Yves Van de Peer
Bioinformatics
VIB Department of Plant Systems Biology, UGent

Yves Van de Peer PhD: Univ. of Antwerp, Antwerp, Belgium, '95 VIB Group leader since 2002 VIB Division Coordinator since 2003

e-mail phone +32 9 331 38 07 ADDRESS

Current team members
Group leader: Yves Van de Peer
Experts: Pierre Rouzé, Tom Michoel
Postdoctoral scientists: Eric Bonnet, Guy Baele, Jens Hollunder, Klaas Vandepoele, Lieven Sterck, Sara Groeneboer, Vanessa Vermeirssen, Xin-Ying Ren, Yvan Saeys
Ph.D. Students: Anagha Joshi, Bing Li, Cindy Martens, Elisabeth Wischnitzki, Evangelia Dougali, Irina Lambertz, Jeffrey Fawcett, Kevin Vanneste, Michiel Van Bel, Pedro Pattyn, Phuong Thi Ngoc Cao, Plus Lin, Sandra Botelho, Sara Movahedi, Sebastian Proost, Sofie Van Landeghem, Thomas Abeel, Yao Yao, Ying He
Support personnel: Sophie Maebe, Stephane Rombauts, Thomas Van Parys

Keywords
comparative genomics - gene prediction and annotation - gene and genome evolution - algorithm and software development - database

Science
Yves Van de Peer, in close collaboration with Pierre Rouzé, leads the Bioinformatics and Evolutionary Genomics (BEG) Division. The BEG division is a centre of excellence in the field of gene and genome annotation and in the field of comparative and evolutionary genomics.  In the future, our research group would also like to engage more in what we would refer to as ‘evolutionary systems biology’ by studying the evolution of entire biological processes and networks through gene duplication and divergence of transcriptional regulation. We also try to integrate our research within a system biology perspective, by linking our genome models with experimental genomics information as well as in silico functional predictions, miRNAs and cis-acting transcriptional modules, being typical examples.

During the past few years, novel gene prediction and modelling tools have been developed, making a wider use of machine learning algorithms but also of comparative approaches using sequence information from other genomes. The annotation tools that have been developed so far have been mainly used for re-annotating the Arabidopsis genome, and to obtain the first preliminary annotations of two novel genomes, namely that of the unicellular green alga Ostreococcus tauri and that of the poplar tree. For the coming years, we will further improve our gene prediction software, making use of feature subset selection techniques that are currently being developed, in order to speed up annotation efforts and to further increase the reliability and efficiency of genome annotation projects. Genome annotation will continue to be a major driver for our research (see further) since we will be involved in future gene prediction and genome annotation projects such as those of tomato, Medicago, a different Ostreococcus strain, two mycorrhizal fungi (Laccaria and Glomus), a brown alga (Ectocarpus), and a moss (Physcomitrella).  Therefore, further development of efficient gene annotation platforms and pipelines is of crucial importance.
These new genomes will provide us with a large amount of new sequence information that we will exploit for further research during the coming years.  In particular these new genomes will be applied in a comparative way to:
• Identify conserved non-coding RNA genes
• Identify conserved cis-regulatory elements in promoter regions
• Delineate gene families across plant species
• Identify syntenic and collinear regions between different genomes
• Trace evolutionary history of some major genes, pathways and networks

One of the biological processes we would like to study in more detail, using an evolutionary systems biology approach, is the cell cycle.   The availability of many new genomes will allow us to study all genes involved in the cell cycle across different species and will allow studying how the cell cycle has evolved through time and over the tree of life.  Functional genomics data and comparative approaches will allow us to study the transcriptional network underlying the cell cycle, from more simple organisms to more complex ones.

Thirty-five years ago, Susumu Ohno´s seminal book entitled “Evolution by Gene Duplication” outlined the potential role of gene duplication as the driving force behind the evolution of increasingly complex organisms. Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has indeed been rampant. Moreover, next to a continuous mode of small-scale gene duplications, in many organisms, the complete genome – or at least large portions thereof – has been duplicated in their evolutionary past. In particular such large-scale gene duplication events have been associated with important evolutionary transitions and are considered a major driving force for evolution and the increase of biological complexity, and adaptive radiations of species. However, the mechanisms underlying evolutionary innovation through these genome duplications and the overall consequences for evolution and complexity remain unclear. We have recently started to develop full-fledged mathematical models that quantitatively simulate the population dynamics of duplicate genes. Such a model estimates the birth and death rates of genes, taking into account both major, genome-wide duplication events and a continuous mode of gene duplication and gene loss in a coupled differential equation framework. By applying the computational model to different functional categories of Arabidopsis genes, we can assess the importance of different gene duplication events for the evolution of specific gene functions or biological processes and pathways. Our model has already shown that decay rates for genes of most functional Gene Ontology categories are vastly different for large-scale and small-scale duplication events. Furthermore, it allows correlating gene duplication events with decisive moments in evolution.  Applying such mathematical models will allow us to speculate on the evolution of important biological processes and can provide working hypotheses for the further study of biological networks and evolution of transcriptional regulation. 

Press Release
See also press release (23/03/2009): DNA duplication: a mechanism for ‘survival of the fittest’ - based on a publication in PNAS (Fawcett et al., PNAS, 2009)

See also press release (05/03/2008): Secrets of cooperation between trees and fungi revealed - based on a publication in Nature (Martin et al., Nature, 2008)

De Schutter K, Lin Y, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouzé P, Van de Peer Y, Callewaert N
Genome sequence of the recombinant protein production host Pichia pastoris
NAT BIOTECHNOL 27, 561-6, 2009



Martin F, Aerts A, Ahrén D, Brun A, Danchin E, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro H, Wuyts J, Blaudez D, Buée M, Brokstein P, Canbäck B, Cohen D, Courty P, Coutinho P, Delaruelle C, Detter J, Deveau A, Difazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger P, Jain P, Kilaru S, Labbé J, Lin Y, Legué V, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq M, Peter M, 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 P, Richardson P, Rouzé P, Sanders I, Stajich J, Tunlid A, Tuskan G, Grigoriev I
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
NATURE 452, 88-92, 2008



Carlton J, Hirt R, Silva J, Delcher A, Schatz M, Zhao q, Wortman J, Bidwell S, Alsmark U, Besteiro S, Sicheritz-Ponten T, Noel C, Dacks J, Foster P, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton G, Westrop G, Müller S, Dessi D, Fiori P, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera F, Simoes-Barbosa A, Brown M, Hayes R, Mukherjee M, Okumura C, Schneider R, Smith A, Vanacova S, Villalvazo M, Haas B, Pertea M, Feldblyum T, Utterback T, Shu C, Osoegawa K, De Jong P, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik S, Logsdon J, Henze K, Gupta A, Wang C, Dunne R, Upcroft J, Upcroft P, White O, Salzberg S, Tang P, Chiu C, Lee Y, Embley T, Coombs G, Mottram J, Tachezy J, Fraser-Liggett C, Johnson P
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
SCIENCE 315, 207-12, 2007



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, Bhalerao p, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman j, Chen G, 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, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson D, Nelson C, Nieminen K, Nilsson O, Pereda V, 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
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
SCIENCE 313, 1596-604, 2006



Van de Peer Y
Computational approaches to unveiling ancient genome duplications
NAT REV GENET 5, 752-763, 2004

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