Lieven Sterck
ResearchI first came into contact with bioinformatics during my Master-thesis, entitled "In silico detection of cis-acting regulatory elements through phylogenetic footprinting of plant promoters". The main aim of this project was to test the applicability of the phylogenetic footprinting approach on plants and so I needed sets of orthologous genes (in their genomic context) from as much plant-species as possible. Back then only the genome sequence of Arabidopsis was available (and annotated) and a limited amount of genomic BAC-sequences of other plants (mostly non-annotated), so the first part of the thesis mainly consisted of annotating 'putative' othologous genes in other plant-species. Doing so I soon realized that a good (structural) gene-annotation is one of the cornerstones of bioinformatics and that gene-prediction could only become more important as more and more genomes become available. Thatâ¬"s briefly the background of the bioinformatics research-topics I focus on in my PhD studies: genome-annotation and comparative & evolutionary genomics. Genome annotationWhile in the beginning I talked about gene-prediction I now prefer to call it genome annotation, this is because I switched from (manually) annotation a few genes to applying sophisticated programs to predict all genes in whole genome sequence. Moreover it is more and more becoming 'genome-annotation' because we not longer focus solely on the protein-coding genes in a genome but also on other biological relevant features (transposable elements, RNA-genes, cis-acting promoter elements,⬦) that are present in genome sequences. If I had to describe what I mean with genome-annotation in 1 sentence it would sound something like "finding the biological relevant features in a genomic sequence in a high-throughput manner". For more information on which genomes I'm currently working I would like to point you to the genome-projects section on our group-website. From the number of genome projects we are involved in it's clear that it is my colleagues and my mission to evolve towards a center of excellence in gene and genome annotation. Comparative & evolutionary genomicsThe other main research topic of my PhD is, to me, a logical consequence of the previous one. An annotated whole genome sequence is the starting point of a wealth of other bioinformatics analyses especially when genome sequences from more and more species are becoming available. That's way I developed a more than average interest in understanding how evolution shaped and/or shapes genomes of different species. I try to achieve this by looking for large-scale duplication events in genome sequences and by analyzing the collinearity between different genomes. I believe that comparative genomics is an ideal way to start to tackle these important questions. In general I consider myself a true 'genomics'-man, with an interest in lots of things as long as they are genome-wide and preferably high-throughput. Besides the purely scientific topics I also like to develop programs and tools that can be applied in the field of genome-annotation (eg programs/pipelines to detect biological features in a genome) or comparative genomics (eg. visualization tools to represent the results of comparative studies) Papers(33) Cañas, R., Li, Z., Pascual, M.B., Castro-Rodríguez, V., Avila, C., Sterck, L., Van de Peer, Y., Canovas, F. (2017) The gene expression landscape of pine seedling tissues. The Plant Journal (In Press).(32) Li, Z., R. De La Torre, A., Sterck, L., M. Canovas, F., Avila, C., Merino Sierra, I., Antonio Cabezas, J., Teresa Cervera, M., K. Ingvarsson, P., Van de Peer, Y. (2017) Single-copy genes as molecular markers for phylogenomic studies in seed plants. Genome Biol. Evol. (In Press). (31) Merino, I., Sterck, L., Abrahamsson, M., Craven-Bartle, B., Canovas, F. (2016) Transcript profiling for early stages during embryo development in Scots pine. BMC Plant Biology 16:255. (30) Perazzolli, M., Herrero, J., Sterck, L., Lenzi, L., Pellegrini, A., Puopolo, G., Van de Peer, Y., Pertot, I. (2016) Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat. BMC Genomics 17:838. (29) Cormier, A., Avia, K., Sterck, L., Derrien, T., Wucher, V., Andres, G., Monsoor, M., Godfroy, O., Lipinska, A., Perrineau, M.-M., Van de Peer, Y., Hitte, C., Corre, E., Coelho, S., Cock, M. (2016) Re-annotation, improved large-scale assembly and establishment of a catalogue of non-coding loci for the genome of the model brown alga Ectocarpus. New Phytologist 214(1):219-232. (28) Potenza, E., Luisa Racchi, M., Sterck, L., Coller, E., Asquini, E., Tosatto, S.C. E., Velasco, R., Van de Peer, Y., Cestaro, A. (2015) Exploration of alternative splicing events in ten different grapevine cultivars. BMC Genomics 16:706 . (27) Morel, N., Sterck, L., Swennen, D., Marcet-Houben, M., Onesime, D., Levasseur, K., Jacques, N., Mallet, S., Couloux, A., Labadie, K., Amselem, J., Beckerich, J., Henrissat, B., Van de Peer, Y., Wincker, P., Souciet, J., Gabaldon, T., Tinsley, C.R., Casaregola, S. (2015) Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Scientific Reports 5:11571. (26) Vanneste, K., Sterck, L., Myburg, A.A., * Van de Peer, Y., * Mizrachi, E. (2015) Horsetails are ancient polyploids: Evidence from Equisetum giganteum. The Plant Cell 27(6):1567-78. *contributed equally (25) Ahmed, S., Cock, M., Pessia, E., Luthringer, R., Cormier, A., Robuchon, M., Sterck, L., Peters, S., Dittami, S., Corre, E., Valero, M., Aury, J., Roze, D., Van de Peer, Y., Bothwell, J., Marais, GAB., Coelho, S.M. (2014) A haploid system of sex determination in the brown alga Ectocarpus sp. Current Biology 24(17):1945-1957. (24) Myburg, A.A., Grattapaglia, D., Tuskan, G., Hellsten, U., Hayes, R.D., Grimwood, J., Jenkins, B., Lindquist, E., Tice, H., Bauer, D., Goodstein, D., Dubchak, I., Poliakov, A., Mizrachi, E., Kullan, A.R.K., van Jaarsveld, I., Hussey, S.G., Pinard, D., van der Merwe, K., Singh, N., Silva-Junior, O.B., Togawa, R.C., Pappas, M.R., Faria, D.A., Sansaloni, C.P., Petrol, C.D., Yang, X., Ranjan, P., Tschaplinski, T.J., Ye, Z., Li, T., Sterck, L., Vanneste, K., Murat, C., Soler, M., San Clemente, H., Saidi, N., Cassan-Wang, H., Dunand, C., Hefer, C.A., Bornberg-Bauer, E., Kersting, A.R., Vining, K., Amarasinghe, V., Ranik, M., Naithani, S., Elser, J., Boyd, A.E., Liston, A., Spatafora, J.W., Dharmwardhana, P., Raja, R., Sullivan, C., Romanel, E., Alves-Ferreira, M., Külheim, C., Foley, W., Carocha, V., Paiva, J., Kudrna, D., Brommonschenkel, S.H., Pasquali, G., Byrne, K., Rigault, P., Tibbits, J., Spokevicius, A., Jones, R.C., Steane, D.A., Vaillancourt, R.E., Potts, B.M., Joubert, Y., Barry, K., Pappas Jr., G.J., Strauss, S.H., Jaiswal, P., Grima-Pettenati, J., Salse, J., Van de Peer, Y., Rokhsar, D., Schmutz, J. (2014) The genome sequence of Eucalyptus grandis. Nature 510(7505):356–362. (23) * 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 (22) 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. (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) Zambounis, A., Elias, M., Sterck, L., Maumus, F., Gachon, C. (2012) Highly dynamic exon shuffling in candidate pathogen receptors... What if brown algae were capable of adaptive immunity?. Mol. Biol. Evol. 29(4):1263-76. (19) Malacarne, G., Perazzolli, M., Cestaro, A., Sterck, L., Fontana, P., Van de Peer, Y., Viola, R., Velasco, R., Salamini, F. (2012) Deconstruction of the (paleo)polyploid grapevine genome based on the analysis of transposition events involving NBS resistance genes . PLoS One 7(1):e29762. (18) 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. (17) Grenville-Briggs, L., Gachon, C., Strittmatter, M., Sterck, L., Küpper, F.C., van West, P. (2011) A molecular insight into algal-oomycete warfare: cDNA analysis of Ectocarpus siliculosus infected with the basal oomycete Eurychasma dicksonii. PLoS One 6(9):e24500. (16) 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. (15) Delage, L., Leblanc, C., Nyvall Collén, P., Gschloessl, B., Oudot, M-P., Sterck, L., Poulain, J., Aury, J., Cock, M. (2011) In Silico Survey of the Mitochondrial Protein Uptake and Maturation Systems in the Brown Alga Ectocarpus siliculosus. PLoS One 6(5):e19540. (14) 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. (13) 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. (12) * Proost, S., * Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., Vandepoele, K. (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. The Plant Cell 21(12):3718-31. *contributed equally (11) Van de Peer, Y., Fawcett, J., Proost, S., Sterck, L., Vandepoele, K. (2009) The flowering world: a tale of duplications. Trends Plant Science 14(12):680-8. (10) 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. (9) 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. (8) Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008) i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics 24(1):127-8. (7) Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., Pruss, D., Pindo, M., FitzGerald, L.M., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell, B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J.T., Perazzolli, M., Eldredge, G., Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C., Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., Si-Ammour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev, V., Fawcett, J., Sterck, L., Vandepoele, K., Grando, M.S., Toppo, S., Moser, C., Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana, P., Gutin, A., Van de Peer, Y., Salamini, F., Viola, R. (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLoS One 2(12):e1326. (6) Rohde, A., Ruttink, T., Hostyn, V., Sterck, L., Van Driessche, K., Boerjan, W. (2007) Gene expression during the induction, maintenance, and release of dormancy in apical buds of poplar. J. Exp. Bot. 58(15-16):4047-60. (5) 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. (4) * 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 (3) 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 (2) Morreel, K., Goeminne, G., Storme, V., Sterck, L., Ralph, S., Coppieters, J., Breyne, P., Steenackers, M., Georges, M., Messens, W., Boerjan, W. (2006) Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. Plant J. 47(2):224-37. (1) 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. |
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