Symbiosys & BiomagnetBrothers-in-arms

Bart De MoorESAT-SCD, Katholieke Universiteit Leuven

bart.demoor@esat.kuleuven.be

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 bart.demoor@esat.kuleuven.be

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, ….