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
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
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)
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.
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
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 ).
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.
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
).
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:
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.
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).
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.
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
Next
to the Meeting Office there is a board for messages.
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.
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).
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.
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.
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.
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.
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
Breakfast 7:00
- 8:30 am
rinciples
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
rinciples
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 and David Krakauer
Breakfast 7:00
- 8:30 am
ools
and methods (part 1) Lectures 8:30 am -
12:30 pm
Chair: Karl Kuchler
Co-chair: Igor Goryanin
T-L1 Rudi
Aebersold 8:30
- 9:15
Quantitative
Proteomics: An essential component of systems biology
T-L2 Roland
Eils 9:15
- 10:00
Modelling and
simulation of large-scale signal transduction networks
Coffee &
Refreshment Break 10:00
- 10:20
T-L3 Shoshana
Wodak 10:20
- 11:05
Analysing networks
of biochemical processes: Bioinformatics meets systems biology
T-L4 Charlie
Boone 11:05
- 11:50
Global mapping of
synthetic genetic interactions in yeast
Break 11:50
– 12:00
Guided General Discussion: Identifying
issues; Tools, Methods 12:00 -
12:30
Lunch &
Afternoon Break 12:30
- 4:30 pm
Coffee and Tea Break 4:00
– 4:30 pm
Chalk/Blackboard teaching 4
in parallel (repeat) 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
ools
and methods Workshop
& Short talks 5:15
- 7:00 pm
Chair: Igor Goryanin
Co-chair: Karl Kuchler
T-W1 An-Ping
Zeng 5:15
- 5:35
An integrated
interaction network of Escherichia coli for studying genotype-phenotype relationship
T-S1 Sune
Danø 5:35
- 5:50
Oscillatory
mechanisms derived from phase and amplitude information
Coffee & Refreshment Break 5:50
- 6:15
T-S2 Adrienne James 6:15
- 6:30
Application of
modelling and simulation to drug discovery: The ErbB system
T-S3 Konstantin
Kozlov 6:30
- 6:45
Combined
optimization technique for biological data fitting
T-S4 Balázs
Papp 6:45-
7:00
Systematic
identification and characterisation of synthetic lethal interactions in the
metabolic network of yeast
Resumed General Discussion: Addressing the issues Tools &
Methods 7:00
- 7:30
Dinner 7:30
- 9:00 pm
Poster
Session 2 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
T-S01 Oscillatory mechanisms derived from phase
and amplitude information
Sune Danø,
Mads Madsen and Preben G. Sørensen
T-S02 Application of modelling and simulation to
drug discovery: The ErbB System
Bart Hendriks,
Gareth Griffiths, Jack Beusmans, Adrienne James,
Julie Cook, Jonathan Swinton and David De
Graaf
T-S03 Combined optimization technique for
biological data fitting
Konstantin N. Kozlov,
Alexander M. Samsonov and John Reinitz
T-S04 Systematic
identification and characterisation of synthetic lethal interactions in the
metabolic network of yeast. Balázs Papp,
Richard Harrison, Daniela Delneri, Csaba Pál and
Stephen Oliver
P-P02 Metabolic footprinting: its role in systems
biology
Marie Brown,
Rick Dunn, Julia Handl and Douglas Kell
P-P05 Multiscale modelling of a cell
Gianni De Fabritiis and Peter Coveney
P-P08 Metabolic quorum sensing: experiments with S. cerevisiae
Francesco d'Ovidio, Silvia De Monte, Sune Danø and Preben Graae Sørensen
P-P11 Discovering compound mode of action with
CutTree
Kristofer Hallén,
Johan Björkegren and Jesper Tegnér
P-P14 Secondary metabolites can create
coexistence in the chemostat
Julia Heßeler,
Julia K. Schmidt, Udo Reichl and Dietrich Flockerzi
P-P17 Linlog Modeling Approach: Theoretical
Platform for System Biology
M.T.A. Penia Kresnowati,
Wouter van Winden and Sef Heijnen
P-P20 Systems analysis of yeast glucose sensing
system
Hisao Moriya and Hiroaki Kitano
P-P23 Kinetic models of phosphorylation cycles:
the role of protein-protein interactions
Carlos Salazar and Thomas Höfer
P-P26 First steps towards a multi-dimensional
iron regulatory network
Yevhen Vainshtein,
Martina Muckenthaler, Alvis Brazma and Matthias W. Hentze
T-P02 Relational
learning of biological networks
Cyril Combe, Florence d'Alché-Buc, Vincent Schachter
and Stan Matwin
T-P05 Technical variance, quality control and
scaling: necessary steps towards meta-analyses on large expression databases. Martin Eisenacher, Harald Funke, Thomas Vogl,
Christoph Cichon, Kristina Riehemann, Clemens Sorg and
Wolfgang Koepcke
T-P08 Simulation
of epidermal homeostasis including barrier formation
Niels Grabe and
Karsten Neuber
T-P11 Software
components for analysis of DNA microarray and quantitative proteomics data
Sergii Ivakhno and
Olexander Kornelyuk
T-P14 Autonomous
oscillations in Saccharomyces cerevisiae during batch cultures on trehalose.
Matthieu Jules, Jean-Marie Francois and Jean-Luc Parrou
T-P17 Data
visualization for gene selection and modeling in cancer bioinformatics
Minca Mramor, Gregor Leban and Blaž Zupan
T-P20 SCIpath
- an integrated environment for systems biology analysis and visualisation.
Manish Patel
T-P23 Database
Support for Yeast Metabolomics Data Management
Irena Spasic, Warwick Dunn and Douglas Kell
T-P26 Identification of the C-terminal signal peptides for GPI modification and prediction of the
cleavage sites. Yu Zhang, Thomas
Skoet Jensen, Ulrik de Lichtenberg and Soeren Brunak
U-P02 Gene
expression and adaptive responses of in
situ fermentation
Herwig Bachmann,
Michiel Kleerebezem and Johan E. van Hylckama Vlieg
U-P05 Comparative metabolomics of Saccharomyces
yeasts. Robert P. Davey1,
G Lacey1, DA MacKenzie,
M Defernez, FA Mellon, K Huber, V Moulton and
IN Robert
U-P08 Unravelling
new metabolic metworks in LAB via the thioredoxin system
L. Mariela Hebben-Serrano, Eddy Smid and Willem M. de Vos
U-P11 Systematic computational modelling reveals
a key operating principle of TOR signalling in yeast Lars Kuepfer, Matthias Peter, Jörg Stelling and
Uwe Sauer
U-P14 Natural
sweetening of food products: engineering Lactococcus
lactis for glucose production
Wietske
A. Pool, Ana R. Neves, Jan Kok, Helena Santos and Oscar
P. Kuipers
U-P17 Adaptation
of yeast glycolysis to temperature changes.
Jarne Postmus, Jildau Bouwman, Rick Orij, Stanley Brul and Gertien Smits
U-P20 A
Systems Biology approach for the optimization of recombinant protein production
in E. coli
Eugénio Ferreira
and Isabel Rocha
U-P23 The
effect of oxygen tension on yeast glycolysis
Isil Tuzun, Klaas Hellingwerf and M. J. Teixeira de
Mattos
U-P26 High-throughput screening of Saccharomyces cerevisae knockout
library: method development and stoichiometric profiling. Vidya R. Velagapudi, Christoph Wittmann, Thomas Lengauer,
Priti Talwar and Elmar Heinzle
M-P02 Regulation
of the INF-Gamma/JAK/Stat1 signal transduction pathway
Stephan Beirer, Thomas Meyer, Uwe Vinkemeyer and
Thomas Höfer
M-P05 A domain-oriented approach to the reduction
of combinatorial complexity in signal transduction networks Holger Conzelmann, Julio Saez-Rodriguez, Thomas Sauter, Boris Kholodenko and Ernst-Dieter Gilles
M-P08 System
Properties of the Core Reactions of Apoptosis
Thomas Eißing, Carla Cimatoribus, Frank Allgöwer,
Peter Scheurich and Eric Bullinger
M-P11 Repression
of SOX6 transcriptional activity by SUMO modification
Fernandez-Lloris Raquel, Osses Nelson, Jaffray Ellis,
Shen LinNan, Vaughan Owen Anthony, Girdwood David,
Bartrons Ramon, Rosa Jose Luis and Ventura Francesc
M-P14 Modeling
the synchronization of circadian oscillators in the suprachiasmatic nucleus
Didier Gonze, Samuel Bernard, Christian Waltermann,
Achim Kramer and Hanspeter Herzel
M-P17 BOOLEAN analysis of the signaling network
triggered by neurotrophic factors and extracellular matrix in sensory neurons. Mikhail Paveliev, Maria Lume and Mart Saarma
M-P20 Analysis
of the signaling network involved in the activation of T-Lymphocytes
Julio Saez-Rodriguez,
Xiaoqian Wang, Birgit Schoeberl, Steffen Klamt, Jonathan Lindquist,
Stefanie Kliche, Buckhart Schraven and Ernst Dieter Gilles
M-P23 Retroelement
insertion polymorphism in cell line identification.
Svetlana
V. Ustyugova, Anna L. Amosova, Yuri B. Lebedev and
Eugene D. Sverdlov
Power Poster
Presentations
P-PoP2 Effects of noise in
metabolic flux analysis. Visakan Kadirkamanathan, Steve Billings, Sarawan Wongsa,
Jing Yang and
Philip Wright
P-PoP5 An adaptive system approach for the modelling
of genetic regulatory networks. Glucose metabolism study in the yeast. Sinisa Zampera and Todor Vujasinovic
T-PoP2 Single cell mechanics and mechano signal transduction using a micro-force loading device. Hao Zhang, Zhiqing Feng, Ning Fang, Vincent Chan
and Kin Liao
T-PoP5 Regulatory Network Reconstruction by
Integrative Analysis of Cross-Platform Microarray Data. Jasmine Zhou,
Ming-Chih Kao, Haiyan Huang, Angela Wong,
Juan Nunez-Iglesias, Michael Primig, Oscar Aparicio,
Caleb Finch, Todd Morgan and Wing Wong
U-PoP2 Some changes in the composition of nuclear
components during cereal seeds germination.
Liya
A. Minasbekyan and Poghos H. Vardevanyan
M-PoP2 SYMBIONIC: A European initiative on the
Systems Biology of the neuronal cell Ivan Arisi
M-PoP5 Experimental design for model discrimination
in cellular signal transduction
Clemens Kreutz,
Jörg Stelling, Thomas Maiwald and Jens Timmer
Breakfast 7:00
- 8:30 am
ools
& Methods (part 2) Lectures 8:30 am -
10:00 pm
Chair: Karl Kuchler
T-L5 Jacky
Snoep 8:30
- 9:15
The Silicon Cell
approach to building detailed kinetic models of biological systems
T-L6 Ursula
Kummer 9:15
- 10:00
Mathematical
modelling: Choosing the right simulation method
Coffee &
Refreshment Break 10:10
- 10:20
nicellular
Organisms (part 1) Lectures 10:20 am -
12:35 pm
Chair: Stefan Hohmann
U-L1 Edda Klipp 10:20 - 11:05
Mathematical
modeling of stress response in yeast
U-L2 Matthias
Reuss 11:05
- 11:50
Hiding behind the
population average - cell cycle dynamics
of energy metabolism during the lifelines of individual yeast cells
U-L3 Jörg
Stelling 11:50
- 12:35
Knowledge and data
requirements for systems analysis of cellular networks
Lunch &
Afternoon Break 12:35
– 13:15
VISIT to SALZBURG 13:30
– 23:00 pm
Buses will leave Hotel at 13:30
pm
Dinner
in Salzburg
Return from Salzburg to
the venue 22:00
pm
Breakfast 7:00
- 8:30 am
nicellular Organisms (part 2) Lectures 8:30 am -
12:30 pm
Chair: Stefan Hohmann
Co-chair:Matthias Reuss
U-L4 Uwe
Sauer 8:30
- 9:15
In vivo
operation of metabolic pathways
U-L5 Uri
Alon 9:15
- 10:00
Simplicity in
biology
Coffee &
Refreshment Break 10:00
- 10:20
U-L6 Barry
Wanner 10:20 - 11:05
Stochastic
activation of the response regulator PhoB by noncognate histidine kinases
U-L7 Masaru
Tomita 11:05
- 11:50
Metabolome
analysis and systems biology
Break 11:50
– 12:00
Guided General
Discussion: Identifying issues;
unicellular organisms 12:00 -
12:30
Lunch &
Afternoon Break 12:30
- 4:30 pm
Coffee and Tea Break 4:00
– 4:30 pm
nicellular
Organisms Workshop
& Short Talks 4:30
- 6:50 pm
Chair: Matthias Reuss
Co-chair: Stefan Hohmann
U-W1 Guillaume
Beslon 4:30
- 4:50
Modelling
evolution of prokaryotic genomes: an integrative approach
U-W2 Victor
Sourjik 4:50
- 5:10
Signal processing
in bacterial chemotaxis
U-W3 Bas
Teusink 5:10
- 5:30
Combining experimental data and in silico analysis to model the
metabolic and regulatory network of Lactobacillus plantarum
Coffee & Refreshment Break 5:30
- 5:50
U-S1 Attila
Csikasz-Nagy 5:50
- 6:05
Modelling fission
yeast morphogenesis
U-S2 Silvia
De Monte 6:05
- 6:20
Metabolic quorum
sensing: onset of density-dependent oscillations
U-S3 Ana
Sofia Figueiredo 6:20-
6:35
Integration of software tools for the in silico design of metabolic
pathways using flux balance analysis
U-S4 Douglas
Murray 6:35-
6:50
Uncovering the
control of the respiratory clock in yeast
Resumed General
Discussion: Addressing the issues; unicellular organisms 6:50- 7:30
Dinner 7:30
- 9:00 pm
Poster
Session 3 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
U-S01 Modelling fission yeast morphogenesis.Attila Csikasz-Nagy,
Bela Gyorffy, Wolfgang Alt, John J. Tyson and Bela Novak
U-S02 Metabolic
quorum sensing: onset of density-dependent oscillations
Silvia De Monte, Francesco d'Ovidio, Sune Danø and Preben Grae Sørensen
U-S03 Integration of software
tools for the in silico design of metabolic pathways using flux balance
analysis. Ana Sofia Figueiredo, Pedro Fernandes, Pedro Pissarra and
António Ferreira
U-S04 Uncovering
the control of the
respiratory clock in yeast
Douglas B. Murray and
Hiroaki Kitano
M-S01 Inferring
feedback mechanisms in cellular transformation due to oncogenic RAS
Nils Bluethgen, Christine Sers, Jana Keil, Szymon
M. Kielbasa, Reinhold Schaefer and Hanspeter Herzel
M-S02 Regulation
of MAPK signalling determining cell fate in PC-12 cells - a step beyond
biochemistry
Silvia D. Santos, Eli Zamir, Peter Verveer and
Philippe Bastiaens
M-S03 Mathematical
modeling of neuronal response to neuropeptides: Angiotensin II signaling via
G-protein coupled
receptor. Thomas Sauter, Rajanikanth Vadigepalli and James Schwabe
P-P03 Genetic network model for the AP-1 system. David Camacho and
Roland Eils
P-P06 A
genetical genomics approach to gene network
inference. Alberto de la Fuente, Bing Liu and
Ina Hoeschele
P-P09 Phylogenetic analysis based on structural
information of metabolic networks
Oliver Ebenhöh, Thomas Handorf and
Reinhart Heinrich
P-P12 Scopes: A new concept for the structural
analysis of metabolic networks
Thomas Handorf, Oliver Ebenhöh and
Reinhart Heinrich
P-P15 Two Numerical Model Analyses for the
Movement of a Restriction Enzyme.
Noriko Hiroi, Akira Funahashi and
Hiroaki Kitano
P-P18 Knowledge
discovery by integrated analysis of metabolic and regulatory networks
Hong-Wu Ma and
An-Ping Zeng
P-P21 Investigating
the structure of integrated biological networks
Venkata Gopalacharyulu Peddinti, Erno Lindfors and Matej Oresic
P-P24 Modelling transient dynamics of osmo-stress
response in Yeast.Jörg Schaber,
Bodil Nordlander and Edda Klipp
P-P27 Nutrient
starvation in baker’s yeast, and the implication of protein degradation for Vertical Genomics. Karen van
Eunen, Jildau Bouwman, Sergio Rossell, Rob J.M. Spanning,
Barbara M. Bakker and Hans V. Westerhoff
T-P03 A new Information System to manage and
analyse information on biochemical interactions
Holger Dach, Juliane Fluck, Kai Kumpf and
Rainer Manthey
T-P06 Genomic rearrangements : influence of the
genetic context on chromosomal dynamics
Emilie Fritsch, Jean-luc Souciet, Serge Potier and
Jacky de Montigny
T-P09 Modelling protein motions
for systems biology.Benjamin
A Hall and
Mark Sansom
T-P12 Systemic models for metabolic dynamics and
regulation of gene expression – easy access, retrieval and search for publicly available
gene expression data.Per
Harald Jonson and M.
Minna Laine
T-P15 Automated
construction of genetic networks from mutant data
Peter Juvan, Gad Shaulsky and Blaz Zupan
T-P18 Accelerating the construction of genome-scale metabolic models: a test case for Lactococcus
lactis. Richard A. Notebaart, Frank H.J. van Enckevort, Bas Teusink and Roland
J. Siezen
T-P24 Fokker-Planck equations for IP3
mediated Calcium dynamics.Rüdiger Thul and
Martin Falcke
T-P27 The Genevestigator gene function
discovery engine.Philip Zimmermann, Matthias Hirsch-Hoffmann, Lars Hennig and
Wilhelm Gruissem
U-P03 Metabolic
functions of duplicate genes in Saccharomyces cerevisiae
Lars M. Blank, Lars Küpfer and
Uwe Sauer
U-P06 Metabolic
network analysis in six microbial species. Tobias Fuhrer, Eliane Fischer and Uwe Sauer
U-P09 The
regulatory circuitry of arabinases in Bacillus subtilis .José
M. Inácio and
Isabel de Sá-Nogueira
U-P12 Dynamic
on-line investigation of lactic acid
bacteria.
Ann Zahle Larsen, Lars Folke Olsen and Frants
Roager Lauritsen
U-P15 Adaptative
response of the central metabolism in Escherichia coli to quantitative modulations of a single
enzyme: glucose-6-phosphate dehydrogenase.Cécile Nicolas, Fabien Létisse and Jean-Charles Portais
U-P18 Progressive
adaptation of Lactococcus lactis to stress.
Emma Redon, Pascal Loubière and
Muriel Cocaign-Bousquet
U-P21 Some
properties and partial purification of Candida
Guilliermondii NP-4 and Paramcium Multimcronucleatum glutaminase. Ara H. Tamrazyan, Misak A. Davtyan and Susanna A. Karapetyan
U-P24 Vertical
genomics in baker’s yeast: adaptation of respiring cells to anaerobic
sugar-excess conditions. Joost van den Brink,
Pascale Daran-Lapujade, Han de Winde and Jack Pronk
U-P27 A
Sysytems Biology Strategy For Understanding The Genome-wide Control Of Growth
Rate And Metabolic Flux In Yeast. Jian Wu, Nianshu Zhang, Andy Hayes, Douglas Kell, Stephen Oliver and Jian Wu
M-P03 Comprehensive
analysis of the cancer Tyrosine
Kinome & Phosphatome
Martin Bezler, Christian Mann, Detlev T. Bartmus,
Pjotr Knyazev, Tatjana Knyazeva, Sylvia Streit and Axel Ullrich
M-P06 Model
building in a systems biology company: the cell cycle and
apoptosis
Cathy Derow, Chris Snell, Christophe Chassagnole,
John Savin and David Fell
M-P09 Meshfree
modelling of biological transport processes in complex domains
Martin Eigel and
Markus Kirkilionis
M-P12 Network
synchronization from population to cell level
Laurent Gaubert and
Magali Roux-Rouquié
M-P15 Modelling,
Enzyme kinetics & Fluorescence Imaging of the NF-kappaB Signalling Pathway Adaoha EC. Ihekwaba, Rachel Grimley, Neil Benson,
David Broomhead and Douglas B. Kell
M-P18 A
topological analysis of the human transcription factor interacting network
Carlos Rodríguez-Caso, Miguel Ángel Medina and Ricard V Solé
M-P21 Flavo-di-iron
proteins: role in microbial detoxification by NO
Francesca Maria Scandurra, Paolo Sarti, PierLuigi Fiori,
Elena Forte, Alessandro Giuffrè, P. Rappelli, G. Sanciu,
Daniela Mastronicola, Miguel Teixeira and Maurizio Brunori
M-P24 RNAi screening for novel components of mammalian Hedgehog and Wnt pathways
Markku Varjosalo, Antti Oinas and Jussi Taipale
Power Poster
Presentations
P-PoP3 A new dynamic complexity reduction method
for biochemical reaction networks
Dirk Lebiedz, Jürgen Zobeley, Julia Kammerer and
Ursula Kummer
T-PoP3 Connectivity
matrix for describing all the atom-level connectivities in a given metabolic
network and its use for analysis of the network structure.Jun Ohta
T-PoP6 Oxygen
consumption and glycolytic redox state in skeletal muscle
Bjørn Quistorff, Sune Danø, Mads Madsen, Brian Lindegaard Petersen and
Peter Fæster Nielsen
U-PoP3 Differentiation
in a genetic network with duplicate repressors: simulating evolutionary
pathways based on Lac mutational data. Frank Poelwijk,
Daniel Kiviet and Sander Tans
M-PoP3 In
vitro systems for modelling of signal transduction in hepatocytes
Patricio Godoy, Katja Breitkopf, Loredana Ciuclan,
Eliza Wiercinska and Steven Dooley
M-PoP6 Integration of
genomics and proteomics with metabolic/signaling pathways for
generating/improving novel anti-cancer drug targets.
He Yang
Breakfast 7:00
- 8:30 am
ulticellular Organisms Lectures 8:30 am -
12:30 pm
Chair: Hiraoki
Kitano
Co-chair: Marta
Cascante
M-L1 Michel Eichelbaum 8:30
- 9:15
Pharmacogenomics:
a holistic approach to drug organism interaction
M-L2 Boris
Kholodenko 9:15
- 10:00
Systems biology of
receptor tyrosine kinase signaling
Coffee &
Refreshment Break 10:00
- 10:20
M-L3 Nicolas Le Novere 10:20 - 11:05
Computational
systems biology of neuronal signalling
M-L4 Ursula
Klingmüller 11:05
- 11:50
Signal
transduction and cancer – generation of high quality quantitative data
Break 11:50
– 12:00
Guided
General Discussion: Identifying issues; multicellular organisms 12:00 - 12:30
Lunch &
Afternoon Break 12:30
- 4:30 pm
Coffee and Tea Break 4:00
– 4:30 pm
ulticellular
Organisms Workshop
& Short Talks 4:30
-5:55 pm
Chair: Marta Cascante
Co-chair: Hiraoki Kitano
M-W1 Mariko
Hatakeyama 4:30
- 4:50
Computer
simulation analysis of ErbB signaling for understanding of cellular
transformation mechanism
M-W2 Thomas
Höfer 4:50
- 5:10
Integration of signal transduction and cytokine expression in T
lymphocytes
M-S1 Nils
Bluethgen 5:10
- 5:25
Inferring feedback
mechanisms in cellular transformation due to oncogenic RAS
M-S2 Silvia
Santos 5:25
- 5:40
Regulation of MAPK signalling determining cell fate in PC-12 cells - a step beyond
biochemistry
M-S3 Thomas
Sauter 5:40-
5:55
Mathematical
modeling of neuronal response to neuropeptides: Angiotensin II signaling via
G-protein coupled receptor
Coffee & Refreshment
Break 5:55
- 6:15
Resumed General
Discussion:Addressing the issues; multicellular organisms 6:15 - 6:45
NovoNordisk Closing Lecture
Denis Noble 7:00
pm – 8:00 pm
Highlights of
SysBio2005: From
genes to whole organs
Vertical integration using mathematical simulation
Banquet and
Farewell Party 8:00
pm - open end
Presentation of “Gosau YOUNG SysBio INVESTIGATOR AWARDS” 8:30 - 8:45
Marta Cascante, Lilia Alberghina, Roel van
Driel, Stefan Hohmann
Official Course Closure 8:45 - 9:00
Hans Westerhoff and Karl Kuchler
Breakfast 7:00
- 8:30 am
Hotel Check-Out
& Departure 7:00
- 11:00 am
End of SysBio 2005 11:00
am
Shuttle Buses to Salzburg (detailed schedule to be announced)
