Programme: Sunday 20 April 2008
| 09:30 | Registration and refreshments |
| 10:45 | Conference Opening and Keynote Session I Chair: James Brown, University of Cambridge, UK |
| 10:45 | Welcome Richard Kitney, Imperial College London, UK |
| 11:00 | Keynote Address 1 - Title to be confirmed Tom Knight, Computer Science and Artificial Intelligence Lab, MIT |
| 12:00 | Keynote Address 2 -
From Molecular Machines to Gene-Regulatory Networks in Mammalian Cells Thomas Höfer, German Cancer Research Center, Heidelberg, Germany |
| 13:00 | Lunch |
| Session 1 - Synthetic Biology Chair: Jim Haseloff, University of Cambridge, UK |
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| 14:00 | (1.1) Title to be advised J Haseloff, University of Cambridge, UK |
| 14:20 | (1.2) Rational Design of a Set of Versatile Synthetic Biological Modules |
| 14:45 |
(1.3) GenoCAD: A Formal Language Tool to Quickly Design and Verify Synthetic Genetic Constructs Y Cai, J Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA, C Gustafsson, DNA2.0, Inc., USA |
| 15:10 | (1.4) Automatic Design Tools for Synthetic Biology G Rodrigo, J Carrera, IBMCP-UPV Spain, M Suarez, A Jaramillo, École Polytechnique, France |
| 15:35 | (1.5) In Vitro Synthetic Oscillators J Kim, CbsBioscience Inc., Republic of Korea, E Winfree, California Institute of Technology, USA |
| 16:00 | Refreshments |
| 16:30 | Session 2 - Bioinformatics & Computational Biology I Chair: Jean Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA |
| 16:30 |
(2.1) From Registries of Biological Parts to IDE of Genetic Systems J Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA |
| 17:15 | (2.2) A Spatio-Temporal Algorithm for Resolving Time-Lapse Imaging of Bacteria A Demarez, M Primet, F Taddei, A B Lindner, L Moisan, Paris Descartes University, France |
| 17:40 | (2.3) Transcription Factor Heterogeneity in Single Human Embryonic Stem Cells M Hemberg, Children's Hospital Boston, USA, A Stahlberg, H Semb, Lund University, Sweden, M Bengtsson, Oxford University, UK, M Barahona, Imperial College London, UK |
| 18:05 | (2.4) Modelling the Endothelial Cell Response to Fluid Flow R J Allen, I D L Bogle, University College London, UK, A J Ridley, King's College London, UK |
| 18:30 | Sponsors’ Reception and Poster Session |
| Poster series 1 - Synthetic Biology | |
| P1.01 - Riboswitch Development: Design of in Vivo Circuits N Kelley-Loughnane, S Harbaugh, Y Chushak, M O Stone, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force, USA |
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| P1.02 - The E. coli Integrated Network and the Self Contained Regulatory Loops H Ma, I Goryanin, University of Edinburgh, UK | |
| P1.03 - Data Integration to Constrain Computational Modelling in Synthetic Biology J S Hallinan, M Pocock, A Wipat, Newcastle University, UK | |
| P1.04 - Self-Assembly of Protein Amyloid C F Lee, Oxford University, UK | |
| P1.05 - An RNAi-Enhanced Logic Circuit: Cancer-Specific Detection and Destruction A Swaminathan, J Monk, P Cowgill, R Weiss, P Purnick, P Guye, Princeton University, USA | |
| P1.06 - YeSOil A Yeast Sensor for Real Extra Virgin Olive Oil R Bergamasco, M Graziano, M A Ricci, G Russo, L Marucci, M di Bernardo, University of Naples Federico II, Italy, I Cantone, G Cuccato, V Siciliano, M P Cosma, D di Bernardo, TIGEM Telethon Institute of Genetics and Medicine, Italy | |
| P1.07 - Computational Design of Synthetic Molecular Clocks with Targeted Cell Growth G Rodrigo, J Carrera, Instituto de Biologia Molecular y Celular de Plantas, CSIC-UPV, Spain, B Canton, D Endy, MIT, USA, A Jaramillo, École Polytechnique, France | |
| P1.08 - Biological Implementation of Algorithms A Becerra, F Castro, L Martinez, Y Robles, F Ramirez, P Padilla, E Samra, University of Mexico (UNAM), Mexico, R Palma, Mexican Institute of Technology (IPN), Mexico | |
| P1.09 - Variety of Dynamics Regimes in Synthetic Genetic Oscillators A Koseska, J Kurths, Potsdam University, Germany, A Zaikin, University of Essex, UK, J Garcia-Ojalvo, Universitat Politecnica e Catalunya, Spain, E Volkov, Lebedev Physical Institute, Russia | |
| Poster series 2 - Bioinformatics & Computational Biology | |
| P2.01 - Molecular and Comparative Modelling and Docking Analysis of CDC4 Proteinin Homo sapiens A Khanzode, PT. Ravishankar Shukla University, India | |
| P2.02 - Identifying the Features of co-translational Protein Folding R J K Saunders, C M Deane, University of Oxford, UK |
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| P2.03 - Use of Virtual Environments and Selection of Measurement Parameters for the Application in the Phobia Treatment M Plaza, Universidad Libre, Colombia | |
| P2.04 - ConFunc - Functional Annotation in the Twilight Zone M N Wass, M J E Sternberg, Imperial College London, UK |
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| P2.05 - Development of an Extensible System for the Capture and Storage of Experimental Enzyme Kinetics Data N Swainston, K Smallbone, F Khan, H L Messiha, I Spasic, D B Kell, University of Manchester, UK, M Golebiewski, S Mir, I Rojas, EML Research, Germany | |
| P2.06 - Morphogenesis in Cellular Automata Models of Non-Linear Media G Juarez Martinez, P Padilla Longoria, University of the West of England, UK | |
| P2.07 - Hierarchy, Abstraction Levels and Emergent Behaviours in Agent-based Simulations of Complex Biological Systems C C Chen, University College London, UK | |
| P2.08 - NetBuilder’ - Evolving Genetic Regulatory Networks K Wegner, J F Knabe, C L Nehaniv, M J Schilstra, University of Hertfordshire, UK | |
| P2.09 - Software Development in Modelling and Virtual Exploration of Proteins: an Alternative of IT in Central America A Orozco, UNA, Costa Rica | |
| P2.10 - Predicting the Function of the Protein-Tristetraproline N Pillai, A Kumar, Deemed, India | |
| P2.11 - A Process Model of Actin Polymerisation O Kahramanogullari, E Caron, P Gardner, Imperial College London, UK, L Cardelli, Microsoft Research, UK | |
| P2.12 - Protein Network Alignment for Functional and Structural Annotation W Ali, C Deane, Oxford University, UK | |
| P2.13 - Improving Loop Prediction by Improving Loop Selection Y J Choi, C Deane, Oxford University, UK | |
| P2.14 - Environment-Specific Substitution Tables for Membrane Proteins S Kelm, C M Deane, University of Oxford, UK, J Shi, UCB Celltech Ltd, UK | |
| P2.15 - Quantitative PCR Primer Database for Terpene Synthesizing Genes in Selected Aromatic Plants M Pattanayak, S K Gupta, F N Jaffery, Industrial Toxicology Research Centre, India | |
| P2.16 - Error Tolerance of Gene Networks and their Robustness to Different Timescales S Yeniterzi, C Atilgan, A R Atilgan, Sabanci University, Turkey | |
| P2.17 - The Determination of the Basis of HLA Class I Associated Protection in HTLV-I Infection A MacNamara, B Asquith, C Bangham, Imperial College London, UK | |
| P2.18 - HIV-1 Escape from Cytotoxic T-Lymphocytes in Gag, but not in Other Genes, is Detrimental to the Host U Kadolsky, B Asquith, Imperial College London, UK | |
| P2.19 - A General Model for Inferring Boolean Networks from Sparse Gene Expression Data L Yu, S Marshall, University of Strathclyde, UK, P Ghazal, S Watterson, University of Edinburgh, UK | |
| P2.20 - Statistical Analysis of Time Series of Gene Expression Response to Mycobacterium tuberculosis Infection M Berk, G Montana, Imperial College London, UK | |
| P2.21 - Evolution of the G+C Content Frontier in the Rat Cytomegalovirus Genome, and its Effect on Gene Length D Gatherer, MRC Virology Unit, UK | |
| P2.22 - A New Approach to Calculate the Measure of Similarity of 3D Structures in Proteins R Yeniterzi, S Yeniterzi, A Kucukural, U Sezerman, Sabanci University, Turkey | |
| P2.23 - GeneTrail - Statistical Evaluation and Visualization of Biological Pathways C B Backes, A C K Keller, J K Küntzer, H P L Lenhof, Saarland University Germany, A G Gerasch, M K Kaufmann, Eberhard Karls University, Germany | |
| P2.24
- Predicting and Understanding Gene Interaction Networks based on Sequence Information
F Schubert, V Pancaldi, J Bahler, Wellcome Trust Sanger Institute, UK |
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| P2.25
- Prediction of Glycosylation Sites using Random Forests
S E Hamby, J D Hirst, University of Nottingham, UK |
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| P2.26
- Selection of Algal Strain by Sequence Analysis for Biodiesel
N Pillai, A Kumar, Deemed, India |
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| P2.27
- Placental Malaria in Different HLA Alleles
P B Karau, University of Nairobi, Kenya |
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| P2.28
- Making Sense of Microarray Gene Lists using Text Mining and Over-Representation Analysis
H S Leong, P Giles, S Menon, D Kipling, Cardiff University, UK |
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| P2.29
- Spatial Knowledge Retrieval and Discovery in Chromosomes
A Martin Pittock, University of Edinburgh, UK |
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| P2.30
- Semi Supervised Spectral Clustering for Regulatory Module Discovery
A Mishra, D Gillies, Imperial College London, UK |
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| P2.31
- Biomarker Discovery using Genetic Algorithms
A Küçükural, D Yörükoğlu, U Sezerman, Sabanci University, Turkey |
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| P2.32
- Synthetic Cis-Regulatory Bio-Logic Gates in Escherichia Coli
Z Jian, Z Yun, H Y Liu, University of Science and Technology of China, China |
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| P2.33
- Using Annotation for the Integration and Interpretation of Microarray Data
S Menon, P Giles, I Brewis, H S Leong, D Kipling, Cardiff University, UK |
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| Poster series 3 - iGEM | |
| P3.01 - Promoter Calibrator: One Possible Application for a Biological Comparator P Aparicio, O Cuenca, J Garzon, R Soriano, A Ferrando, J Pereto, Universidad de Valencia, Spain, D Das, S K Maiti, A Montagud, H Mosquera, M Baguena, E Navarro, P Fernandez-de-Cordoba, J Urchueguia, Universidad Politécnica de Valencia, Spain, A Jaramillo, École Polytechnique, France | |
| P3.02 - ElectrEcoBlu: A Novel Self-Powering Electrochemical Biosensor X Gu, S Ramsay, D Gilbert, University of Glasgow, UK | |
| P3.03 - University of Edinburgh iGEM 2007 Projects: A Cell Division Detector, and Self-Flavouring Yoghurt C Dahl, L Gerosa, S Hollingshead, A Marshall, P Ravindranath, J Rokicki, X Wang, D Yin, A Elfick, C French, H Ma, University of Edinburgh, UK | |
| Poster series 4 - Systems Biology | |
| P4.01 - Comparative Study of Mathematical Models for Gene Regulatory Networks A Polynikis, M di Bernardo, S J Hogan, University of Bristol, UK | |
| P4.02 - Systematically Identifying the Key Controllers of Growth Rate in a Eukaryotic Cell K Gkargkas, S G Oliver, University of Cambridge, UK | |
| P4.03 - Cold Glycerol-Saline: The Promising Quenching Solution for Accurate Intracellular Metabolite Analysis of Microbial Cells S G Villas-Boas, P Bruheim, University of Auckland, New Zealand | |
| P4.04 - Dynamic Transcription Modelling Identifies Gene Networks using Time Course Expression Data and Transcript Turnover Rates M Barenco, E Papouli, M Hubank, University College London, UK, D Brewer, Institute of Cancer Research, UK, J Stark, Imperial College London, UK | |
| P4.05 - Evolution of Evolvability in Gene Regulation Networks A B M Crombach, P Hogeweg, Utrecht University, Netherlands | |
| P4.06 - Glycomic Analysis of O-Gycosylation in Knockout Mice M N Ismail, M Panico, S Haslam, A Dell, Imperial College London, UK | |
| P4.07 - Gene Regulatory Network Inference in the Fission Yeast Schizosaccharomyces Pombe S D Kane, F Schubert, L Maury, Wellcome Trust Sanger Institute, UK | |
| P4.08 - Reconstraction of Saccharomyces Cerevisiae and Schizosaccharomyces Pombe Metabolic Pathways Base on Enzyme Nomenclature Database K-Y Lo, A Dalby, University of Oxford, UK | |
| P4.09 - Model Discrimination and Robustness for Cyanobacterial Circadian Oscillators M Hafner, H Koeppl, École Polytechnique Fédérale de Lausanne, Switzerland, A Wagner, University of Zurich, Switzerland | |
| P4.10 - Bottlenecks in Escherichia Coli-based Glyoxylate Production Revealed by 13C-Flux Analysis S Noack, M Kunze, K Nöh, Research Centre Jülich, Institute of Biotechnology, Germany | |
| P4.11 - Robust Stability of Metabolic Networks H Koeppl, M Hafner, École Polytechnique Federale de Lausanne (EPFL), Switzerland, A Wagner, University of Zurich, Switzerland | |
| P4.12 - Modelling the IP3 / Calcineurin / NFAT Pathway in the Cardiac Myocyte M T Cooling, P J Hunter, E J Crampin, University of Auckland, New Zealand | |
| P4.13 - Understanding Chemotaxis in R. Sphaeroides M A J Roberts, E August, J P Armitage, P McSharry, P K Maini, A Papachristodoulou, University of Oxford, UK | |
| P4.14 - Diffusion Simulation of Protein Molecules through the Cytoplasm of Escherichia Coli Y D Yu, Y J Choi, A Dalby, University of Oxford, UK | |
| P4.15 - Modelling of Methylglyoxal Detoxification in Bacteria C Almeida, E Ozyamak, I R Booth, C Grebogi, A Moura, University of Aberdeen, UK | |
| P4.16 - Bridging the Gap between Constraint-based and Kinetic Modelling K Smallbone, E Simeonidis, D S Broomhead, D B Kell, Manchester Centre for Integrative Systems Biology, UK | |
| P4.17 - From QconCAT to Molecules per Cell: Accurate Quantification of Absolute Enzyme Concentrations in Yeast by Mass Spectrometry K M Carroll, D Simpson, C E Eyers, C Knight, S J Gaskellm, R J Beynon, D B Kell, University of Manchester, UK | |
| P4.18 - Stochastic Parameter Estimation using Minimum Entropy: Application to the RKIP Regulated ERK Signalling Pathway G Papadopoulos, M Brown, University of Manchester, UK | |
| P4.19 - Information-Theoretic Analysis for Exploring Death-Survival Signalling in Glioblastoma Y C Tang, Singapore-MIT Alliance, Singapore, G Stephanopoulos, Massachusetts Institute of Technology, USA, H-P Too, National University of Singapore, Singapore | |
| P4.20 - Global Sensitivity Methods for Identifiability Analysis and Model Reformulation in Systems Biology M Rodriguez-Fernandez, J R Banga, IIM-CSIC, Spain, A Kremling, Max-Planck-Institute for Complex Technical Systems, Germany | |
| P4.21 - Inference and Modelling of Regulatory Networks from Transcriptomic Data J Carrera, G Rodrigo, Instituto de Biologia Molecular y Celular de Plantas, CSIC-UPV, Spain, A Jaramillo, École Polytechnique, France | |
| P4.22 - An Accelerated Algorithm for the 3D Poisson-Nernst-Planck Calculations of Ion Fux through Membrane Channels W W Dyrka, M Kotulska, Wroclaw University of Technology, Poland, A T Augousti, Kingston University, UK |
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| P4.23 - Parameter Estimation for Gene and Protein Interaction Networks R K Shelton, W T Baumann, Virginia Polytechnic Institute and State University, USA, J Peccoud, Virginia Bioinformatics Institute at Virginia Tech, USA | |
| P4.24 - Biochemical Reaction Kinetic Parameters Identification by means of Evolutionary Algorithms: Application to EGFR Pathway F Menolascina, G Bevilacqua, D Naso, G Mastronardi, Polytechnic of Bari, Italy |
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| P4.25 - Integrated Statistical and Optimization Analysis of Nonlinear Systems with Noisy and Sparse Data, an Application to Biochemical Pathways X Gu, M Barrett, D Gilbert, University of Glasgow, UK |
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