1st FEBS Advanced Lecture Course on
Systems Biology:

From Molecules & Modeling to Cells
 Gosau, Austria, EU, March 12-18, 2005

 

 

 

 

 

 

 

Organizers


                                                         Anneke (J.G.) Koster (course director)

                                                         Institute for Systems Biology Amsterdam

                                                        

                                                         Roland Eils

                                                         Intelligent Bioinformatics Systems

                                                         Deutsches KrebsForschungsZentrum

                                                         Heidelberg

 

                                                         Karl Kuchler

                                                         Department of Medical Biochemistry

                                                         Max F. Perutz Laboratories

                                                         Campus Vienna Biocenter

                                                         Medical University Vienna

 

                                                         Hans V. Westerhoff (program chair)

                                                         Departments of Molecular Cell Physiology and              Mathematical Biochemistry, BioCentrum            Amsterdam, Free University Amsterdam and

                                                         University of Amsterdam

 

 

 

 

 

 

 


 

Teacher-Members of the Scientific Advisory Board

 

 

 


Lilia Alberghina

Uri Alon

Marta Cascante 
Igor
 Goryanin

Stefan Hohmann

Hiroaki Kitano

Ursula Kummer

Uwe Sauer

Masaru Tomita

Barry Wanner

Roel van Driel

Shoshana Wodak


 

                                                       

Technical Support & Registration & Course Office


FEBS
- Sysbio Course Office:     Anneke (J.G.) Koster

                                                        Amsterdam Systems Biology Institute 

                                                        Charlie Parkerstraat 25

                                                        NL-1066 GV Amsterdam, EU          
                                                        Phone:         +31-20-6143163
                                                        FAX:            +31-20-6143163
                                                        e‑mail:         hweste@bio.vu.nl
                                                        wweb:          http://www.febssysbio.net

At the Venue in Gosau:                Anneke (J.G.) Koster

                                                        Sport und Erlebnis Hotel**** Gosau
                                                        A-4824 Gosau am Dachstein 713, Austria

                                                        Phone:         +43-6136-8811-390

                                                        Mobile:         +43 676 572 4348
                                                        FAX:            +43-6136-8811-352

                                                        e‑mail:        
hweste@bio.vu.nl

                                                        wwweb:       http://www.febssysbio.net

FEBS
-SysBio2005 Hotlines:        +43 676 572 4348 and +43 676 572 4349

 

 

 

 

 


 

FEBS-SysBio2005 received generous financial support from


FEBS [The Federation of the European Biochemical Societies]

BMBF [German Bundesministerium für Bildung und Forschung]

NWO-ALW [Netherlands Organization for Scientific Research, NL]
DKFZ [Deutsche Krebsforschungszentrum]

AstraZeneca

NovoNordisk

Teranode

BioCentrum Amsterdam

EMBL [European Molecular Biology Laboratories]

ESF [European Science Foundation]

BioSim NoE-EU

The Systems Biology Institute

 

 

Additional Donations and Contributions came from

DSM 

  EUSYSBIO-EU

FEBS Journal 

 

Purac

Amsterdam Systems Biology Institute

 

EML (European Media Laboratory)

  GENome Research in AUstria

Merck A.G.

Unilever


Table of Contents  

Organizers. 1

Teacher-Members of the Scientific Advisory Board. 2

Technical Support & Registration & Course Office. 2

FEBS-SysBio2005 received generous financial support from.. 3

Additional donations and contributions came from.. 4

Willkommen in Gosau, Welkom in Gosau, Welcome to Gosau! 6

Scientific Program - its principles. 9

Symposia. 9

Morning: Plenary Lectures - Discussion of the Issues. 9

Break for Lunch, Physical Activities, Tea. 9

Black-Board Teaching. 9

Workshop (W) & Short Talks (S) 10

Late Afternoon Discussion. 10

Poster Presentations, Poster Committees, Analyses, Discussions. 10

Power Poster Presentations (PoP’s) 10

Participant Task List: Contribution of each Participant and its Timing. 11

Course Book - its Principles. 15

Abstracts. 15

Course (‘Abstract’) Book - Paper 15

Course Book - Electronic. 15

Systems Biology Young Investigator Awards. 15

Web Site. 16

Technical Local Information. 16

Connections – You and the World. 16

Departure. 16

FEBS Evaluation Form.. 16

FEBS-SysBio2005 Course Office. 16

Help. 17

Message Board. 17

Meals, Beverages & Lunch Packages. 17

Payments. 17

Presentations. 17

Skiing and Outdoor Leasure. 18

Social Program.. 18

Sport & Erlebnis Hotel Facilities. 19

Scientific Program.. 21

Speaker abstracts. 35

Abstracts of Posters & Power Posters. 105

Principles. 106

Tools and Methods. 124

Unicellular Organisms. 142

Multicellular/mammalian. 159

Address list 177

Author and Subject Index. 186

 


 

Willkommen in Gosau, Welkom in Gosau, Welcome to Gosau! 

 

 

In this snowy environment, we warmly welcome you to the first European Advanced Course on Systems Biology.  Around the turn of the previous century, Biology was revolutionized:  the sequence of complete genomes became available.  Almost immediately many high-throughput,  genome-wide analyses sprung up, which will soon enable us also to measure the expression levels of all genes at most levels of the cellular hierarchy.  Perhaps never before, there has been such a sense of urgency.  Never before did we seem to be so close to knowing how Life functions in terms of the properties of its molecules.  Never before could we begin to think of the rational engineering of drugs targeting pathophysiology rather than individual molecules.  Yet, when confronted with massive data sets about the molecules of living cells, one tends to get confused rather than illuminated; the function of living cells cannot easily be read from what happens to the molecules.  Much of functioning depends on many molecules simultaneously, which engage in complex interactions.

 

In parallel, biochemistry and biophysics focused more and more on the experimental assessment of molecular interactions.  Together with mathematical biochemistry, these disciplines generated new paradigms for understanding how functional properties arise in interactions.  These paradigms remained limited however, because not all components of the cellular systems were considered in the analyses, and because most components could not be accessed experimentally.

 

In 2005 much excitement lies in the synergy of the two above developments:  functional genomics gleans from biochemistry, biophysics and mathematical biology how new function arises in nonlinear interactions, whereas the latter three may engage in functional genomics in order to measure all components that are important for the living cell.   In fact all these paradigms are now merging into what one might call Integrative Systems Biology.  Integrative Systems Biology is here defined as the science investigating how much of the functioning of living organisms comes about in the nonlinear interactions of all their molecules.

 

From this definition, from the large size of even the smallest genomes, and from the multitude and diversity of nonlinear interactions in Biology, it is readily understood that the challenge that Integrative Systems Biology poses is enormous.  This young Science will require so much expertise in both experimental molecular biology and mathematics, in a highly interactive mode, that the way of doing Biology is being revolutionized.  As Physics was in the 1950’s, Biology is now becoming Big Science, i.e. Systems Biology.   A new generation of scientists is needed.  These scientists should be at ease with both experimental molecular biology and complex mathematics, and with almost anything that is in between.  They should also be able to interact strongly and productively with each other, in large teams.  This Course is meant to catalyze the formation of this new generation of scientists, from very young Ph D students, but also from established researchers.  In this way the course should contribute to the development of science, also for the sake of humanity. 

 

The need for training in Systems Biology was well recognized by our main sponsor, i.e.  the Federation of European Biochemical Societies (FEBS).  We appreciate the strong support through the FEBS Advanced Course Committee, in particular its previous chairman Karel Wirtz. 

 

The need for training is also recognized by the national European organizations that fund modern biological and medical research.  Indeed, the German Ministry for Education and Research (BMBF) and the Dutch Organization for Scientific Research, in particular its section on Earth and Life Sciences (NWO-ALW), have generously supported the course largely through student registration waivers.

 

The European Science Foundation (ESF), which aims to make the activities of the National European Science Funding Organizations synergize, has likewise given strong support.  The ESF engages in a Forward Look study on Systems Biology, which will prepare its final report during the two days following this course, also in Gosau.

 

The 6th Framework Program of the European Union has funded a similar reconnaissance study on Systems Biology, through a Specific Support Action EUSYSBIO.  EUSysBio also supports this course, as it will help define the Systems Biology field.  A network of Excellence recently funded by the EU and partly directed at Systems Biology, i.e. BioSim coordinated by Erik Mosekhilde, has immediately assimilated this Course into its program of furthering excellent Systems Biology in Europe.

 

The number of new drugs that reach the market, and the number that thereafter survive, is diminishing.  The cost of developing the drugs is becoming astronomical, largely because it is too difficult to choose between the large numbers of promising drug leads at an early stage.  The ones that are plagued by ‘side effects’ and will not interact optimally with their target in the context of the living organism, are identified so late in the process that they absorb most of the budget.  The critical issues here are again Systems Biology issues, and modern pharmaceutical companies are engaging strongly in this new field.  Two of these, i.e., AstraZeneca and NovoNordisk, enthusiastically support this meeting, both in terms of its lectures and AstraZeneca also in terms of the USB-sticks provided to all participants.  Of course, various Software companies engage strongly in Systems Biology, not the least in interaction with these companies and the top Systems Biology Centers (see below).  Of these, Teranode co-supports the USB sticks and their formatting. 

 

It is unbelievable how ill-defined some of the food is that we enjoy on a daily basis.  Both in terms of food safety, and in terms of improvements in their contribution to health, food production methodology is a field that may also be revolved by Systems Biology developments.  After all, the production of food by living organisms and its use by human beings, abounds of interacting molecules in the context of living cells.  DSM and Purac are supporting this Course.

 

The European Journal of Biochemistry (EJB) has been a pillar under Biochemistry in more than one way.  First, it has always published scientific articles of high quality and significance.  Second, it has always earned much of the money that is used to subsidize FEBS courses.  At present, the journal is even more relevant to the emerging field of Systems Biology:  (i) it is one of the earliest journals that highlighted the topic, such as through the direct link to the siliconcell model-base (www.siliconcell.net ), and (ii) it has just undergone a facelift, becoming the FEBS Journal and orienting itself more towards quantitative cell biology and systems biology.  To celebrate this, the journal offers us drinks at the Welcome Mixer.

 

Europe already has a number of Centers for Systems Biology.  Of these, the BioCentrum Amsterdam, the Deutsche Krebsforschungszentrum, the European Molecular Biology Laboratory, and the European Media Laboratory, support this course financially.  We expect that many Systems Biologist of the future will have been nurtured at these institutions.  Likewise Japan has very important institutes, one of which has been world-leading for systems biology, including activities in California.  We are pleased that The Systems Biology Institute is generously sponsoring this course.

 

Of course, the home institutions of the organizers have contributed rather importantly to the organization, i.e. the BioCentrum Amsterdam, the DKFZ and the Max F. Perutz Laboratories of the Vienna Biocenter.  We also thank the Institute of Molecular Pathology (IMP) and the Vienna Veterinary University for providing poster walls, and the Institute for Molecular Cell Biology, Amsterdam for lending some of the additional equipment.  Likewise the Teachers of the course (i.e. the Lecturers and the members of the Scientific Advisory Board: Drs. Aebershold, Alberghina, Alon, Boone, Cascante, Doyle, Eichelbaum,  Goldbeter,  Goryanin, Heinrich,  Hohmann, Kell, Kholodenko, Kitano, Klingmüller, Klipp, Kummer,  LeNovere, Noble, Reuss, Sauer, Schuster, Snoep, Stelling, Tomita, Van Driel, Wanner, and Wodak) have spent quite some time in order to optimize their teaching at this course; their institutes have thereby also contributed.

 

A course is a matter of human beings, much more than of institutions.  This course is possible thanks to the enthusiasm of the many people involved in the actual organization.  Jacky L. Snoep has provided us with much of the artwork for the abstract book.  We thank Maria Bausback for secretarial assistance during the course, Walter Glaser for helping with the adaptation of the web page, and Hannes Davidek of helping with graphic design.   Of course the local organizing committee is quite important: we thank Karen van Eunen, Frank Bruggeman, Richard Notebaart, and all others for their contribution to the dynamics of the course.   The director and staff of the Sport und Erlebnis Hotel Gosau are thanked for the professional way they arrange for infrastructure and food.  And we thank Emilia, for her patience.


But of course, we should not forget the all-but-silent majority, i.e. the participants and their supporters (institutions and mentors), who contributed much effort and inspiration.  Reading the abstracts we found that a great many innovative ideas were going to be contributed by the participants in spe.  This course was the first of its kind in Systems Biology.  Because of the novelty of the field we had applied to FEBS
 for a course of 120 students.  When the number of registrants exceeded 200, we were pleased because it demonstrated great interest and enthusiasm, but saddened because we had to deny many high quality applicants participation.  Because quality and potential of most abstracts was high, we also had to select on the basis of more technical parameters, e.g. we limited the number of students coming from any same institution.  We hope that the students we could not admit will come to a next course.  Likewise, we have to admit that although our speakers/teachers are excellent Systems Biologists, we have not been able to attract all excellent Systems Biologist to the course: we had too few speaker slots.

 

What is next?  An exciting course here in Gosau with lots of excellent teaching.  The teaching program is special in that it hosts a number of unconventional teaching elements.  The latter include the systematic discussion of each poster contribution by a number of senior scientists, black-board teaching, power-poster presentations, discussion sessions formulating key questions and subsequent sessions trying to address them.  Equally importantly, new and more established Systems Biologists from various science directions will meet and discuss science intensively.  We expect that Gosau will be the cradle of a network of excellent Systems Biologists who will know to find each other in the future for advice and collaboration.  Thus, the interdisciplinary activities that are so important for Systems Biology, take off and make excellent new Science.     

 

The organizers,

 

 

 

 

 

 

 

 

and

her troika (i.e.., Roland Eils , Karl Kuchler , and Hans V. Westerhoff)

 

 

 

 

 

 

 

 

 

 

 

 

 


 

 

 

Scientific Program - its principles

 

Symposia

The course has been organized in terms of 4 Symposia, dedicated to areas within Systems Biology, i.e.Principles’, Tools and Methodology’, Unicellular Organisms and (Cells from) Multicellular Organisms.   Each symposium has its dedicated day.  On that day the symposium is kicked off with a number of plenary lectures in the morning.  Discussions, Workshop talks by invited Principal Investigators, Short talks by invited poster presenters, and a Discussion follow.  The posters and power posters corresponding to the symposium are have been grouped together, and will be presented in sequel on the three poster evenings (Sunday, Monday and Wednesday).

Tuesday morning has two extra lectures for symposium T and three extra for symposium U, before the cultural break.

Morning: Plenary Lectures - Discussion of the Issues

Each symposium is kicked off with four plenary lectures in the morning.  The lecturer presents an oral presentation for 35 minutes, with a subsequent 10 minutes discussion period.  This oral presentation should spend 5 minutes to introduce the field/topic, 15 minutes to teach a few important principles relevant to that topics, and then 15 minutes to report on recent work in which the principles are used in generating some excellent Systems Biology.  It is important to realize that it is better to teach little well, than all not at all!

This is followed by a discussion session in which the most cogent Systems Biology questions related to the symposium topic are formulated. 

Break for Lunch, Physical Activities, Tea

Lunch will be in the hotel restaurant.  Course teachers are requested not to seat together.  They should rather sit at their own table and be joined by students.  Similarly, students are kindly requested not to sit together with other students from their own institute, but with Teachers, or with students and principal investigators of other institutes.

After lunch there is a break for physical activities, such as ski-ing, rock climbing, chess, or hang gliding.  Be back for tea (coffee if you wish) at 16h00 to engage in the afternoon session that begins at 16h30.

Black-Board Teaching

On Sunday and on Monday, Blackboard teaching sessions will be held after the physical activity break and tea.  These are optimized for interactive teaching.  Key concepts for Systems Biology will be explained, in interactive mode, using blackboard and chalk, or equivalent.  4 Blackboard presentations will be held in parallel, such that each should be expected to host some 30 students. As a rule, each Blackboard teacher (-couple) presents his Blackboard presentation twice, i.e. on Sunday and then again on Monday.  Each student is expected to be present at 2 out of 4 Black-board talks.

The following topics have been agreed to: 

·         Motifs and networks (Alon)

·         Stability and flux mode analysis (Heinrich, & Schuster)

·         Control analysis and silicon cells (Snoep & Westerhoff)

·         Robustness (Stelling & Bruggeman)


 

Workshop (W) & Short Talks (S)

The topics of workshop presentations and short talks during the afternoon sessions, fall within the area of the main symposium of that particular day (or, in the case of M, of the day thereafter). These talks are usually delivered by principal investigators (W) and students (S), respectively. These speakers have been invited on the basis of their poster abstracts.

Late Afternoon Discussion

During the late-afternoon discussion, the questions raised during the morning discussion session will be addressed by the Lecturers and other Teachers of that symposium.  This will be followed by a general discussion.  The results of the discussion will be noted down and reported to FEBS, ESF and EUSYSBIO.

Poster Presentations, Poster Committees, Analyses, Discussions

The posters are up throughout the meeting; they should be mounted Sunday evening and removed Thursday evening.

Each poster will be presented for at least an hour by its prime author.  Poster numbers n-2 will be presented/analyzed/discussed Sunday evening from 21h00 for at least an hour.  Numbers 3n-1 will be presented/analyzed/discussed Monday evening.  Numbers 3n-3 will be presented/analyzed/discussed Wednesday evening.  Also the presenters of short talks are requested to present their poster, on the day of their short talk.

Authors presenting posters are asked to indicate on their poster additional times when they will be available at their poster for discussion.

Every student will get to speak the teachers in her/his symposium:  each symposium has a corresponding Poster Committee, which consists of all lecturers at that symposium plus:

Symposium Principles: Alberghina (chair), Westerhoff plus P lecturers

Symposium Tools: Cascante (chair), Goryanin plus T lecturers

Symposium Unicellular organisms: Hohmann (chair), Kuchler plus U lecturers

Symposium Mammalian systems: Van Driel (chair), Kitano plus M lecturers.

During the first 45 minutes of each of the three poster sessions, this committee will inspect the one third of the posters belonging to their symposium that is being presented by their author that evening (i.e. up to ten posters).  At the end of the poster session, i.e. from 22h30 – 23h00), i.e. in the ‘poster round table discussion’, the poster committee will discuss in a session with all poster presenters of their symposium all the posters they have seen that evening (i.e. this will be a non-plenary session with approximately 6 committee members and 10 poster presenters). 

Power Poster Presentations (PoP’s)

Principal investigators who have not been asked to give an oral presentation as Lecture or Workshop Talk, are requested to give a so-called PowerPoster Presentation (PoP).   This is a 5 minutes’ powerpoint presentation on one of five computers available in the poster halls.  They will be asked to run this presentation repeatedly for any PoP viewer interested during the time slot allotted to the PoP presenter.  PoP’s occur in parallel to the poster presentation by students. 


Participant Task List: Contribution/Timing of each Participant

Tasks are AC: Award Committee, B: Black board teaching, C: Chair, L: Lecture, O: Organizer, P: Poster, PC: Poster committee; PoP: Power Poster, S: Short talk plus poster, W: Workshop talk.

 

Full name

Date

Task

Symposium-Contrib.Number

Ronald Aardema

Sunday

Poster

 P-P01

Niels Aarsaether

Sunday

PowerPoster

 M-PoP01

Rüdi Äbersold

Monday, S, M, W

Lecture + Poster committee

 T-L01 + T-PC

Charles Affourtit

Sunday

Poster

 M-P01

Lilia Alberghina

Sunday + S, M,W, Th

Chair + Poster Committee Chair + Award Committee

 P-C02 + P-PC  + AC

Uri Alon

Wedn + S,M + SMW

Lecture +Blackboard+ Poster Committee

 L05 + PT-B1 + U-PC

Ole Herman Ambur

Sunday

Poster

 U-P01

Ivan Arisi

Monday

PowerPoster

 M-PoP02

Herwig Bachmann

Monday

Poster

 U-P02

Stephan Beirer

Monday

Poster

 M-P02

Guillaume Beslon

Wednesday

Workshop Talk

 U-W01

Martin Bezler

Wednesday

Poster

 M-P03

Lars M. Blank

Wednesday

Poster

 U-P03

Nils Blüthgen

Thursday

Short Talk + Poster

 M-S01

Charlie Boone

Monday + S, M, W

Lecture + Poster committee

 T-L04 + T-PC

Irina Borodina

Sunday

Poster

 T-P01

Marc Breit

Sunday

Poster

 M-P04

Marie Brown

Monday

Poster

 P-P02

Frank J. Bruggeman

S, M + S, M + t

Short Talk + Black bpres+Orgr

 P-S01, PT-B4

Marina Caldara

Sunday

Poster

 U-P04

David Camacho

Wednesday

Poster

  P-P03

Marta Cascante

Thurs+ S, M, W + Th

Ch+Post commCh+Aw commCh

 M-C02 + M-PC + AC

Cyril Combe

Monday

Poster

 T-P02

Holger Conzelmann

Monday

Poster

 M-P05

Attila Csikasz-Nagy

Wednesday

Short Talk + Poster

 U-S01

R. Keira Curtis

Sunday

Poster

 P-P04

Holger Dach

Wednesday

Poster

 T-P03

Sune Danø

Monday

Short Talk + Poster

 T-S01

Robert P. Davey

Monday

Poster

 U-P05

Gianni De Fabritiis

Monday

Poster

 P-P05

Alberto de la Fuente

Wednesday

Poster

 P-P06

Silvia De Monte

Wednesday

Short Talk + Poster

 U-S02

Cathy Derow

Wednesday

Poster

 M-P06

Helena Diaz-Cuervo

Sunday

Poster

 P-P07

Claudia Donnet

Sunday

Poster

 M-P07

Francesco d'Ovidio

Monday

Poster

 P-P08

John Doyle

Sunday + S,M,W

Lecture + Poster committee

 P-L02, P-PC

Oliver Ebenhöh

Wednesday

Poster

 P-P09

Michael Ederer

Sunday

Poster

 T-P04

Michel Eichelbaum

Thursday + S, M,W

Lecture + Poster committee

 M-L01, M-PC

Thomas Eißing

Monday

Poster

 M-P08

Martin Eigel

Wednesday

Poster

 M-P09

Roland Eils

Monday +  S, M

Lecture + Poster committee

 T-L02 + T-PC

Martin Eisenacher

Monday

Poster

 T-P05

Graham P. Feeney

Sunday

Poster

 M-P010

Raquel Fernandez-Lloris

Monday

Poster

 M-P011

Ana Sofia Figueiredo

Wednesday

Short Talk + Poster

 U-S03

Emilie S. Fritsch

Wednesday

Poster

 T-P06

Tobias Fuhrer

Wednesday

Poster

 U-P06

Akira Funahashi

Sunday

Poster

 T-P07

Laurent Gaubert

Wednesday

Poster

 M-P12

Subhendu Ghosh

Saturday + Sunday

Music + PowerPoster

 O-M + T-PoP01

Sergio Giannattasio

Sunday

Poster

 U-P07

Adi Gilboa-Geffen

Sunday

Poster

 M-P13

Patricio Godoy

Wednesday

PowerPoster

 M-PoP03

Albert Goldbeter

Sunday

Lecture + Poster committee

 P-L03 + P-PC

Didier Gonze

Monday

Poster

 M-P14

Igor Goryanin

Monday + S, M, W,

Chair  + Poster committee

 T-C02 + T-PC

Niels Grabe

Monday

Poster

 T-P08

Reingard Grabherr

 

 

 

Ioan Grosu

Sunday

PowerPoster

 P-PoP01

Vitaly V. Gursky

Sunday

Poster

 P-P10

Benjamin A Hall

Wednesday

Poster

 T-P09

Kristofer Hallén

Monday

Poster

 P-P11

Thomas Handorf

Wednesday

Poster

 P-P12

Franz Hartner

Sunday

Poster

 T-P10

Mariko Hatakeyama

Thursday

Workshop Talk

 M-W01

Feng He

Sunday

Poster

 P-P13

Mariela Hebben-Serrano

Monday

Poster

 U-P08

Reinhart Heinrich

Sunday

Lect + Blackb pres+Post comm

 P-L01 + PT-B2 + P-PC

Julia Heßeler

Monday

Poster

 P-P14

Noriko Hiroi

Wednesday

Poster

 P-P15

Thomas Höfer

Thursday

Workshop Talk

 M-W02

Stephan Hohmann

Tu-,Wedn+S,M,W+Th

Chair+PostCommCh+AwComm

U-C01 + U-PC + AC

Adaoha EC. Ihekwaba

Wednesday

Poster

 M-P15

José M. Inácio

Wednesday

Poster

 U-P09

Sergii Ivakhno

Monday

Poster

 T-P11

Adrienne C. N. James

Monday

Short Talk + Poster

 T-S02

Per Harald Jonson

Wednesday

Poster

 T-P12

Paula Jouhten

Sunday

Poster

 T-P13

Matthieu Jules

Monday

Poster

 T-P14

Peter Juvan

Wednesday

Poster

 T-P15

Visakan Kadirkamanathan

Monday

PowerPoster

 P-PoP02

Douglas B. Kell

Saturday

Opening Lecture

 O-L01

Alexander Kern

Sunday

Poster

 U-P10

Boris N. Kholodenko

Thursday + S, M, W

Lecture + Poster committee

 M-L02 + M-PC

Hiraoki Kitano

Thursday +  S, M, W

Chair + Poster committee

 M-C01 + M-PC

Ursula Klingmüller

Thursday + S, M, W

Lecture + Poster committee

 M-L04 + M-PC

Edda Klipp

Tuesday + S, M, W

Lecture + Poster committee

 U-L01, U-PC

Tetsuya J. Kobayashi

Sunday

Poster

 P-P16

Markus Kollmann

Sunday

Short Talk + Poster

 P-S02

Anneke  Koster

throughout

Organizer

 O

Konstantin N. Kozlov

Monday

Short Talk + Poster

 T-S03

M.T.A. Penia Kresnowati

Monday

Poster

 P-P17

Albert Kriegner

 

 

 

Karl Kuchler

Sun+S, M, W +throug

Chair+Poster Comm +Organizer

 T-C01 + T-PC + O

Ursula Kummer

Tuesday + S, M, W

Lecture + Poster committee

 T-L02 + T-PC

Lars Küpfer

Monday

Poster

 U-P11

Ann Zahle Larsen

Wednesday

Poster

 U-P12

Nicolas Le Novere

Thursday + S, M, W

Lecture + Poster committee

 M-L03 + M-PC

Dirk Lebiedz

Wednesday

PowerPoster

 P-PoP03

Kin Liao

Monday

PowerPoster

 T-PoP02

Junli Liu

Sunday

PowerPoster

 P-PoP04

Hong-Wu Ma

Wednesday

Poster

 P-P18

Shaukat Mahmood

Sunday

Poster

 M-P16

Asawin Meechai

Sunday

PowerPoster

 U-PoP01

Thomas Millat

Sunday

Poster

 P-P19

Liya A. Minasbekyan

Monday

PowerPoster

 U-PoP02

Robert Modre-Osprian

Sunday

Poster

 T-P16

Hisao Moriya

Monday

Poster

 P-P20

Minca Mramor

Monday

Poster

 T-P17

Dirk Müller

Sunday

Poster

 U-P13

Douglas B. Murray

Wednesday

Short Talk + Poster

 U-S04

Leo Neumann

 

 

 

Ana R. Neves

Monday

Poster

 U-P14

Cécile Nicolas

Wednesday

Poster

 U-P15

Denis Noble

Thursday

Closing Lecture

 O-L02

Richard A. Notebaart

Wednesday +through

Organizer + Poster

 T-P18 + O

Jun Ohta

Wednesday

PowerPoster

 T-PoP03

Rick Orij

Sunday

Poster

 U-P16

Karen Page

Sunday

PowerPoster

 M-PoP04

Balázs Papp

Monday

Short Talk + Poster

 T-S04

Ainslie B. Parsons

Sunday

Poster

 T-P19

Manish Patel

Monday

Poster

 T-P20

Mikhail Paveliev

Monday

Poster

 M-P17

Venkata G. Peddinti

Wednesday

Poster

 P-P21

Esa Pitkänen

Sunday

Short Talk + Poster

 P-S03

Jarne Postmus

Monday

Poster

 U-P17

Bjørn Quistorff

Wednesday

PowerPoster

 T-PoP06

Emma Redon

Wednesday

Poster

 U-P18

Matthias Reuss

Tues + W + W, S, M

Lecture+Chair+Poster comm

 U-L02 + U-C02 + U-PC

Riccarda Rischatsch

Sunday

Poster

 U-P19

Isabel Rocha

Monday

Poster

 U-P20

Juan-Carlos Rodriguez

Sunday

Poster

 P-P22

Carlos Rodríguez-Caso

Wednesday

Poster

 M-P18

Susana Ros

Sunday

Poster

 M-P19

Julio Saez-Rodriguez

Monday

Poster

 M-P20

Carlos Salazar

Monday

Poster

 P-P23

Silvia D. Santos

Thursday

Short Talk + Poster

 M-S02

Uwe Sauer

Wednesday

Lecture + Poster committee

 U-L04 + U-PC

Thomas Sauter

Thursday

Short Talk + Poster

 M-S03

Francesca Maria Scandurra

Wednesday

Poster

 M-P21

Jana Schütze

Sunday

Poster

 T-P22

Jörg Schaber

Wednesday

Poster

 P-P24

H. Schmidt-Glenewinkel

Sunday

Poster

 M-P22

Stefan Schuster

Sunday +S,M+S,M,W

Lecture+Blackb+Poster comm

 P-L04 + PT-B2 + P-PC

Jacky L. Snoep

Tuesd+ S,M + S,M,W

Lecture+Blackb+Poster comm

 T-L05 + PT-B3 + T-PC

Victor Sourjik

Wednesday

Workshop Talk

 U-W02

Irena Spasic

Monday

Poster

 T-P23

Christian Spieth

Sunday

Poster

 P-P25

Dan Staines

Monday

PowerPoster

 T-PoP4

Jörg Stelling

Tuesday+S,M+S,M,W

Lecture+Blackbpres+Postcomm

 U-L03 + PT-B4 + U-PC

Ara H. Tamrazyan

Wednesday

Poster

 U-P21

Sander Tans

Wednesday

PowerPoster

 U-PoP3

Bas Teusink

Wednesday

Workshop Talk

 U-W03

Rüdiger Thul

Wednesday

Poster

 T-P24

Jens Timmer

Monday

PowerPoster

 M-PoP5

Masaru Tomita

Wednesday + S,M,W

Lecture + Poster committee

 U-L07 + U-PC

Nicolas Tourasse

Sunday

Poster

 U-P22

Isil Tuzun

Monday

Poster

 U-P23

Renata Usaite

Sunday

Poster

 T-P25

Svetlana V. Ustyugova

Monday

Poster

 M-P23

Yevhen Vainshtein

Monday

Poster

 P-P26

Joost van den Brink

Wednesday

Poster

 U-P24

Roel van Driel

Sun, Mon, Wed, Th

Poster Com Chair+Award Com

 M–PC+ AC

Frank H.J. van Enckevort

Sunday

Poster

 U-P25

Karen van Eunen

Wednesday+through

Poster + Organizer

 P-P27 + O

Markku Varjosalo

Wednesday

Poster

 M-P24

Vidya R. Velagapudi

Monday

Poster

 U-P26

Dennis Vitkup

Sunday

Workshop Talk

 P-W01

Todor Vujasinovic

Monday

PowerPoster

 P-PoP5

Barry L. Wanner

Wednesday + S,M,W

Lecture + Poster committee

 U-L06 + U-PC

Hans V. Westerhoff

Sa,Su,Th + S,M + thr

Chair + Blackboard + Organizer

P-C-1 + PT-B3 + O

Shoshana Wodak

Monday + S, M, W

Lecture + Poster committee

 T-L03 + T-PC

Jian Wu

Wednesday

Poster

 U-P27

He Yang

Wednesday

PowerPoster

 M-PoP6

Sinisa Zampera

Sunday

Workshop Talk

 P-W02

An-Ping Zeng

Monday

Workshop Talk

 T-W02

Yu Zhang

Monday

Poster

 T-P26

Hao Zhu

Sunday

Poster

 M-P25

Philip Zimmermann

Wednesday

Poster

 T-P27


 

Course Book - its Principles

 

Abstracts

All scientists present at the Course have been asked to formulate an abstract of their work or interests in Systems Biology, even those that are too new to the field to have much to report on Systems Biology itself.   Most have complied.  Accordingly the abstracts vary widely in content and quality.  Constructive criticism will be formulated for all student abstracts, and it is in this constructive mode that all discussions should proceed; after all this is a Course, not just a conference.  Please note that all abstracts, posters as well as oral presentations, must be considered “privileged personal communications”.  No data may be cited or used in any kind of verbal or written scientific correspondence with third parties without explicit permission of the presenting author.

Course (‘Abstract’) Book - Paper

The Course book on paper is meant to serve as an in-hand tool at the course.   It contains:

-          Most Course information

-          A list of when each participant has to present her/his work, or fulfill some other function

-          The program, described linearly in time, with all presentation represented by their authors and titles

-          Abstracts:

o        first the abstracts of the oral presentations in the sequence of the (day-time) program

o        then the abstracts of the poster presentations (including the ones also presented as short talks, and power posters), ordered per Symposium, then per type and then alphabetically.

-          List of addresses with presentation code

Abstracts have been giving codes.  The first letter refers to the symposium (P, T, U, M; for Principles, Tools, Unicellular and Multicellular, respectively).  The second letter denotes to the type of presentation (L for lecture, W for workshop talk, S for short talk, P for poster, PoP for ‘power poster’).  Then a sequence number follows.  For instance P-P22 refers to poster number 22 in the Symposium on Principles.

-          a subject list referring to the abstracts in which the subject is mentioned

-          an authors list referring to anywhere where that participant is mentioned in this Course book

-          a list of addresses

Course (‘Abstract’) Book - Electronic

The Course book can also be found as a pdf file on the USB stick provided.  The file should be considered non-citable ‘preprints’.  The program will also be published on the world wide web site (www.FEBSsysbio.net ).

Systems Biology Young Investigator Awards

The scientific merit of all abstracts (posters and oral presentations) submitted by graduate students and postdoctoral researchers as first authors will be evaluated by the teachers in the corresponding symposium.  The best abstracts will be awarded a surprise prize, the "Gosau Young Investigator Award" during the Farewell Party.  Also two short talk speakers will be awarded such a prize.

Web Site

The course has a website (www.FEBSsysbio.net ), which will be live before, during and after the meeting.  The website can be checked using the wireless network in many areas of the hotel, and using any of the host computers in the poster halls.  The abstract book can also be found as a pdf file on the USB stick provided.  The poster file should be considered a non-citable ‘preprint’.  The program will also be published on the world wide web site (www.FEBSsysbio.net ).

 

Technical Local Information

We wish you a very pleasant stay at the venue of the 1st FEBS Advanced Lecture Course on Systems Biology in Gosau.  We need to draw your attention to the following points:

Connections – You and the World

The meeting office has a laser printer, a copy machine, as well as phone (+43-6136-8811-390) and FAX (+43-6136-8811-352).  Its mobile phone numbers are: +43 676 572 4348 and +43 676 572 4349.  Any incoming FAX and phone call should clearly identify the addressee.  You may not want to use the expensive phone in your hotel room, unless you have a calling card.  When available, you can use our phone/FAX machine at regular post office-rates. At the venue, you can be reached, for urgent matters only, at the following e-mail address: hweste@bio.vu.nl, identifying the addressee by having:  ‘Urgent e-mail for xxx’ on the subject line.  For non-urgent matters use www.mail2web.com to inspect your own e-mail account, or use www.hotmail.com.  At many locations in the hotel there is wireless internet.  Computers, some of which are linked to the internet, are available next to the meeting office, as well as in the poster rooms. 

Departure

Regular departure from the course is Friday morning after breakfast.  At the message board near the Meeting Office there is a ‘Departure sheet’ which contains your name.  Please be so kind to write the date and time of departure you request next to your name.  The organizers will ‘OK’ your name, when they ensured transportation for you to Salzburg airport/train station.  Please allow 90 minutes for the transportation from the hotel to the airport (and then of course more than 60 minutes for boarding the flight).

FEBS Evaluation Form

Most importantly, the FEBS EVALUATION FORM!

Please complete and return the lilac FEBS Evaluation Form you will find in your Meeting Pack to the meeting office no later than Thursday, March 17.  Any and all criticisms (both positive and negative) are highly appreciated, because we are aware that nothing in this world can be perfect, but many things can be improved.  It is imperative that we receive feedback from as many participants as possible (the best of course would be from all of you).  Think about it, no return of evaluation forms - no more FEBS Courses on Systems Biology proteins in the future, and, lack of gratitude to FEBS for sponsoring so much of the present course.

FEBS-SysBio2005 Course Office

The meeting office is located in the basement of the Sport & Erlebnis Hotel**** (please follow the signs). If you need help in any way, please contact the meeting office ((+43-6136-8811-390; do not contact the hotel reception desk, please) or call the 24-hour FEBS-SysBio2005 hotline (++43 676 572 4348 and +43 676 572 4349). Daily office hours are in the morning from 7.30 – 8.30 am, at noon from 12.00 – 13.00 hours and in the evening from 7.30 – 9.00 pm. 

Help

Any member of the local organizing staff, who wear red neck cords, will try to help you anytime with any problem you may encounter.  Alternatively, turn to the Meeting Office, or call the hotline phone: +43 676 572 4348 and +43 676 572 4349

Message Board

Next to the Meeting Office there is a board for messages. 

Meals, Beverages & Lunch Packages

Your registration fee includes all meals (breakfast, coffee and tea during the program’s tea and coffee breaks, lunch, and dinner) and some non-alcoholic beverages at lunch, dinner and in the poster halls during the poster sessions.  Other beverages consumed during lunch and dinner, are not included.  For technical reasons, you cannot charge your beverages to your room:  You must pay for your beverages at the table in cash in €uros.  All beverages and drinks at the Welcome Party (thanks to FEBS Journal) and the Farewell Banquet are free of charge. 

 

If you intend to hit the slopes or otherwise go out early for the afternoon break, you may wish to take a lunch package with you, rather than to eat lunch in the restaurant.  You must then pick up a “Lunch Ticket” at the meeting office.  Each day has a different color-coded Lunch Ticket with your name on it.  You can pick up your Lunch Ticket at the meeting office for any day of the week during regular office hours at the latest, the day before consumption.  IMPORTANT, should you for whatever reason not consume your lunch package, you cannot have regular lunch instead on the same day, because the kitchen prepares a limited number of meals, based on the number of meeting participants.  Lunch packages themselves can be picked up in the HOTEL BAR around noon in exchange for YOUR LUNCH TICKET for that day.

Payments

Any substantial payment to the course organization must have been made by giro/bank transfer before the course (cf. www.febssysbio.net ).  Reimbursements will follow the same route.  The course currency is euros.   We accept cash (€UR/US$/UK£,JP¥) at current exchange rates (plus exchange cost) we collect from the www (no credit cards).  A bank and a cash machine are located on the main road in the nearby village.  Banks are open from 8 AM-12 AM and 2 AM to 5 AM in the afternoon (Mon-Fri).

Presentations

Oral presentations: All participants giving oral presentations are requested to be present in the lecture hall half an hour before their session starts (i.e. at 8.00 a.m. for talks in the morning and at 16h00 for talks in the afternoon; a member of the organizing committee will assist you).  We prefer your files (i.e. Powerpoint) as a directory called ‘’yournameSBcourse’ [e.g. WesterhoffSBcourse] on a USB stick or CD-ROM.  If your presentation links to any other files (e.g. movies), these should be in a single directory with the presentation with appropriate links.  After copying the directory with your name to the hard disk of either of the two presentation computers in the lecture Hall (i.e. a MacIntosh Powerbook and a PC Laptop), you should check whether your presentation and its links actually function.  Alternatively, you may connect your own computer to the LCD projector for your talk, but only if you have checked this with the assistant, half an hour in advance. 

You can use the computers in the poster halls and near the Meeting Office to check your presentation beforehand.

In case of a presentation that uses media other than LCD projection from computer, please inform the organizers well in advance: hweste@bio.vu.nl.

Posters: Course participants presenting Posters (including presenters of Short Talks) are requested to mount their posters in the dedicated poster areas on the poster board with their poster number (follow the signs) on Saturday evening. Your poster number is identical to the number you will find in the Course book next to the title of your abstract, in the Course book in the address list next to your name, and in the task list in the Course book  (e.g. P-P04) (a Poster number always has a ‘P’ for ‘Poster’, or an ‘S’ for ‘Short Talk’ subsequent to the hyphen).  Tape and/or pins must NOT be used to mount posters placed behind acrylic glass.  If necessary, members of the organizing committee will help you mounting your poster on paper sheets first. For all other poster walls, pins are provided and local organizers will be pleased to assist you if necessary.  Posters will stay on display until the evening of Thursday, March 17. The presenting authors needs to be present for at least one hour at the beginning of his poster session.   Poster numbers n-2 will be presented / analyzed / discussed Sunday evening from 21h00 for at least an hour.  Numbers 3n-1 will be presented / analyzed / discussed Monday evening.  Numbers 3n-3 will be presented/analyzed/discussed Wednesday evening.  Presenters of short talks are requested to present their poster on the day of their short talk, upstream the posters of their symposium.  The dates of presentation can also be gleaned from the Participant task list in this course book (cf. above). 

Power posters (‘PopP’s): PoP presenters are requested to load a powerpoint file with their presentation onto one of the PC’s dedicated to PoP’s, which are in the Poster Hall that also houses the PoP’s (follow the signs).  Numbers 3n-2 will be presented Sunday evening from 21h00 for at least an hour.  Numbers 3n-1 will be presented  Monday evening.  Numbers 3n will be presented Wednesday evening.  The dates of presentation can also be gleaned from the Participant task list in this Course book (cf. above). 

Blackboard presentations:  Blackboard Presenters should enquire at the Meeting Office.  LCD projector will be available.  Presenters are expected to connect their own personal computer.  Flipovers will be available as well.

Computer presentations:  Anyone whishing to demonstrate a computer program, can do so on an informal basis by making use of the PoP setup, in time slots not allocated to the PoP’s.

 

Skiing and Outdoor Leasure

A daily bus shuttle to the “Hornspitzbahn” organized by FEBSSysBio2005 will leave the hotel 20 minutes after the last morning lecture. The return shuttle from the "Hornspitzbahn" to the Hotel will leave the "Hornspitzbahn" at 4.00 PM sharp.  A schedule for the daily public ski bus, as well as a ski route map is included in your registration package. On Saturday and Sunday, you can go to the local ski school, located at the chair lift of the "Hornspitzbahn" for rental equipment such as alpine ski sets, snowboards and cross-country skis.  If you show your FEBSSysBio2005 name badge, you will receive a discount on your rental gear.  Moreover, you can sign up for skiing lessons, which usually last three to five days.  We urge you to finish boot fitting and check-in as soon as possible after your registration, in order to avoid delays during the big rush on Monday.

 

Social Program

Salzburg.            On Tuesday, we have scheduled for all course participants to visit Salzburg, the city of Mozart, with lots of surprises.  Buses will leave the hotel at 13h30 and return to the Hotel around 23h30.    There will time available for walks or shopping in romantic downtown Salzburg, but there will also be a common program.  As you might expect, you should not forget to bring your ears, eyes, and taste buds ……  Also be ready to discuss Systems Biology, on the bus, or in the ………..

 

Depending on interest, we may organize the following excursions (Please enquire at the Meeting Office):

 

Bad Ischl:        A trip to Bad Ischl, the favorite retreat of the one-time Austrian Emperor Franz Josef.  Surrounded by a spectacular scenery you can enjoy the rich leisure offered of the magnificent little town Bad Ischl, just like Franz Josef did for more than forty years. 

 

Hallstadt:         A visit to this restored centre of a Salt and Copper mining town is a thrill.

 

Ice Cave:        A visit to the “Koppenbrüller Ice Cave” leading you into the mighty Dachstein mountain range.  Due to expected snowfall, this excursion may not be available.

 

Sport & Erlebnis Hotel Facilities

The hotel offers an indoor pool, two saunas, steam bath, gym, whirl pool, and solarium at no extra charge to the Course participants.  Solarium and whirl pool take tokens that are available free of charge at the hotel reception desk, where further information is also available.  Indoor tennis courts are available for a surcharge; please enquire at the hotel reception desk.

 



 

 

Scientific Program

 of

SysBio2005

 

 

 

 

 

Saturday                                                                   March 12

Course Registration & Hotel Check-In                                                                11:00 am - 6:00 pm

Welcome Reception                                                                                            6:00 pm - 6:45 pm

Official Course Opening                                                                                      6:45 pm - 6:55 pm

Hans Westerhoff and Karl Kuchler                

 

AstraZeneca Opening Lecture

 

Douglas Kell                                                                                       7:00 pm – 8:00 pm

             

Metabolomics, machine learning and modelling in systems biology: towards an understanding of the language of cells

 

 

Welcome Dinner            &                Musical performance                               8:30 pm - open end

          Subhendu Ghosh                    Patterns of Passion


 

Sunday                                                                      March 13

Breakfast                                                                                                                                               7:00 - 8:30 am

Principles of Systems Biology                      Lectures                                      8:30 am - 12:30 pm

Chair: Hans Westerhoff

Co-chair: Lilia Alberghina

P-L1     Reinhart Heinrich                                                                                                8:30 - 9:15

Dynamics and design of cellular reaction networks

P-L2     John Doyle                                                                                                         9:15 - 10:00

Organizational complexity

Coffee & Refreshment Break                                                                                           10:00 - 10:20

P-L3     Albert Goldbeter                                                                                               10:20 -11:55

Computational approaches to cellular rhythms       

P-L4     Stefan Schuster                                                                                                11:05 - 11:50

Fundamentals and applications of metabolic pathway analysis

Break                                                                                                                           11:50 – 12:00

Guided General Discussion:                Identifying issues; SB Principles     12:00 - 12:30 pm

Lunch & Afternoon Break                                                                                            12:30 - 4:30 pm

Coffee and Tea Break                                                                                                  4:00 – 4:30 pm

Chalk/Blackboard teaching                 4 in parallel                                       4:30 – 5:10 pm

PT-B1     Uri Alon                                             Motifs and networks

PT-B2     Reinhart Heinrich/Stefan Schuster        Stability and flux mode analysis

PT-B3     Jacky Snoep/Hans Westerhoff             Control analysis and Silicon cells

PT-B4     Jörg Stelling/Frank Bruggeman            Robustness, network identification and engineering

Principles of Systems Biology                      Workshop & Short Talks                    5:15 – 7:00 pm

Chair: Lilia Alberghina

Co-chair: Hans Westerhoff

P-W1    Dennis Vitkup                                                                                                      5:15 - 5:35

Expression dynamics of a cellular metabolic network

P-S1     Frank Bruggeman                                                                                               5:35 - 5:50

Smart regulation of ammonium assimilation by Escherichia coli: modularity, robustness, and flux regulation

Coffee & Refreshment Break                                                                                              5:50 - 6:10

P-W2    Sinisa Zampera                                                                                                    6:10 -6:30

An adaptive system approach for the modelling of genetic regulatory networks

Glucose metabolism study in the yeast

P-S2     Markus Kollmann                                                                                                 6:30 - 6:45

Design principles of signal transduction pathways to attenuate noise 

P-S3     Esa Pitkänen                                                                                                         6:45- 7:00

On pathways and distances in metabolic networks

Resumed General Discussion:            Addressing the issues; SB principles        7:00 - 7:30

Dinner                                                                                                                         7:30 - 9:00 pm

            Poster Session 1                                                                                          9:00 - 11:00 pm

            Viewing posters                                                                                                    9:00 -  9:45

            Free poster wandering                                                                                          9:45 – 10:30

            Round table poster discussion  (presenters and teachers only)                              10:30 – 11:00

 

Poster Presentations

P-S01     Smart regulation of ammonium assimilation by Escherichia coli: modularity, robustness, and flux regulation. Frank J. Bruggeman, Fred C. Boogerd and Hans V. Westerhoff 

P-S02     Design Principles of Signal Transduction Pathways to attenuate Noise

Markus Kollmann, Kilian Bartholome and Jens Timmer

P-S03     On pathways and distances in metabolic networks

Esa Pitkänen, Ari Rantanen, Juho Rousu and Esko Ukkonen

 

P-P01     The use of accurate mass and time tags to measure yeast’s glycolytic proteome

Ronald Aardema, Henk L. Dekker, Jaap Willem Back, Leo J. de Koning, Luitzen de Jong and Chris G. de Koster 

P-P04     Pathways to analysis of microarray data R. Keira Curtis and Antonio Vidal-Puig

P-P07     A dynamic model of cAMP signal transduction in yeast Dirk Müller, Helena Diaz-Cuervo, Luciano Aguilera-Vazquez, Klaus Mauch and Matthias Reuss

P-P10     Modelling of Drosophila segmentation gene expression with and without usage of attractors

Vitaly V. Gursky, Johannes Jaeger, Konstantin N. Kozlov, John Reinitz and Alexander M. Samsonov

P-P13     Inferring gene regulatory relationships from time series microarray data based on the trend of expression changes. Feng He and An-Ping Zeng 

P-P16     A reductive approach to analyze stochasticity in intracellular networks.

Tetsuya J. Kobayashi and Kazuyuki Aihara

P-P19     Modelling and simulation of dynamic signals in cells. Thomas Millat and Olaf Wolkenhauer

P-P22     An in silico model for the optimization of threonine production in Escherichia coli.

Juan-Carlos Rodriguez, Jerome Maury, Christophe Chassagnole, Josep Centelles, Nic Lindley and Marta Cascante 

P-P25     Inferring regulatory networks from experimental data

Christian Spieth, Felix Streichert, Nora Speer and Andreas Zell

 

T-P01      Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

Irina Borodina, Preben Krabben and Jens Nielsen

T-P04      Reduced order modeling of global regulation - redox regulation in Escherichia coli 

Michael Ederer, Thomas Sauter and Ernst Dieter Gilles

T-P07      CellDesigner2.0: A process diagram editor for gene-regulatory and biochemical networks. Akira Funahashi, Naoki Tanimura, Yukiko Matsuoka, Naritoshi Yoshinaga and Hiroaki Kitano 

T-P10      Speeding up the central metabolism in Pichia pastoris

Franz Hartner, Lars Blank, Alexander Kern, Uwe Sauer and Anton Glieder

T-P13      NMR spectroscopy in systems biology: methods for metabolomics and fluxomics

Paula Jouhten, Minna Perälä, Eija Rintala Laura Ruohonen, Perttu Permi, Merja Penttilä and Hannu Maaheimo

T-P16      An integrative framework for modeling signaling pathways  Robert Modre-Osprian,

Marc Breit, Visvanathan Mahesh, Gernot Enzenberg and Bernhard Tilg

T-P19      Application of yeast genomic strategies to link biologically active compounds to their cellular targets Ainslie B. Parsons, David Williams, Satoru Ishihara, Yoshi Ohya, Raymond Andersen, Timothy Hughes and Charles Boone 

T-P22      Glycolytic oscillations in spatially ordered interacting cells Jana Schütze & Reinhart Heinrich 

T-P25      Global transcriptional response of Saccharomyces cerevisiae to ammonium, alanine,

or glutamine limitation  Renata Usaite, Birgitte Regenberg and Jens Nielsen


U-P01     Neisserial DNA uptake sequences: biased distribution and influence on transformation.

Ole Herman Ambur, Stephan Frye, Tonje Davidsen, Hanne Tuven and Tone Tønjum

U-P04     Experimental manipulation and mathematical modeling of arginine biosynthesis in Escherichia coli. Marina Caldara, K. Verbrugghe, L. De Vuyst, M. Crabeel, G. Dupont, A. Goldbeter and R. Cunin

U-P07     Retrograde response to mitochondrial dysfunction is separable from Tor1/2 regulation of retrograde gene expression. Sergio Giannattasio, Zhengchang Liu and Ronald Butow

U-P10     Extending life by alternative respiration? Alexander Kern, Franz Hartner and Anton Glieder

U-P13     A dynamic model of cAMP signal transduction in yeast. Dirk Mueller, Helena Díaz Cuervo, Luciano Aguilera-Vázquez, Klaus Mauch and Matthias Reuss 

U-P16     Stress induced by weak organic acids in Saccharomyces cerevisiae.

Rick Orij, Jarne Postmus, Gerco van Eikenhorst, Stanley Brul and Gertien Smits

U-P19     Evolutionary conservation and divergence of fungal promoter sequences

Riccarda Rischatsch, Sylvia Voegeli and Peter Philippsen

U-P22     Unusual group II introns in bacteria of the Bacillus cereus group.

Nicolas Tourasse, Fredrik Stabell, Lillian Reiter and Anne-Brit Kolstø

U-P25     LacplantCyc: in silico reconstruction of the metabolic pathways of Lactobacillus plantarum.

Frank H.J. van Enckevort, Bas Teusink, Christof Francke and Roland J. Siezen

 

M-P01     Control of the ATP/ADP ratio in pancreatic beta cells Charles Affourtit and Martin D. Brand

M-P04     Sensitivity analysis with respect to initial values of the TNFalpha mediated NF-kappaB

signalling pathway. Marc Breit, Gernot Enzenberg, Visvanthan Mahesh, Robert Modre-Osprian and Bernhard Tilg

M-P07     Na,K-ATPase regulation via phospholemman phosphorylation

Claudia Donnet, Jia Li Guo, Amy Tucker and Kathleen Sweadner  

M-P10     Generating conceptual models in Zebrafish zinc homeostasis: The first steps towards and

holistic view of zinc metabolism. Graham Feeney, Dongling Zheng, Peter Kille and Hogstrand Christer

M-P13     Impaired gene expression in Sjogren's disease. Adi Gilboa-Geffen and Hermona Soreq

M-P16     Towards a systems biology of signal transduction by insulin and insulin-like growth factors.

Shaukat Mahmood, Jane Palsgaard, Soetkin Versteyhe, Maja Jensen and Pierre De Meyts

M-P19     Molecular dissection of the key LGS residues involved in the control of glycogen biosynthesis. Susana Ros and Joan J. Guinovart

M-P22     Quantitative modeling of EGFR-internalization as a mechanism of signaling specificity

Hannah Schmidt-Glenewinkel, Constantin Kappel and Ivayla Vacheva

M-P25     Modeling emergent networks by dynamic reconstruction in silico.  Hao Zhu and Pawan Dhar

 

 

Power Poster Presentations

P-PoP1   New parameter estimation method with possible application in systems biology Ioan Grosu

P-PoP4   Determination of in vivo non-steady-state fluxes and kinetic information using stable isotope labeling and metabolite pool size data: theory and application. Junli Liu, Alisdair R. Fernie and David F. Marshall

T-PoP1    1/f Noise in Ion Channel: A Theory Based on Self-Organised Criticality

Jyotirmoy Banerjee, Mahendra K. Verma and Subhendu Ghosh 

T-PoP4    Using SRS to develop and populate an information layer for the EMI-CD modeling platform Dan Staines, Daniel Flint and Thure Etzold

U-PoP1   Modeling and analyses of Mycobacterium tuberculosis metabolism

Asawin Meechai, Supapon Cheevadhanalak and Sakarindr Bhumiratana

M-PoP1   Niels Aarsaether

M-PoP4   Module dynamics of the GnRH signal transduction network Karen Page