Download Bioinformatics

Workshop
Bioinformatics and
Computational Biology
Madrid, 25th-26th April 2002
Auditorio BBVA
Paseo de la Castellana, 81
Coordinated by Alfonso Valencia and Roderic Guigó
Post genomic technologies
Genome
Sequencing
Structural
Proteomics
Proteomics
- mass. spec.
- yeast two hybrid
Literature
Functional Genomics /
variability
BIOINFORMATICS
- DNA arrays
- SNPs
Protein-protein interaction networks
- evolution
- new drugs
- cellular organization - cellular factory
- genotyping
- biotecnology
Red de interacción entre proteínas
Extraída de la literatura
(Alma Bionformática)
Experimental (CellZome)
Bioinformatics and Computational Biology in 10 years
Big
challenges
Integration
in biology
Data
management
2000
2010
Information integration
Comparative
genomics
Genomic
information
Gene identification
Functional
relations
Expression
Arrays
Similarity of
expression
patterns
Profiles of
metabolic
products
Genes of interest
2-hybrid
system
Chemistry
Physical interactions
Mass spec. for
protein
complexes
Characterization of
mutants
Phenotypes
SNPs
Biological results
Increasingly complex data
Data management
(databases)
Complex data
(integrated databases)Ontologies
Information
extraction
Mol. Biol. data Genome information
WWW
PostGenomic technology
Next Generation Internet
Distributed GRID computing
Integrative Biology /
Biomedicine / Environment
1980
1990
2000
2010
Top 10 problems
1.
Precise, predictive model of transcription initiation and termination: ability to predict
where and when transcription will occur in a genome
2.
Precise, predictive model of RNA splicing/alternative splicing: ability to predict the splicing
pattern of any primary transcript in any tissue
3.
Precise, quantitative models of signal transduction pathways: ability to predict cellular
responses to external stimuli
4.
Determining effective protein:DNA, protein:RNA and protein:protein recognition codes
5.
Accurate ab initio protein structure prediction
6.
Rational design of small molecule inhibitors of proteins
7.
Mechanistic understanding of protein evolution: understanding exactly how new protein
functions evolve
8.
Mechanistic understanding of speciation: molecular details of how speciation occurs
9.
Continued development of effective gene ontologies - systematic ways to describe the
functions of any gene or protein
10.
Education: development of appropriate bioinformatics curricula for secondary,
undergraduate and graduate education
Reprinted from Genome Technology, issue No. 17, January, 2002
VI Framework Programme (1)
PRIORITY THEMATIC AREAS OF RESEARCH IN FP6
1. Integrating and Strengthening the European Research Area
1.1.1 Genomics and biotechnology for health
The sequencing of the human genome and many other genomes heralds a new age in human biology,
offering unprecedented opportunities to improve human health and to stimulate industrial and
economic activity. In making its contribution to realising these benefits, this theme will focus on
integrating post-genomic research into the more established biomedical and biotechnological
approaches, and will facilitate the integration of research capacities (both public and private) across
Europe to increase coherence and achieve critical mass. Integrated multidisciplinary research, which
enables a strong interaction between technology and biology, is vital in this theme for translating
genome data into practical applications. In addition, an essential element will be to involve key
stakeholders, for example, as appropriate industry, healthcare providers and physicians, policy
makers, regulatory authorities, patient associations, and experts on ethical matters, etc in
implementing the theme. Gender equity in the research will also be ensured.
This thematic priority area will stimulate and sustain multidisciplinary basic research to exploit the full
potential of genome information to underpin applications to human health. The emphasis will be put on
research aimed at bringing basic knowledge through to application, to enable real and consistent
progress in medicine and improve the quality of life. This research may also have implications for
research on areas such as agriculture and environment, which are addressed under other thematic
priorities.
1.1.2 Information Society technologies
1.1.3 Nanotechnologies and nanosciences, knowledge-based multi-functional materials
and new production processes and devices
1.1.4 Aeronautics and space
1.1.5 Food Quality and Safety
1.1.6 Sustainable development, global change and ecosystems
1.1.7 Citizens and Governance in a Knowledge-based society
VI Framework Programme (1)
1.1.1.i Advanced genomics and its applications for health
1.1.1.i.a Fundamental knowledge and basic tools for functional genomics in all organisms
The strategic objective of this line is to foster the basic understanding of genomic information, developing the knowledge base,
tools and resources needed to decipher the function of genes and gene products relevant to human health and to explore their
iinteractions with each other and with their environment. Research actions will encompass the following:
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: Research will focus on: developing model organisms and transgenic tools;
developing genetic sepidemiology tools and standardised genotyping protocols.
Bioinformatics: The objectives are to enable researchers to access efficient tools for managing and
interpreting the ever-increasing quantities of genome data and for making it available to the research
community in an accessible and usable form.
Research will focus on: developing bioinformatic 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: Research will focus on: elucidation of the
mechanisms underlying fundamental cellular processes, to identify the genes involved and to decipher their biological functions in
living organisms.
1.1.1.i.b Applications of knowledge and technologies in the field of genomics and biotechnology for health
1.1.1.ii Combating major diseases
1.1.1.ii.a Application-oriented genomic approaches to medical knowledge and technologies
1.1.1.ii..b Combating cancer
1.1.1.ii.c Confronting the major communicable diseases linked to poverty
Operaciones básicas en
desarrollo de fármacos
600
500
Comercialización
bioinfo
400
Dianas terapeuticas
Ensayos
robotizables
Bioquímicos y
celulares
Año 1
Librerias
combinatoriales
Nuevos fármacos
200
100
7
Síntesis química
0
6
Ensayos clínicos
phase phase phase phase phase phase phase Fase III
1
2
3 54
5
6
7
2
bioinfo
Number of
compounds
9
8
Compuestos purificados
60
50
Librerias
300
de compuestos naturales
3
4
40
30
20
10
Number of
compounds
Global R&D
Billion $
Compuestos
cabeza de serie
Diseño racional
bioinfo
Compuestos
optimizados
Toxicidad /
especificidad
bioinfo
Ensayos clínicos
Fase II
Ensayos clínicos
Fase I
Inversión
0
1996 1997 1998 1999 2000 2001
25th April
Genomics, proteomics and data integration Example Protein “functions”
Temple F. Smith, Boston University
Assembling puzzles by breaking them into smaller pieces
Pavel A. Pevzner, University of California, San Diego
The Evolution of Structure and Function in Protein Superfamilies
Christine Orengo, University College London
Predicting protein functions, pathways from genome sequences
Martijn A. Huynen, Nijmegen Center for Molecular Life Sciences
Statistical design and analysis of DNA microarray experiments
Sandrine Dudoit, University of California, Berkeley
Specificity in protein interactions
Rob Russell, European Molecular Biology Laboratory
26th April
Prediction of orphan protein function
Soren Brunak, The Technical University of Denmark
Comparative modelling of protein structures: advances and pitfalls
Anna Tramontano, University of Rome “La Sapienza”
Comparative gene prediction
Roderic Guigó, Institut Municipal d’Investigació Mèdica
From Microarrays to Gene Networks
Jack Vilo, European Bioinformatics Institute
Structural Proteomics by Machine Learning Methods
Pierre Baldi, University of California, Irvine
Detecting genomic features under weak selective pressure: the example of codon usage in animals and
plants
Laurent Duret, Université Claude Bernard–Lyon 1
Prediction of protein interaction network
Alfonso Valencia, Centro Nacional de Biotecnología
Evolution teaches protein structure prediction
Burkhard Rost, Columbia University
LA SEQÜÈNCIA DEL GENOMA HUMÀ
Computing at Celera Genomics
•200 teraflops
•1000 vegades més potent que deep blue
•Més potent que els 500 ordinadors més potents avui en dia
llei de Moore
creixement de les dades genòmiques