Fundamental knowledge and basic tools for functional genomics in all organisms

1. Fundamental knowledge and basic tools for functional genomics in all organisms Meeting of the National Contact Points 23/10/2002 Brussels Indridi Benediktsson

2. 7 Thematic Priorities M € 1 Life sciences, genomics and biotechnology for health 2255 2 Information society technologies 3625 3 Nanotechnologies and nano-sciences, knowledge- based multifunctional materials & processes1300 4 Aeronautics and space 1075 5 Food quality and safety 685 6 Sustainable development, global change and ecosystems 2120 7 Citizens and governance in a knowledge-based society 225

3. 1.1 Advanced genomics and its applications for health (€ 1,100 M) 1.1.1 Fundamental knowledge and basic tools for functional genomics in all organisms 1.1.2 Application of knowledge and technologies in the field of genomics and biotechnology for health 1.2 Combating major diseases (€ 1,155 M) 1.2.1 Application-oriented genomic approaches to medical knowledge and technologies 1.2.2 Combating cancer 1.2.3 Confronting the major communicable diseases linked to poverty Life sciences, genomics and biotechnology for health

4. Life sciences, genomics and biotechnology for health Fundamental genomics 1.1.1 Fundamental knowledge and basic tools for functional genomics in all organisms  Gene expression and proteomics  Structural genomics  Comparative genomics and population genetics  Bioinformatics  Multidisciplinary functional genomics approaches to basic biological processes

5. Fundamental genomics  Gene expression and proteomics Developing high throughput tools and approaches for monitoring gene expression and protein profiles and for determining protein function and protein interactions  Structural genomics Developing high throughput approaches for determining high-resolution 3-D structures of macromolecules  Comparative genomics and population genetics Developing model organisms and transgenic tools; developing epidemiology tools and standardised genotyping protocols

6. Fundamental genomics  Bioinformatics Developing bioinformatics tools and resources for data storage, mining and processing; developing computational biology approaches for in silico prediction of gene function and for the simulation of complex regulatory networks  Multidisciplinary functional genomics approaches to basic biological processes Elucidation of the mechanisms underlying fundamental cellular processes, to identify the genes involved and to decipher their biological functions in living organisms

7. Criteria: 1. Quality of the rationale, objectives, general approach 2. Need and relevance 3. Excellence 4. For NoE Integration and structuring effect (addressing fragmentation) For IP Integration (delivering specific results) Expressions of Interest Invitation to submit: 20 March 2002 (Electronic submission) Deadline for EoIs: 7 June 2002

8. Expressions of Interest ANALYSIS METHODOLOGY Peer review by panels of high level experts • Remote assessment prior to the panel meeting individual scores and ‘citation lists’ of top 15 EoIs • Discussion at the panel meetingdefinition of priority topics for IP and NoE   - no pre-selection of particular EoIs or consortia

9. Basic biological processes Comparative genomics and population genetics Bioinfor-matics Structural genomics Not relevant (reassigned) Gene expression and proteomics 51 32 96 58 183 103 Fundamental genomics Expressions of Interest: Overall response (total: 523) IP : NoE  approximate ratio 2:1

10. Fundamental genomics • The experts recommended 30 topics in total • Each topic represents on the average 3 EoIs • About 15 topics could be open in each of the two calls • The selected topics will be open only for the call indicated • Competition between topics and within topic areas • Some topic areas which are open might end up not being supported (depending on quality of the proposals)

11. Recommended topics from the EoIs Gene expression and proteomics • Development of advanced array technologies for proteins, DNA and RNA • Development and application of high throughput proteomics technologies for the generation of a large data set of protein-protein interactions • Global in situ gene expression analysis in mouse models and human tissue

12. Recommended topics from the EoIs Structural genomics • High throughput 3D-structure determination of membrane proteins • Supramolecular analysis by 3D-electron microscopy in situ • Development of new hardware and software for the implementation of innovative automated technologies at synchrotron sites • Comparative structural biology of viral replication • Structure determination of large protein complexes

13. Recommended topics from the EoIs Comparative genomics and population genetics • Non-mammalian vertebrates as models for human development and disease mechanisms • Development of in-vivo imaging technologies for phenotyping and functional analysis in cells and animal models

14. Recommended topics from the EoIs Comparative genomics and population genetics • RNA interference screening in Arabidopsis for identification of gene functions relevant to health • Molecular tools for phenotyping human populations • Coordination and standardisation of high throughput genotyping in human populations in Europe • Standardisation and integration of genomic and phenotypic information on bacterial diversity linked to human health

15. Recommended topics from the EoIs Bioinformatics • Developing methods and resources in bioinformatics to focus on human genome annotation • Bioinformatics and genomics grid for European research • Development of an integrated software platform to tackle genomic sequence-structure-function relationships

16. Recommended topics from the EoIs Basic biological processes • Multidisciplinary approaches of functional genomics for : • The cell cycle • Non-human embryonic stem cell differentiation • Erythroid development and disorders • Lymphangiogenesis • Epigenetics: chromatin dynamics, non-coding RNA, imprinting and silencing • Inflammation processes in human disease • Ubiquitin-proteasome and related pathways

17. Recommended topics from the EoIs Basic biological processes • Multidisciplinary approaches of functional genomics for : • Animal models for studying human kidney disease • Peroxisomes in health and disease • Inner ear or retina development and disorders • DNA damage and repair mechanisms in health and disease • Animal models to study human disease of the immune system or muscle • Large epidemiological studies of X-linked syndromes

18. Indicative topics for STREPs and CA • Standardisation of gene expression DNA arrays and proteomics approaches • Deciphering the processes underlying the controlled integration and expression of transgenes in model organisms • Methods for the production of crystals for high throughput structural determination • Transposon mutagenesis methods in the mouse • Co-ordination of functional genomics in the rat model • Role of non-coding RNA in disease • Molecular systems biology approaches for modelling gene functions and complex regulatory networks

19. Indicative topics for STREPs and CA • Detecting low abundance mRNAs and proteins • Identifying new multi-protein “nanomachines” • Comparative genomics in protozoa relating to human health • Programmed cell death across the eukaryotic kingdom • Compiling large data sets on splice variants in humans • Signal transduction pathways mediated via serine/threonine kinases

20. Indicative topics for SSA • Workshops on structuring research activities of fundamental genomics in important fields not yet addressed • Workshops on business opportunities in functional genomics • Bilateral meetings on fundamental genomics issues between scientists from Europe and a third country having an S&T co-operation agreement with the EU • Meetings on integration of candidate countries' researchers in specific activity lines to be supported under this part of the programme • Technology foresight meetings to identify future opportunities within the field of functional genomics