416,156-160.

(5) Wu, H.-J., Gaubier-Comella, P., Delseny, M., Grellet, F., Van Montagu, M., Rouzé, P. (1996) Non-canonical introns are at least 109 years old. Nat. Genet. 14(4):383-384.

(4) Hebsgaard, S., Korning, PG., Tolstrup, N., Engelbrecht, J., Rouzé, P., Brunak, S. (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local & global sequence information. Nucleic Acids Res. 24(17):3439-52.

(3) Korning, PG., Hebsgaard, S., Rouzé, P., Brunak, S. (1996) Cleaning the GenBank Arabidopsis thaliana data set. Nucleic Acids Res. 24(2):316-20.

(2) Renaudin, J.-P., Doonan, J.H., Freeman, D., Hashimoto, J., Hirt, H., Inzé, D., Jacobs, T., Kouchi, H., Rouzé, P., Sauter, M., Savouré, A., Sorrell, D.A., Sundaresan, V., Murray, J.A.H. (1996) Plant cyclins: a unified nomenclature for plant A-, B- and D-type cyclins based on sequence organisation. Plant Mol. Biol. 32, 1003-1018.

(1) Vignal, L., Kawashima, H., Lisacek, F., Mephu, N., Rouzé, P., Quinqueton, J., Thermes, C. (1996) Exon prediction in eucaryotic genomes. Biochimie 78(5):327-34.











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