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
2 Information society technologies
3 Nanotechnologies and nano-sciences, knowledge-
based multifunctional materials & processes 1300
4 Aeronautics and space
5 Food quality and safety
6 Sustainable development, global change and ecosystems 2120
7 Citizens and governance in a knowledge-based society

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

4. Life sciences, genomics and biotechnology for health
1.1.1 Fundamental knowledge and basic tools for functional genomics in all organisms
Fundamental genomics
 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. Expressions of Interest
Invitation to submit: 20 March 2002
(Electronic submission)
Deadline for EoIs: 7 June 2002
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)

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 meeting definition of priority topics for IP and NoE  
- no pre-selection of particular EoIs or consortia

9. Fundamental genomics
Expressions of Interest: Overall response (total: 523)
Bioinfor- matics
Gene expression and proteomics
Structural genomics
Basic biological processes
Not relevant (reassigned)
Comparative genomics and population genetics
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