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Peer Bork
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. Christine Orengo
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 Erik Sonnhammer
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. James McInerney
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. Mar Albà
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 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. Alberto M. R. Dávila
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. |