Symbiosys & Biomagnet Brothers-in-arms Bart De Moor ESAT-SCD, Katholieke Universiteit Leuven...
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Symbiosys & BiomagnetBrothers-in-arms
Bart De MoorESAT-SCD, Katholieke Universiteit Leuven
Come forth into the light of things Let nature be your teacher
William Wordsworth
Program of today
09.00-09.15 Prof. Dr. Ir. Bart De Moor, KULeuven, ESAT/SCD (SISTA) “Symbiosys and Biomagnet: Brothers-in-arms ?”
09.15-09.35 Biomagnet speaker 1: Jacques Van Helden, ULB, Lab. Bioinformatics, Genes and Networks (BiGRe)
“Evaluating the quality of position-specific scoring matrices for predicting transcription factor binding sites”
09.35-10.05 Symbiosys speaker 1: Kathleen Marchal, KULeuven, CMPG-Bioi “Dataintegration based on itemsetmining”
10.05-10.25 Biomagnet speaker 2: Pierre Geurts, Ulg, Electrical Engineering and Computer Science “Preditions of biological interactions by machine learning”
10.25-11.10 Coffee + poster session (44 posters SymBioSys/BioMAGNet)
11.10-11.40 Symbiosys speaker 2: Yves Moreau, KULeuven, ESAT/SCD (SISTA) “Candidate gene prioritization by genomic data fusion”
11.40-12.00 Biomagnet speaker 3: Tom Michoel, Univ. Gent, VIB, Bioinformatics & Evolutionary Genomics “Module Networks revisited : Assessment and prioritization of model predictions”
12.00-12.30 Symbiosys speaker 3: Iven Van Mechelen, KULeuven, Psychology, Research Group quantitative and personality psychology and Lieven Thorrez (KULeuven, ESAT/SCD – SISTA) “A peek into the household of different tissues”
12.30 – 14.00h Lunch Poster Session: Combined SymBioSys/BioMAGNet/BioSCENTer Poster Session + Sandwich lunch (82 posters BioSCENTer, 24 posters SymBioSys/BioMAGNet)
14.00 – 14.20h BioSCENTer, the new Leuven Research Center on BioScience, BioEngineering and BioTechnologyProf. Dr. Ir. Bart De Moor, ESAT-SCD, Department Electrical Engineering, K.U.Leuven
14.20 – 15.35h High-throughput technology drives research in biology, agriculture and biomedicine Dr. Paul Van Hummelen, VIB, The micro-array facilityProf. Dr. Etienne Waelkens, K.U.Leuven,PrometaProf. Dr. Hans Deckmyn, K.U.Leuven, BiomacsProf. Dr. Harry Cuppens, K.U.Leuven, Next generation nucleic acids sequencingDr. Pieter Vanden Berghe, K.U.Leuven, Cell Imaging Core
15.35 - 15.45h K.U.Leuven undergraduate participation in iGEM at MIT Dr. Inge Thijs, Center Microbial and Plant genetics, K.U.Leuven
15.45 – 16.10h Coffee break and poster session
16.10 – 16.35h Evolution and its role in Science and Society Dr. Tom Wenseleers, Animal Ecology and Systematics Section, K.U.Leuven
16.35– 17.10h Vesalius revised: The emerging importance of the neuro-vascular link in health and diseaseProf. Dr. Peter Carmeliet, Vesalius Research Center, VIB/K.U.Leuven
17.10 – 17.20h Address by Prof. Dr. Ir. Karen Maex, vice-rector Group SET, K.U.Leuven
17.20 – 17.55h Tech Transfer : the inspiring patient and consumer Dr. Rudy Dekeyser, Managing Director, VIB
18.00h Reception
Two funding sources
Interuniversity Attraction Poles
Phase VI, 2007-2011, 143 mio euro
44 networks, 324 research teams -Life sciences, 19 networks-Exact and applied sciences, 15 networks-Human sciences, 10 networks
http://www.belspo.be/belspo/iap/index_en.stm
K.U.Leuven Centers of Excellence
Budget defiscalisation +/- 5 mio euro/year, 2005-2009
12 centers of excellence
http://www.kuleuven.be/research/keydomains/excellence/
IAP P6/25 BioMaGNet
Bioinformatics and Modeling: from Genomes to Networks
http://www.kuleuven.be/biomagnet/
• Coordinator (P1): Bart De Moor• K.U.Leuven – EE Dept., (ESAT)/SCD
• Partner 2 (P2): Yves Van de Peer•VIB/U.Gent – Plant Systems Biology – Bioinformatics and Evolutionary Biology
• Partner 3 (P3): Albert Goldbeter•ULB – Chemistry – Unit of Theoretical Chronobiology
• Partner 4 (P4): Louis Wehenkel• ULg, Electrical Engineering & Computer Science – CBIG – Stochastic Methods – Systems and Modeling
• EU-Partner 1 (EU1): Florence d’Alche-buc•Institution Univ. D’Evry-Val d’Essonne – Génopole – Lab. De Méthodes Informatiques – Equipe BioInfo (IBISC)
• EU-Partner 2 (EU2): Denis Thieffry• Université De la Méditerrannée – Aix Marseille II – Faculté des Sciences de Luminy- Bioinformatique
http://www.kuleuven.be/biomagnet/
http://www.kuleuven.be/biomagnet/
Keywords: Bioinformatics, high-throughput data analysis, dynamical modeling, genomics, regulatory interaction, cis-regulations, microRNAs, genotyping, transciptomics, proteomics, interactomics, metabolomics, data integration, gene prioritization, biological networks, regulatory networks, deterministic models, stochastic models, circadian rhythms, cell cycle, pathway, systems biology
http://www.kuleuven.be/symbiosys/
K.U.Leuven Center of Excellence for
Computational Systems Biology
http://www.kuleuven.be/symbiosys/
• Group 1: De Moor Bart (coordinator), Moreau Yves, Faculty of Engineering, Dept. of Electrical Engineering, ESAT-SCD(Bioi)
• Group 2: Van Mechelen Iven, De Boeck Paul, Faculty of Psychology and Educational Sciences, Dept. of Psychology, Research group Quantitative and personality Psychology (QuantPsy)
• Group 3: Verbeke Geert, Lesaffre Emmanuel, Faculty of Medicine, Dept. Public Health, Biostatistical Center (BioStat)
• Group 4: Mathieu Chantal, Verstuyf Mieke, Bouillon Roger, Faculty of Medicine, Dept. of Developmental Biology, Laboratory for Experimental Medicine and Endocrinology (LEGENDO)
• Group 5: 5a. Marchal Kathleen, Faculty of Applied Bioscience and Engineering, Dept. of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG-bioi)
5b. Vanderleyden Jos, De Keersmaecker Sigrid, Faculty of Applied Bioscience and Engineering, Dept. of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG-Salmonella)
• Group 6: Schuit Frans, Resarch group/unit: Faculty of Medicine, Dept. of Molecular Cell Biology, Biochemistry, Research Group: Gene Expression Unit (GEU)
• Group 7: Vermeesch Joris, Faculty of Medicine, Dept. of Human Genetics, CME-UZ Unit (CME)
http://www.kuleuven.be/symbiosys/
Networkinference
Motifanalysis
Primaryanalysis CGH ChIP
chip ProteomicsMetabolomics
Gene prioritization
Module discovery
Network inference
cDNA/Affy
Geneprioritization
Data analysis Data generation
Humangenetics
Endocrinology
Salmonellabiology
Gene
prio
ritiza
tion M
odule
discovery
Networkinference
Human
gene
tics
Salmonella sys. biology
Biological problem
Experiment design
Biological data
Data analysis
Biological validation
Improved method
New biology
Probabilisticmodels
Endocrinology
http://www.kuleuven.be/symbiosys/
Program of today
09.00-09.15 Prof. Dr. Ir. Bart De Moor, KULeuven, ESAT/SCD (SISTA) “Symbiosys and Biomagnet: Brothers-in-arms ?”
09.15-09.35 Biomagnet speaker 1: Jacques Van Helden, ULB, Lab. Bioinformatics, Genes and Networks (BiGRe)
“Evaluating the quality of position-specific scoring matrices for predicting transcription factor binding sites”
09.35-10.05 Symbiosys speaker 1: Kathleen Marchal, KULeuven, CMPG-Bioi “Dataintegration based on itemsetmining”
10.05-10.25 Biomagnet speaker 2: Pierre Geurts, Ulg, Electrical Engineering and Computer Science “Preditions of biological interactions by machine learning”
10.25-11.10 Coffee + poster session (44 posters SymBioSys/BioMAGNet)
11.10-11.40 Symbiosys speaker 2: Yves Moreau, KULeuven, ESAT/SCD (SISTA) “Candidate gene prioritization by genomic data fusion”
11.40-12.00 Biomagnet speaker 3: Tom Michoel, Univ. Gent, VIB, Bioinformatics & Evolutionary Genomics “Module Networks revisited : Assessment and prioritization of model predictions”
12.00-12.30 Symbiosys speaker 3: Iven Van Mechelen, KULeuven, Psychology, Research Group quantitative and personality psychology and Lieven Thorrez (KULeuven, ESAT/SCD – SISTA) “A peek into the household of different tissues”
22
Bart De MoorESAT-SCD, Katholieke Universiteit Leuven [email protected]
BioSCENTer
Leuven Center on Bio-Science, Bio-Engineering and Bio-Technology
BioSCENTer
Leuven Center on Bio-Science, Bio-Engineering and Bio-Technology
Group Science, Engineering & Technologyhttp://gexacte.kuleuven.be
Come forth into the light of things Let nature be your teacher
William Wordsworth
www.kuleuven.be/BioSCENTer
12.30 – 14.00h Lunch Poster Session: Combined SymBioSys/BioMAGNet/BioSCENTer Poster Session + Sandwich lunch
14.00 – 14.20h BioSCENTer, the new Leuven Research Center on ` BioScience, BioEngineering and BioTechnology
Prof. Dr. Ir. Bart De Moor, ESAT-SCD, Department Electrical Engineering, K.U.Leuven
14.20 – 15.35h High-throughput technology drives research in biology, agriculture and biomedicine Dr. Paul Van Hummelen, VIB, The micro-array facilityProf. Dr. Etienne Waelkens, K.U.Leuven, PrometaProf. Dr. Hans Deckmyn, K.U.Leuven, BiomacsProf. Dr. Harry Cuppens, K.U.Leuven, Next generation nucleic acids sequencingDr. Pieter Vanden Berghe, K.U.Leuven, Cell Imaging Core
15.35 - 15.45h K.U.Leuven undergraduate participation in iGEM at MIT Dr. Inge Thijs, Center Microbial and Plant genetics, K.U.Leuven
15.45 – 16.10h Coffee break and poster session
16.10 – 16.35h Evolution and its role in Science and Society Dr. Tom Wenseleers, Animal Ecology and Systematics Section, K.U.Leuven
16.35– 17.10h Vesalius revised: The emerging importance of the neuro-vascular link in health and diseaseProf. Dr. Peter Carmeliet, Vesalius Research Center, VIB/K.U.Leuven
17.10 – 17.20h Address by Prof. Dr. Ir. Karen Maex, vice-rector Group SET, K.U.Leuven
17.20 – 17.55h Tech Transfer : the inspiring patient and consumer Dr. Rudy Dekeyser, Managing Director, VIB
Context
Mission statement
Objectives- Research- Teaching- Valorisation- Branding, recruiting - Science outreach - Strategy development and policy support
Management structure
Some prejudices
Conclusions
Leuven BioSCENTer
Context: 4M research model Biological problem
Experiment design
Biological data
Data analysis
Biological validation
Improved method
New biology
Models: used to formulate hypotheses;
Manipulate: experiment design to generate data; wet lab; clinical;
Measure: technology boosts number of data;
Mine: (in-)validate biological hypotheses;
Leuven Systems Biology Center
Context: Multi-scale complexity in magnitude and time
10 levels of bio-complexity
-9
Molecular dynamics
-8
-7
-6
-5
-4
-3
-2
-1
-10
3
4
5
6
7
8
9
10
11
2
1Atom diameter
nm
Virus
0
1
Bacteria
ChromosomeYeast CellRed blood cell
Human hair diameter
Rat
second
hour
day
month
year
century
millenium
epoch
Circadian rhytms
Cellullar interaction
Embryology
phylogeny Logarithmic scales
m
mm
m
dm
cm
Context: Moore’s law and internet
0
1 109
2 109
3 109
4 109
5 109
6 109
1975 1980 1985 1990 1995 2000 2005 2010
Year
BookkeepingBookkeepingAudioAudio
VideoVideo
3D games3D games
LUILUI
Opera
tions/
seco
nd
Opera
tions/
seco
nd
‘‘Understand’ ?Understand’ ?
Context: technology resolution improves
There was a time…. that biology was data poor !
Nowadays, amount of data increases exponentially due to
- Increasing resolution/sensitivity/accuracy in- imaging, nano-tomography- biodevices and –markers, clinical data - NMR, ….
- Massive parallellization / multiplexing
- Faster computers, larger databases, growing repositories
Conclusion: modern biology and biomedicine is data rich !
Context: High-throughput technology: the ‘omics’
Massive parallellization !
microarray
Context: Dynamics in bio-science fields
Context: Inter-, multi, cross-disciplinarity
The Human Genome Project has catalyzed striking paradigm changes in biology - biology is an information science. [...] Systems biology will play a central role in the 21st century; there is a need for global (high throughput) tools of genomics, proteomics, and cell biology to decipher biological information; and computer science and applied math will play a commanding role in converting biological information into knowledge.
Leroy Hood, Institute for Systems Biology, Seattle, WA, 2002
Systems biology integrates mathematics, systems theory, physics, chemistry, hardand software engineering and other disciplines, to facilitate the understanding of biological and biomedical processes. Systems biology integrates the iterative use of data input, computationalmodeling, simulation, validation and experiments.
Context: integration of heterogenous data sources literature
& databases
genomics
transcriptomics
RNomics
proteomics
metabolomics
DNA-protein
fluxomics
phenomics
predictions
Transcriptional network
Protein interaction network
Metabolic network
Transcript & protein expression
Expression & metabolite profile
Expression & phenome
ph
eno
me
pro
fili
ng
inte
ract
om
e
protein-protein
in s
ilic
o
Comprehensivenetwork
model
Structural network
Network behavior
Info
rmat
ion
sou
rces
…
…
literature& databases
genomics
transcriptomics
RNomics
proteomics
metabolomics
DNA-protein
fluxomics
phenomics
predictions
Transcriptional network
Protein interaction network
Metabolic network
Transcript & protein expression
Expression & metabolite profile
Expression & phenome
ph
eno
me
pro
fili
ng
inte
ract
om
e
protein-protein
in s
ilic
o
Comprehensivenetwork
model
Structural network
Network behavior
Info
rmat
ion
sou
rces
…
…
Context: integration of heterogeneous data sources
Candidategenes
?Information sources
Candidate prioritization
Validation
• Bayesian inference• Kernel methods
• Component models• Simultaneous optim.
Wetlab data validation
-omics data generation
Context: A wealth of potential applications
- Areas: food, health, farma, agro, environment, sustainability
- Examples:
-Science: biological systems understanding -Health: disease management -Farma: in silico drugs discovery – customized medicine -Food/health: nutraceuticals – functional food -Safety: biofilms, infectious disease management (bird flu, malaria,..)-Environment: microbial ecology -Energy: biofuels -Ecology: protected area conservation, integrated forest management-Agro: novel crop design- ….
BioSCENTer mission statement To integrate available expertise on biology and biomedicine, stimulate the interactivity within the Group and foster cross-fertilization between disciplines;
To add new dimensions in the way that research is traditionally being done in the sciences dealing with life, health and environment;
To strive for excellence in these fields in research, teaching and valorisation;
To create visibility by appropriate branding and research;
To provide decisions makers with policy support and to participate in strategic initiativesin the domains of biology, biotechnology and biomedicine.
BioSCENTer Partners: 4 clusters
Biochemistry
Virtual life
Evolutionary biology
Bioinformatics
BioMIntCMPG, LICEB
Bioi@SCDBioi@CMPG
Leuven InterdisciplinaryCommunity on
Evolutionary Biology (LICEB)
Virtual life group
BioSCENTer Objectives Science
Scientific research:
Do 4M over several levels of biocomplexity
Projects
Scientific objectives
Biochemistry
BioMIntCMPG, LICEB
Bioinformatics
Bioi@SCDBioi@CMPG
-Develop high impact tools for breakthroughs in biology, biomedicine, disease management (multifactorial diseases) and drugs discovery; -Understand the signal processing mechanisms (e.g. quorum sensing)-Sustainable microbial ecology (biofuels, biodegradability, ….)
Virtual life
Virtual life group
Evolutionary biology
Leuven Interdisc.Community on
Evol. Biology
-High resolution microscopy surpassing the defraction limits-Integration of multiple interaction in the cell: the cell as a system -Integration towards the tissue level
-Multiscale models for biological systems -Technological breakthroughs on micro- and nanoscale
- Exploit the notion of evolution as an organizing paradigm in biology
BioSCENTer objectives: science
BioSCENTer
- creates inter-/multi-/cross-disciplinary opportunities
- leverage platform for funding (joint proposals)
- stimulating and monitoring scientific output (co- and top-pubs
- allows for integrated scientific research plan
- platform for international benchmarking - Flanders: VIB, IMEC, … - Europe: Freiburg, Dutch Genomics Initiative, …- World: Institute for Systems Biology, Seattle, …
Basic
Research
Strategic
Valorisation
BOF
IOF FP6/7
SME
BioSCENTer Objectives Teaching
-Generation of excellent scientists; retain talented researchers
-Bachelor-Minor bio ?
-Master Programs-Cross-fertilize and rationalize-Exchange teachers and best practices
-Graduate School
BioSCENTer Objectives Teaching Masters
-Master Bioinformatics
-Master Mathematical Engineering
-Master Biomedical Engineering
-Master Artificial Intelligence
-Master in Cell and Gene Technology
-Master in Biosystems Engineering
-Master in Molecular and Cellullar Biophysics
-Master in Biochemistry and Biotechnology
-Master in Biology
-….
BioSCENTer Objectives Teaching: Graduate School
-Provide ‘body’/content to the Arenberg Doctoral School
-Organize annual co-promotor assignment session
-Coordinate graduate school organizing committee
-Collaborate for graduate school courses with- VIB- Group Biomedical Sciences- IAP (e.g. BioMagnet,….) - ….
- Examples - Course on Technology (how, what, cost, spec’s, trends,…)- Biology course for engineers - Bioinformatics course for biologists - ….
BioSCENTer Objectives Branding and recruiting
-Acknowledgment on publications
-Website -Partners and links-Research news-Announcements (seminars, PhDs,…)
-Seminars and workshops-Kick off -Annual branding seminar – X-mas lecture-International conferences
-Recruitment -Youngsters (science outreach activities) -Platform for master theses-Local and international recruitment -Postdocs-International visitor program
BioSCENTer Objectives Valorisation
-Economic valorisation: -Current spinoffs as role models
- www.algonomics.com, www.silicos.com, www.remynd.be, …
-New ventures: best practices, valorisation seminars (LRD),multidisciplinary start-up teams
-Create Valorisation Interface Platform under LRD
-Societal valorisation -Science outreach -Scientific support in ethical debates
BioSCENTer Objectives Science outreach
-Get involved in activities targeted to youngsters
-Inspire young people for a career in S&T
-Reach teachers
-Reach the general public
-Reach politicians
-Science sharing – open access
BioSCENTer Objectives: Strategy development and policy support
To create vision on convergence of technologies: BANG = bits, atoms, neurons, genes
To share and look for synergies and economy of scale (e.g. Hercules heavy equipment)
Seize opportunities in K.U.LeuvenFlandersBelgiumEuropeWorld
BioSCENTer Objectives: strategic opportunities
K.U.Leuven- omics facilities (MAF, Prometa, BioMacs, GenCor,…)- Leuven Network for Translational Medicine- Leuven Cancer Institute- Strategic initiatives UZ- CD3 - …
Flanders- Witboek Life Sciences- Hercules - VRWB: 6 strategic areas - e-onderzoek: pilootproject bioinformatica - Flanders Bio – BioScope-IT- VIB- IMEC – Human ++
Belgium- GIGA: Interdisciplinary Cluster for Applied
Geno-proteomics (Liege)- IAPs
BioSCENTer Objectives: strategic opportunities
-Europe-ESF: Systems Biology: A grand challenge for Europe, policy paper-ERASYSBIO: www.erasysbio.net -EMBRACE: A European Model for Bioinformatics Research and
Community Education, www.embracegrid.be -European Bioinformatics Institute, www.ebi.ac.uk -European Molecular Biology Center, www.embl.org -Institute of Systems Biology, www.systemsbiology.org -The Wellcome Trust Sanger Institute, www.sanger.ac.uk -ESRF, European Synchrotron Radiation Facility, www.esrf.eu-…
-World-Computational and Systems Biology @ MIT, scbi.mit.edu-Systems Biology at Harvard Medical School
sysbio.med.harvard.edu
BioSCENTer Management structure
PI (bi-)-Annual Meeting - general concertation - doctoral school suggestions- defining cross-promotorship - ….
Executive committee (execom)- Set and guard strategic lines - Monitor performance- Budget allocation (if applicable)- Meets 4 times/year - Hire coordinator ?
Scientific Advisory Board - Needed ? - Several SABs already active and installed
(e.g. Symbiosys, BioMagnet,…)
Many prejudices ? A lot of scepticism ? More suggestions ?
- Overlap with other SET research centra ?
- Exclusivity of BioSCENTer within SET ?
And so, my fellow Americans: ask not what your country can do for you—ask what you can do for your country.
John F. Kennedy, Inaugural address, January 1961
Conclusions
Strong points of BioSCENTer: - everything in house (complete university) - large number of PIs and junior researchers - streamlined in 4 lines:
bioinformatics, biophysics, biochemistry, evolution - top quality research: present and future - attractive to potential new students - achieve economics of scale in co-using large equipment
Opportunities for BioSCENTer:- enormous perspectives for science and valorisation - profiling in Europe and world: e.g. LERU, ESF, ….