Frontiers of Multidisciplinary Research: Mathematics, Engineering and Biology 21 – 24 SEPTEMBER 2010 | REED HALL, UNIVERSITY OF EXETER Sponsors Front cover image reproduced with the kind permission of Eckhard Völcker. Welcome... to this unique meeting that aims to facilitate Finally, Frontiers aims to motivate and attract young interaction and scientific exchange among talent to interdisciplinary research. Some of the mathematicians, physicists, engineers and invited and most of the selected speakers are early- biologists. The Frontiers workshop aspires career academics, and we believe that they are to be unique for several reasons. indeed at the frontiers of interdisciplinary research. To foster such research in the coming generation of Firstly, it aims to achieve an unprecedented academics we will record all presentations (subject scientific breadth whilst maintaining focus and to speaker consent) and make them publicly coherence. This is not an easy goal but we aim available on the internet for the use of the wider to realise it by selecting a large number of invited scientific community. speakers who are leading scientists in their specific fields, yet maintain a broad view of science in Meetings are about people; no organisational other fields and the connections of their work aspiration can be met in a meeting without the to those fields. right mix of participants. This fact is particularly true for Frontiers given its scientific breadth. We believe Secondly, Frontiers aims to place “interaction” first that with you, we have indeed gathered the right and foremost. To achieve this we tried hard to mix of people. provide a relaxed scientific platform with ample free time for both free and structured discussions. We look forward to seeing you at the next Half of the attendees will present a talk and posters Frontiers meeting. will be at the centre stage of the meeting, being on display in the break out area at all times. The Orkun S Soyer, full daily program is set in an idyllic mansion in the on behalf of the organising committee campus of University of Exeter, with planned after- September 2010, University of Exeter lunch walks that will allow for stretching the legs and mind. FRONTIERS 1 Organisers and Sponsors Orkun S Soyer Ruth Baker University of Exeter University of Oxford Steven Porter Nicolas Buchler Özgür Akman University of Exeter Duke University University of Exeter EPSRC Engineering and Physical Sciences Research Council University SIGNET of Exeter Microsoft Company of The Cell Signaling Science Strategy Research Biologists Network Systems Biology Theme In addition to our official sponsors, we would like to thank all academic members of University of Exeter systems biology managerial board, Professor Nick Talbot and Professor David Butler. We would also like to acknowledge the support of the Research & Knowledge Transfer Office, and especially thank Maggie Smith, Andrew Richards and Pete Hodges. 2 Programme * Indicates Invited Speaker Tuesday, 21 September 12.00 -13.50 Registration 13.50 -14.00 Conference Open and Welcome Professor Nick Talbot, Deputy Vice Chancellor for Research & Knowledge Transfer, University of Exeter 14.00 - 14.30 Pristionchus Pacificus – A Nematode Model for Integrative Studies in Evolution and Ecology, *Ralf Sommer, Max Planck Institute for Developmental Biology, Germany 14.35 - 15.05 Parasite Driven Redundancy in Signaling Networks, Orkun Soyer, University of Exeter 15.10 - 15.40 Complex Light Response in a One-Loop Model of the Ostreococcus Tauri Circadian Clock, Carl Troein, University of Edinburgh 15.40 - 16.10 Coffee Break 16.10 - 16.40 The Origins of Evolutionary Innovations, *Andreas Wagner, University of Zurich 16.45 - 17.15 Two-Domain DNA Strand Displacement, *Luca Cardelli, Microsoft Research 17.15 – 18.30 Posters session and free discussion with drinks reception Wednesday, 22 September 09.00 - 09.30 Modelling and Analysis Tools for Biochemical Networks, Antonis Papachristodoulou, Oxford University 09.35 - 10.05 Phenotypes in the Design Space of Biochemical Systems, *Michael Savageau, UC Davis 10.05 - 10.35 Coffee Break 3 10.35 - 11.05 Multidimensional Optimality of Microbial Metabolism, *Uwe Sauer, ETH Zurich 11.10 - 11.30 Uncovering the Design Principles of Polyamine Regulation in Yeast: An Integrated Modelling and Experimental Study, Svetlana Amirova, University of Exeter 11.35 - 12.05 A Synthetic Biology Approach to Recombinase Mediated Metabolic Pathway Engineering, *Susan Rosser, University of Glasgow 12.10 - 12.30 Surpassing Evolution: Using Synthetic Biology to Rewire and Repurpose Biological Systems, Travis Bayer, Imperial College London 12.30 - 13.30 Lunch 13.30 - 14.00 After lunch walk 14.00 - 14.30 Stochastic and Controlled Accumulation of Dynein at Microtubule Ends Prevents Endosomes from Falling off the Track, Gero Steinberg, University of Exeter 14.35 - 15.05 A Dynamic Spindle-Like Apparatus that Segregates Low Copy Number Plasmids, *Martin Howard, John Innes Centre 15.05 - 15.35 Coffee Break 15.35 - 16.05 Combinatorial Stress Responses in Yeast, Ken Haynes, University of Exeter. 16.10 - 16.40 The Gene Circuits of Plant Clocks, and the Infrastructure for Systems Biology, *Andrew Millar, University of Edinburgh 16.40 - 17.30 Discussion 1: Modelling in Light of Current Experimental Developments 17.30 - 18.30 Posters session and free discussion with drinks reception Thursday, 23 September 09.00 - 09.30 The Propagation of Perturbations in Rewired Gene Networks, *Mark Isalan, Centre for Genomic Regulation (CRG), Barcelona, Spain 09.35 - 10.05 Cell-to-Cell Variability in the E. Coli TorS/TorR Signaling System, *Mark Goulian, University of Pennsylvania 4 10.05 - 10.35 Coffee Break 10.35 - 11.05 Measuring Dynamics, Noise and Heterogeneity in Genes and Networks, *David Rand, University of Warwick 11.10 - 11.30 An Integrated Framework for Inference, Identifiability, Sensitivity and Robustess in Stochastic Models of Biochemical Reactions, Michal Komorowski, Imperial College London 11.35 - 12.05 Looking After the Neighbourhood: Noise Abatement and Genome Evolution, *Laurence Hurst, University of Bath 12.10 - 12.30 Transcriptional Noise Reduction and the Evolution of Negative Auto-Regulation, Max Reuter, University College London 12.30 - 13.30 Lunch 13.30 - 14.00 After lunch walk 14.00 - 14.30 Ultrasensitivity and Cellular Decision-Making, *Peter Swain, University of Edinburgh 14.35 - 15.05 Decision Making in Bacterial Chemotaxis, *Judy Armitage, Oxford University 15.05 - 15.35 Cream Tea Break 15.35 - 15.55 Robust Signal Processing in Living Cells, Ralf Steuer, Berlin 16.00 - 16.20 Chaste: A Computational Framework for Multiscale Modelling in Systems Biology, Alexander Fletcher, Oxford University 16.25 - 16.55 ... The Rest are Details: Model Selection in Systems and Evolutionary Biology, *Michael Stumpf, Imperial College London 16.55 - 17.30 Discussion 2: Experiment in Light of Current Theoretical Developments 17.30 Day session closes 17.30 Bar opens – Reed Hall. 19.00 Pre-dinner drinks – Reed Hall 19.30 Gala Dinner – Woodbridge Suite, Reed Hall 5 Friday, 24 September 09.00 - 09.30 The Statistical Physics of Decision-Making in Insect Colonies, Patrick Hogan, University of Bristol 09.35 - 10.05 Social Evolution in Microbes, *Kevin Foster, Harvard University 10.05 - 10.35 Coffee Break 10.35 - 11.05 Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence, Sam Brown, Oxford University 11.10 - 11.30 Microbial Evolution in Theory and Practice, Ivana Gudelj, Imperial College London 11.35 - 12.05 The Evolutionary Systems Biology of HIV-1 Drug Resistance, *Sebastian Bonhoeffer, ETH Zurich. 12.15 - 13.00 Final thanks and conference closes 6 Posters 1. Evolutionary Signatures of Mutagenic Processes Co-authors: Leslie Aichaoui ¹, Lieke van Associated with Transcription, Peter Arndt, Gijtenbeek ², Maria de Vries ², Vincent Max Planck Institute for Molecular Genetics, Fromion ¹, Jan Maarten van Dijl ², Germany (¹ Laboratoire de Genetique Microbienne, France; ² University Medical Center Groningen Co-authors: Paz Polak, Max Planck Institute for and University of Groningen, Netherlands) Molecular Genetics, Germany 5. Inferring Hidden Transcription Factor Profiles 2. Inferring Partially-Known Scale-Free Interaction by Thermodynamic Modelling of GFP-derived Networks from Noisy Data, Carlo Cosentino, Promoter Activities, Luca Gerosa, ETH Zurich University of Catanzaro, Italy Co-authors: Bart Haverkorn van Rijsewijk ¹, Co-authors: Francesco Montefusco ¹ ², Karl Kochanowski ¹, Matthias Heinemann ¹, Jongrae Kim ³, Declan G. Bates ², Francesco Uwe Sauer ¹, (¹ Institute of Molecular Systems Amato ¹ (¹ University of Catanzaro, Italy; Biology, ETH Zurich, Switzerland) ² University of Exeter, UK; ³ University of Glasgow, UK) 6. The Mathematical Structures of the Brain. Category Theory in Neural Science, Manuel G 3. A Kinetic Model for Predicting MHC Class Bedia, University of Zaragoza, Spain I Presentation of Competing Peptides, Neil Dalchau, Microsoft Research, UK Co-authors: Ricardo Sanz ¹, Jaime Gonzalez- Ramirez ¹ (¹ Technical University Madrid, Co-authors: Andrew Phillips ¹, Leonard D Spain) Goldstein ², Mark Howarth ³, Luca Cardelli ¹, Tim Elliott 4, Joern M Werner 4 (¹ Microsoft Research, UK; ² University of Cambridge, UK; 7. On Types and Roles of Interdisciplinarity within 4 ³ University of Oxford, UK; University of Systems Biology Research, Karen Kastenhofer, Southampton, UK) Austrian Academy of Sciences 4. Modelling the Oxidative Stress Response