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Focus Group on Computational Molecular Biology
Genetic Regulatory Mechanisms for Cell Growth and Division, Signal Transduction and
Circadian Rhythms
Convened by John J. Tyson and Béla Novák

Focus Group Participants

  • Béla Novák (convener), Biology - Budapest
  • John J. Tyson (convener), Biology - Blacksburg (USA)
  • Wolfgang Alt (visiting scholar), Biology - Germany
  • Dennis Bray (visiting scholar), Biology - England
  • Laurence Calzone (junior fellow), Biology - France
  • Kathy Chen (visiting scholar), Biology - USA
  • Andrea Ciliberto (junior fellow), Biology - Italy
  • Emery Conrad (junior fellow), Biology - USA
  • Attila Csikász-Nagy (junior fellow), Bio-engineering - Hungary
  • Albert Goldbeter (visiting scholar), Chemical Physics - Belgium
  • Béla Györffy (junior fellow), Bio-engineering - Hungary
  • Christian Hong (junior fellow), Biology - USA
  • Lee Segel (visiting scholar), Applied Mathematics - Israel
  • Jason Zwolak (junior fellow) Biology - USA

General Goal

The fundamental goal of post-genomic molecular biology is to understand the genetic basis of cell physiology. How do the complex networks of genes and proteins determine the behavior of living cells in their natural environments? New techniques provide the life sciences with massive quantities of data about DNA sequences, gene expression, protein profiles, etc. Besides the evident problems of curating and searching these databases, novel computational tools are needed to connect molecular mechanisms (networks of interacting proteins) to cell behavior. The goal of the focus group is to develop and employ modeling tools to understand some basic dynamical properties of eukaryotic cells: spatial and temporal control of cell growth and division, signal transduction pathways that regulate cell proliferation in response to internal and external milieus of the cell, and generation of an autonomous circadian clock that synchronizes cellular activities to the externally imposed 24-h rhythm of light and darkness.

Concrete research plans

The modelling efforts concentrate on following topics in molecular cell biology:

Temporal Patterns of Cell Growth and Division

  • Budding yeast cell cycle
  • Fission yeast cell cycle
  • Meiosis
  • Morphogenetic checkpoint
  • Septation and cell division
  • Early embryogenesis
  • Mammalian cell division

Spatial Patterns of Cell Growth and Division

  • Microtubule dynamics
  • Actin dynamics
  • Signal Transduction Pathways
  • Bacterial chemotaxis
  • Budding yeast signaling
  • Apoptosis

Output of the Focus Group

We have been invited by Stefan Hohmann, Editor of Topics in Current Genetics, to organize a special issue of the journal, on the topic of "Systems studied with theoretical an experimental approaches." We plan to use this invitation as an opportunity to produce a published record of the accomplishments of the Focus Group. Members of the focus group will prepare articles on the following subjects:

  • Cell cycle regulation
  • Patterns of cell growth
  • Circadian rhythms
  • Bacterial chemotaxis
  • Apoptosis
  • Growth factor signaling
  • Immune surveillance
  • Pattern formation in development
  • Motility
  • Evolution of regulatory systems

Mini-Workshops

A series of mini-workshops were organised to bring together leading experimental molecular biologists with the modelling team. To encourage dialog, the workshops were kept small, intimate, and highly focussed. Each one lasted 2-3 days, with three parts: (1) the experimentalists introduced the modelers to the latest facts and speculations about a control system, (2) the theoreticians introduced the experimentalists to the basic ideas behind modeling the control system, and (3) the two groups jointly developed plans for the immediate future of model development and experimental tests.

I Workshop 28 February - 2 March
Morphogenesis in fission yeast
Béla Novák (Budapest), John J. Tyson (Blacksburg, USA) Kathy Chen (USA), Laurence Calzone (France), Andrea Ciliberto (Italy) Jason Zwolak (USA), Attila Csikász-Nagy (Hungary), Béla Györffy (Hungary), Christian Hong (USA), Stefania Castagnetti (UK), Klaus Leonhard (UK), Rafael Carazo-Salas (UK), Mercedes Pardo (UK), Jacky Hayles (UK), Ákos Sveiczer (Hungary), Sir Paul Nurse (Cancer Research UK, 2001 Nobel-prize in Physiology or Medicine)

II Workshop 14-16 March
Cell cycle of budding yeast
Béla Novák (Budapest), John J. Tyson (Blacksburg, USA) Laurence Calzone (France), Kathy Chen (USA), Andrea Ciliberto (Italy) Jason Zwolak (USA), Attila Csikász-Nagy (Hungary), Béla Györffy (Hungary), Christian Hong (USA), Wolfgang Alt (Germany), Lee Segel (Israel)
Mike Mendenhall (University of Kentucky, USA), Frank Uhlmann (London), Wolfgang Zachariae (Dresden)

III Workshop 25-30 April
Apoptosis
Béla Novák (Budapest), John J. Tyson (Blacksburg, USA) Laurence Calzone (France), Dennis Bray (England), Andrea Ciliberto (Italy) Jason Zwolak (USA), Attila Csikász-Nagy (Hungary), Béla Györffy (Hungary), Christian Hong (USA), Yuri Lazebnik (Cold Spring Harbor Laboratory, NY, USA)

IV Workshop 5-6 June
Filamentous fungi
Béla Novák (Budapest), John J. Tyson (Blacksburg, USA) Laurence Calzone (France), Andrea Ciliberto (Italy) Jason Zwolak (USA), Attila Csikász-Nagy (Hungary), Béla Györffy (Hungary), Christian Hong (USA), Albert Goldbeter (Belgium), Emery Conrad (USA), Peter Philippsen (Switzerland)

 

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