Special issue of
FEMS Yeast
Research

Recollections

 

   
ISSY25 PROGRAM
(Final Programme.pdf)
    
Speakers include Roger Brent, USA; Bernard Dujon, France; James Galagan, USA; Vassily Hatzimanikatis, USA; Takashi Ito, Japan; Hiroaki Kitano, Japan; Edda Klipp, Germany; Jens Nielsen, Denmark; Bela Novak, Hungary; Stephen Oliver, UK; Bernhard Palsson, USA; Matthias Reuss, Germany; Han de Winde, The Netherlands; Jacky Snoep, South Africa
   
SUNDAY 18.6.
12.00 Registration starts
18.00 Get-together
19.30 Welcome (Merja Penttilä, VTT Technical Research Centre of Finland, Finland)
 

KEYNOTE LECTURES

19.45

Theoretical and practical systems biology
(Pertteli Varpela, Medicel Ltd and University of Helsinki, Finland)

20.25

New 'dimensions' in genome annotation
(Bernhard Palsson, Department of Bioengineering, UCSD, USA)

    
MONDAY 19.6.
Comparative Genomics & Genome-wide analyses
(Chairs: Stefan Hohmann, Sweden and Kalervo Hiltunen, Finland)
9.00

Yeasts illustrate the mechanisms of eukaryotic genome evolution
(Bernard Dujon, Institut Pasteur, Paris, France)

9.40

Integrative genomics of fungi
(James Galagan, The Broad Institute of MIT and Harvard, USA)

10.20

Genome-wide identification and analysis of biological systems in yeast
(Stephen Oliver, The University of Manchester, UK)

11.00 Coffee
11.25

Further exploration of the budding yeast transcriptome
(Takashi Ito, University of Tokyo, Japan)

12.05

Understanding the quantitative physiology of a eukaryotic cell fate decision system
(Roger Brent, The Molecular Sciences Institute, Berkeley, USA)

12.45 Lunch
    
Omics data & Cell Function
(Chairs: Markus Herrgård, USA and Peter Philippsen, Switzerland)
14.10

Evolutionary origin of novel short transcripts in S. cerevisiae
(Eugenio Mancera, European Molecular Biology Laboratory, Germany)

14.30

Conditional perturbations for GDP-mannose related genes in S. cerevisiae
(Risto Renkonen, Biomedicum, University of Helsinki, Finland)

14.50

Interactive Proteomics of Membrane Protein Assemblies
(Igor Stagljar, University of Toronto, Canada)

15.10

Vertical genomics: fast dynamic response of central metabolism and glycolytic genes to glucose availability in S. cerevisiae
(André Canelas, Delft University of Technology, The Netherlands)

15.30

Determination of the transcriptional networks controlling pseudohyphal growth in Saccharomyces cerevisiae and their comparison to related yeast species
(Anthony Borneman, The Australian Wine Research Institute, Australia)

15.50

The time-dependent response of S. cerevisiae to oxidative stress
(Vladimir Shulaev, Virginia Bioinformatics Institute, USA)

16.10 Coffee
16.30 Poster session I
18.30 Dinner
20.00

Workshops: New -omics approaches & bioinformatics
(Chairs: Igor Stalgljar, Canada and David Ussery, Denmark)

21.30 Sauna
     
TUESDAY 20.6.
Modelling: Theory & Practise
(Chairs: Matej Oresic, Finland and Masanori Arita, Japan)
9.00

Dynamic modeling of cAMP signal transduction in Saccharomyces cerevisiae
(Matthias Reuss, Institute of Biochemical Engineering, Germany)

9.40

Construction and analysis of kinetic models of Saccharomyces cerevisiae; applications to glycolysis, cell cycle and mixed populations studies
(Jacky Snoep, University of Stellenbosch, South Africa)

10.20

Metabolic control analysis of yeast central carbon metabolism under uncertainty
(Vassily Hatzimanikatis, Northwestern University, Evanston, USA)

11.00 Coffee
11.25

Dynamic modeling of yeast cell stress response
(Edda Klipp, Max Planck Institute for Molecular Genetics, Berlin, Germany)

12.05

Exit from mitosis in budding yeast: models and experiments
(Bela Novák, Hungarian Academy of Sciences, Hungary)

12.45 Lunch
 
Modelling & Cell Function
(Chairs: Uwe Sauer, Switzerland and Friedrich Srienc, USA)
14.10

Physiological response of Saccharomyces cerevisiae to change in oxygen provision
(Hannu Maaheimo, VTT Technical Research Centre of Finland, Finland)

14.30

Monitoring fast dynamic combined response metabolome and transcriptome of S. cerevisiae to a glucose pulse
(Made Kresnowati, Delft University of Technology, The Netherlands)

14.50

Automated flow cytometry for studying population dynamics
(Friedrich Srienc, BioTechnology Institute, University of Minnesota, USA)

15.10

Deciphering condition dependent metabolic regulation in Saccharomyces cerevisiae by 13C flux analysis
(Lars Blank, University of Dortmund, Germany)

15.30

Functional implications of changes in gene expression
(Jildau Bouwman, Vrije Universiteit, The Netherlands)

15.50

Comparative computational modelling reveals a novel logic of tor signalling in yeast
(Joerg Stelling, Institute of Molecular Systems Biology, ETH Zurich, Switzerland)

16.10 Coffee
16.30 Poster session II
18.30 Dinner
20.00

Workshop: Quantitative data acquisition & modelling
(Chairs: Pedro Mendes, USA and Douglas Kell, UK)

21.30 Sauna
      
WEDNESDAY 21.6.
Systems Biology Applications (Chairs: Lilia Alberghina, Italy and Hans Westerhoff, The Netherlands/UK)
8.30

Adaptation of Saccharomyces cerevisiae to a changing environment: a vertical genomics approach
(Han de Winde, Delft University of Technology, Delt, The Netherlands)

9.05

Application of system biology on brewer’s yeast
(Naoyuki Kobayashi, Sapporo Breweries Ltd, Japan)

9.45

Chemical combinations as multi-target therapeutics and biological probes
(Joseph Lehar, CombinatoRx Inc. and Boston University, USA)

10.20 Coffee
10.40

Reporter features: A tool for mapping of global control in metabolism through model driven analysis of ome data
(Jens Nielsen, Technical University of Denmark, Denmark)

11.20 Panel: Industrial expectations of systems biology
(Chairs: Hans van Dijken, The Netherlands and Pirkko Suominen, USA)
12.20 Lunch
   
Physiology & Metabolic Engineering
(Chairs: Sylvie Dequin, France and Laura Ruohonen, Finland)
13.20

Metabolic engineering of yeasts for production of bulk fermentation products from xylose: ethanol and lactic acid
(Pirkko Suominen, NatureWorks LLC, Minnetonka, USA)

13.40

L-ascorbic acid production from D-glucose in metabolic engineered Saccharomyces cerevisiae and its effect on strain robustness
(Paola Branduardi, University of Milano-Bicocca, Italy)

14.00

Metabolic engineering of S. cerevisiae for overproduction of succinic acid
(Jose Manuel Otero, Technical University of Denmark, Denmark)

14.20

Comparative 13C flux analysis of two Saccharomyces cerevisiae strains reveals substantial differences in the flux through the PP pathway
(Carole Camarasa, UMR-Sciences pour l’Enologie, INRA, France)

14.40

Zero growth product formation in Saccharomyces cerevisiae
(Leonie van Dijk, Delft University of Technology, The Netherlands)

15.00 KEYNOTE LECTURE :
Biological robustness

(Hiroaki Kitano, Sony Computer Science Laboratories Inc, Japan)
15.40 Concluding remarks
(Merja Penttilä, VTT Technical Research Centre of Finland, Finland)
16.00 Coffee
17.30 Boat trip and sightseeing at the forstress island Suomenlinna
19.00 Dinner at the Restaurant Walhalla at the forstress island Suomenlinna