Senior researcher of EMBL-Heidelberg. His research interest centers on prediction of protein function, protein and genome evolution, domain analysis, sequence and structural analysis of proteins and genes, comparative genome and proteome analysis, bridging genotype and phenotype.

Relevant publications:

Korbel JO, Jensen LJ, von Mering C, Bork P. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol. 2004 Jul;22(7):911-7.

von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P. Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15428-33.

Group leader and senior researcher at the University College London (UK). Dr. Orengo has research interest on algorithms for protein structure comparison, classification and recognition. Over the past four years a major research interest has been the development of protocols for classifying protein domain structures according to their (C)lass, (A)rchitecture, (T)opology or fold and (H)omology (CATH database). Individual folds within multidomain proteins are identified by a consensus assignment method, developed together with S. Jones, M. Stewart and J. Thornton.

Relevant publications:
Bray JE, Marsden RL, Rison SC, Savchenko A, Edwards AM, Thornton JM, Orengo CA. A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics. 2004 Sep 22;20(14):2288-95. Epub 2004 Jun 16.

Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA. From structure to function: approaches and limitations. Nat Struct Biol. 2000 Nov;7 Suppl:991-4

Professor of Bioinformatics and Director of the Center for Genomics and Bioinformatics, Karolinska Institutet. His group is mainly involved in research and development of new methods for sequence analysis, focussed on protein function predition, and applying them to genomics research. These include automated and graphical tools for homology analysis, methods for analyzing protein domain families, and methods for predicting and visualizing sequence features.

Relevant publications:

O'Brien KP, Remm M, Sonnhammer EL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D476-80.

Storm CE, Sonnhammer EL. Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res. 2003 Oct;13(10):2353-62.

Senior lecturer at the National University of Ireland Maynooth. Dr. McInerney works on understanding two important evolutionary trends – adaptive evolution in protein-coding genes and horizontal gene transfer. He has developed methods to detect selection and has also been involved in the development of phylogenetic supertree software and software to parallelise algorithms for inferring phylogenetic trees. Dr. McInerney has organized and taught courses in bioinformatics and molecular evolution for the past ten years, having previously organized three EMBO-funded bioinformatics course. For the course in this proposal, Dr. McInerney will teach new mathematical methods for phylogeny reconstruction and how they can be used to study reassortment in viruses, the development of disease resistance in bacteria and adaptation of parasites to their hosts. Dr. McInerney will give a seminar on the first day of the course.

Relevant publications:

Kinsella, R.J., Fitzpatrick, D.A., Creevey, C.J. and McInerney J.O. (2003). Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution and gene duplication. Proceedings of the National Academy of Sciences USA, 100, 10320-10325.

Creevey, C.J. and McInerney, J.O. (2005). CLANN: Investigating Phylogenetic Information Through Supertree Analysis. Bioinformatics 21 (3) 390-392.

Research Professor at Pompeu Fabra University (Barcelona, Spain) and Coordinator of the Spanish Bioinformatics Network. Dr. Albà works on diverse aspects of comparative genomics, including the analysis of gene regulation sequences in
genomes, the evolution of tandem repeats in proteins and the variability of evolutionary rates across genes. She has been a Lecturer of the BSc and PhD Bioinformatics Courses at Pompeu Fabra University for the past five years. She has also taught at the European Master on Genomics of the University of Paris .

Relevant publications:

Albà, M.M., Guigó, R. (2004). Comparative analysis of amino acid repeats in rodents and humans. Genome Research, Vol. 14: 549-554.

Holzerdlandt, R., Orengo, C.A., Kellam, P., Albà, M.M. (2002). Identification of novel herpesvirus homologues in the human genome. Genome Research, Vol. 12:1739-1748.

Associate researcher at the Oswaldo Cruz Institute (FIOCRUZ) and co-ordinator of the BiowebDB (comparative genomics) consortium in Brazil. His is also member of the IAEA collaborating center for Animal Genomics and Bioinformatics and the editor in chief of the “Kinetoplastid Biology and Disease” journal. Dr. Dávila research centers on the molecular evolution of kinetoplastids, functional annotation and mining of those genomes.

Relevant publications:

Davila AM, Lorenzini DM, Mendes PN, Satake TS, Sousa GR, Campos LM, Mazzoni CJ, Wagner G, Pires PF, Grisard EC, Cavalcanti MC, Campos ML. GARSA: genomic analysis resources for sequence annotation. Bioinformatics. 2005 Dec
1;21(23):4302-3. Epub 2005 Oct 6.

Davila AM, Majiwa PA, Grisard EC, Aksoy S, Melville SE. Comparative genomics to uncover the secrets of tsetse and livestock-infective trypanosomes. Trends Parasitol. 2003 Oct;19(10):436-9.