Cedric Simillion

Postdoc
(Group member from 2001 until 2011)


+ 32 (0) 9 33 13 823

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

Research

Genome Archeology

It has long been suggested that large-scale duplication events, such as genome duplications, provide the necessary genetic material for evolution to act upon to evolve new structures. Next to this, genomes also undergo rearrangements which are thought to be linked to the divergence of species. The goal of my research is to uncover these ancient events that shaped today's genomes. In order to accomplish this, we are developing software that allows the detection of very ancient homology relations in and between genomes.

Papers

(14) Passos, J.F., Nelson, G., Wang, X., Richter, T., Simillion, C., Proctor, C.J., Miwa, S., Olijslagers, S., Hallinan, J., Wipat, A., Saretzki, G., Rudolph, K.L., Kirkwood, T.B., von Zglinicki, T. (2010) Feedback between p21 and reactive oxygen production is necessary for cell senescence. Mol. Syst. Biol. 6:347.

(13) Passos, J.F., Simillion, C., Hallinan, J., Wipat, A., von Zglinicki, T. (2009) Cellular senescence: unravelling complexity. Age (Dordr) 31(4):353-63.

(12) 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.

(11) Carlton, J.M., Hirt, H., Silva, E.P., Delcher, A.L., Schatz, M., Zhao, Q., Wortman, J.R., Bidwell, S.L., Alsmark, C.M., Besteiro, S., Sicheritz-Ponten, T., Noel, C.J., Dacks, J.B., Foster, P.G., Simillion, C., Van de Peer, Y., Barton, G.J., Westrop, G.D., Müller, S., Dessi, D., Fiori, L.P., Paulsen, I., Zhang, J., Bastida-Corcuera, F.D., Barbosa, A., Brown, M.T., Hayes, R.D., Mukherjee, M., Okumura, C.Y., Schneider, M., Villalvazo, M., Haase, G., Pertea, M., Feldblyum, T., Utterback, T.R., Shu, C.-L., Osoegawa, K., de Jong, P.J., Dolezal, P., Hrd, I., Malik, S.-B., Logsdon, Jr., Henze, K., Gupta, A., Wang, X., Dunne, R.L., Upcroft, J.A., Upcroft, P., White, O., Salzberg, S.L., Tanghe, K., Chiu, C.-H., Embley, T.M., Coombs, G.H., Mottram, J.C., Tachezy, J., Fraser-Liggett, C.M., Johnson, P.J. (2007) Draft Genome Sequence of the Sexually-Transmitted Pathogen Trichomonas vaginalis. Science 315(5809):207-12.

(10) Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., Van de Peer, Y. (2006) The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 7(5):R43.

(9) Gevers, D., Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol. 12(4):148-54.

(8) Simillion, C., Vandepoele, K., Saeys, Y., Van de Peer, Y. (2004) Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. 14(6):1095-106.

(7) Vandepoele, K., Simillion, C., Van de Peer, Y. (2004) The quest for genomic homology. Curr. Genomics 5(4):299-308.

(6) Simillion, C., Vandepoele, K., Van de Peer, Y. (2004) Recent developments in computational approaches for uncovering genomic homology. BioEssays 26(11):1225-35.

(5) Vandepoele, K., Simillion, C., Van de Peer, Y. (2003) Evidence that rice, and other cereals, are ancient aneuploids. The Plant Cell 15(9):2192-202.

(4) Raes, J., Vandepoele, K., Saeys, Y., Simillion, C., Van de Peer, Y. (2003) Investigating ancient duplication events in the Arabidopsis genome. J. Struct. Func. Genomics. 3(1-4):117-29.

(3) Simillion, C., Vandepoele, K., Van Montagu, M., Zabeau, M., Van de Peer, Y. (2002) The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99(21):13627-32.

(2) Vandepoele, K., Simillion, C., Van de Peer, Y. (2002) Detecting the undetectable: Uncovering duplicated segments in Arabidopsis through rice. Trends Genet. 18(12):606-8.

(1) Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., Van de Peer, Y. (2002) The Automatic Detection of Homologous Regions (ADHoRe) and its application to microcolinearity between Arabidopsis and Rice. Genome Res. 12(11):1792-801.











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!