Computational Genomics

Research Interests

We are interested in the evolutionary mechanisms underlying the origins and evolution of cellular life and the complex structures within the cell, the transitions to multi-cellularity, and the medical applications of evolutionary genomics.

Our research encompasses themes that are broadly classified as evolutionary cell biology, systems biology, pathogenomics, and translational or medical bioinformatics.

Group Members

Research Project

Evocell – the evolution of cellular structures and compartments

We are interested in the origins and evolution of eukaryotic cell organization, and are pursuing two lines of research currently:

i) The evolution of protein traffic pathways and cellular compartments, aiming to understand the origins of this system, as well as the mechanisms for pathway specialization. This project is a collaboration with the Cellular pathogenesis of Malaria Group at the IGC.

ii) The evolution of centrioles, which form the basal body of cilia and flagella, as well as the centrosome. This project is a collaboration with the cell cycle regulation laboratory at the IGC.

Research Project

Genome Evolution

We are interested in understanding how the evolution of genomes and protein repertoires drives the evolution of organisms. Our research in these topics ranges from studying the relative extent of specific types of changes in proteins, to the study of gene loss in parasitic organisms.

Research Project

Bacterial sporulation

Endospores are the most resistant cell types known to man, and the product of a complex differentiation program. They are also the infectious gents of a variety of human diseases and vectors for bioterrorism. We are collaborating with the Bacterial Development group at the ITQB in the study of the mechanisms of assembly, in time and in space, of the endospore.

Publications

(Selected) Updated January (2009).

Pereira Leal, J.B., Levy, E.D. (2008). Evolution and dynamics of protein interactions and networks Curr Opin Struct Biol 18(3) :349-57

Pereira Leal, J.B. (2008). The Ypt/Rab family and the evolution of trafficking in fungi Traffic 9(1) :27-38

Pereira Leal, J.B., Levy, E.D., Kamp. C. and Teichmann, S.A. (2007). The evolution of protein complexes by duplication of homomeric interactions Genome Biol. 8(4) :R51v

Rasteiro, R, Pereira Leal, JB. (2007). Multiple domain insertions and losses in the evolution of the Rab prenylation complex BMC Evol Biol 7 :140

Pereira Leal, J.B., Levy, E.D., Teichmann, S.A. (2006). The origins and evolution of functional modules: lessons from protein complexes Philos Trans R Soc Lond B Biol Sci 361(1467) :507-17

Levy, E.D., Pereira Leal, J.B., Chothia, C. and Teichmann (2006). 3D Complex: a structural classification of protein complexes PLoS Comp. Bio. 2(11) :e155

Mosedale, G., Niedzwiedz, W., Alpi, A., Perrina, F., Pereira Leal, J.B., Johnson, M., Langevin, F., Pace, P., Patel, K.J. (2005). The vertebrate Hef ortholog is a component of the Fanconi anemia tumor-suppressor pathway Nature Struct. Mol. Biol. 12(9) :763-71

El-Sayed, N.M., Myler, P.J., Blandin, G., Berriman, M., Crabtree, J., Aggarwal, G., Caler, E., Renauld, H., Worthey, E.A., Hertz-Fowler, C., Ghedin, E., Peacock, C., Bartholomeu, D.C., Haas, B.J., Tran, A.N., Wortman, J.R. Alsmark, U.C., Angiuoli, S., Anupama, A., Badger, J., Bringaud, F., Cadag, E., Carlton, J.M., Cerqueira, G.C., Creasy, T., Delcher, A.L., Djikeng, A., Embley, T.M., Hauser, C., Ivens, A.C., Kummerfeld, S.K., Pereira Leal, J.B., Nilsson, D., Peterson, J., Salzberg, S.L., Shallom, J., Silva, J.C., Sundaram, J., Westenberger, S., White, O., Melville, S.E., Donelson, J.E., Andersson, B., Stuart, K.D., Hall, N. (2005). Comparative genomics of trypanosomatid parasitic protozoa Science 309(573 :404-9

Pereira Leal, J.B. and Teichmann, S.A. (2005). Novel specificities emerge by step-wize duplication of functional modules Genome Res. 15(4) :552-9

Pereira Leal, J.B.*, Enright, A.*. and Ouzounis, C.A. (2004). Identification of Functional Modules from Protein Interaction networks Proteins - Structure function and Genetics 54(1) :49-57