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Biosysbio Full Programme

Biosysbio Full Programme

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Published by A Roy

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Published by: A Roy on Apr 10, 2008
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09/27/2012

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 Sunday, 20 April 200809:30 Registration and Refreshments10:45 13:00 Conference Opening and Keynote Session 1
Chair: James Brown
, University of Cambridge, UK 
 
10:45 Welcome
Richard Kitney,
Imperial College London, UK 
 11:00 Keynote Address 1Title – To be advised
Tom Knight,
Computer Science and Artificial Intelligence Lab, MIT, USA
12:00 Keynote Address 2From Molecular Machines to Gene-Regulatory Networks in Mammalian Cells
Thomas Höfer,
German Cancer Research Center, Heidelberg, Germany 
 
13:00 Lunch14:00 16:00 Session 1 - Synthetic Biology
Chair: Jim Haseloff,
University of Cambridge, UK 
 
14:00 1.1Title – To be advised
J Haseloff,
University of Cambridge, UK 
 14:20 1.2Rational Design of a Set of Versatile Synthetic Biological Modules
B Wang, V Rouilly, R Kitney,
Imperial College London, UK 
, C L Poh,
Nanyang Technological University, Singapore
 A set of modular synthetic biological parts and devices, including NOT, AND, NANDgates, Amplifier etc., are rationally designed by making use of the Hrp regulatorynetwork of Pseudomonas syringae type III secretion system.
14:45 1.3GenoCAD: A Formal Language Tool to Quickly Design and Verify SyntheticGenetic Constructs
Y Cai, J Peccoud,
Virginia Bioinformatics Institute at Virginia Tech, USA
, CGustafsson,
DNA2.0, Inc., USA
 Genomic Computer Assisted Designer (GenoCAD) is a formal language based toolfor design and verification of synthetic genetic constructs. Please visitwww.genocad.org for more information.
15:10 1.4Automatic Design Tools for Synthetic Biology
G Rodrigo,
 
J Carrera,
IBMCP-UPV,
 
Spain,
M Suarez,
 
A Jaramillo,
ÉcolePolytechnique,
 
France
We describe our set of computational tools to design biological parts and deviceswith targeted behaviour. We also show the experimental validation of several of our 
 
designs.
15:35 1.5In Vitro Synthetic Oscillators
J Kim,
CbsBioscience Inc.,
 
Republic of Korea,
E Winfree,
California Institute of Technology,
 
USA
We constructed and characterized three kinds of artificial transcriptional oscillatorscomprising synthetic DNA switches regulated by RNA signals and only twoenzymes.
16:00 Refreshments16:30 18:30 Session 2 - Bioinformatics & Computational Biology I
Chair: Jean Peccoud,
Virginia Bioinformatics Institute at Virginia Tech, USA
 
16:30 2.1From Registries of Biological Parts to IDE of Genetic Systems
J Peccoud,
Virginia Bioinformatics Institute at Virginia Tech, USA
 
17:15 2.2A 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
To reduce costly human post-processing in the image analysis of bacterial micro-colony movies, we propose an automatic algorithm, based on cell shape priors andmotion likelihood, that solves segmentation and tracking issues simultaneously.
17:40 2.3Transcription 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 
We present a simple stochastic model which describes the distribution of mRNA of six core transcriptional regulators in single human embryonic stem cells.
18:05 2.4Modelling the Endothelial Cell Response to Fluid Flow
R J Allen, I D L Bogle,
University College London,
 
UK,
A J Ridley,
King's CollegeLondon,
 
UK 
The abstract describes my research in simulating how endothelial cells change their shape in response to a mechanical signal.
18:30 20:00 Sponsors’ Reception and Poster Session1 - Synthetic BiologyP1.01Riboswitch 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
Bacterial cells expressing the riboswitch containing a theophylline aptamer domainupstream of TEV protease and FRET fusion protein showed a marked opticaldifference and in silico studies revealed mutant riboswitches that permit novel ligand
 
binding.
P1.02The E. coli Integrated Network and the Self Contained Regulatory Loops
H Ma, I Goryanin,
University of Edinburgh,
 
UK 
We reconstructed an integrated network of E. coli which includes different types of cellular interactions. Based on it, we introduced the concept of self contained loopand studied the dynamic behaviour of such loops.
P1.03Data Integration to Constrain Computational Modelling in Synthetic Biology
J S Hallinan, M Pocock, A Wipat,
Newcastle University,
 
UK 
This paper describes describes ongoing work using data integration andevolutionary computation for designing and modelling genetic circuits. The aim is toproduce designs which are biologically plausible enough to be useful in syntheticbiology.
P1.04Self-Assembly of Protein Amyloid
C F Lee,
Oxford University,
 
UK 
This work studies the thermodynamical properties of protein amyloid self-assemblyand the mechanical properties of amyloid fibrils.
P1.05An RNAi-Enhanced Logic Circuit: Cancer-Specific Detection and Destruction
A Swaminathan, J Monk, P Cowgill, R Weiss, P Purnick, P Guye,
PrincetonUniversity,
 
USA
We developed an RNAi based logic circuit that detects cancer by evaluating internalcell state through mRNA expression patterns. The circuit controls translation of apro-apoptotic factor, allowing targeted destruction specific to cancer cells.
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 PCosma, D di Bernardo,
TIGEM Telethon Institute of Genetics and Medicine,
 
Italy 
The goal of our project is to transform Saccharomices cerevisie in a BiologicalSensor able to distinguish between Extra Virgin Olive Oil and not Edible Olive Oilconstructing a synthetic network.
P1.07Computational Design of Synthetic Molecular Clocks with Targeted CellGrowth
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
We have designed synthetic molecular clocks following a computational evolution of circuits. In addition, we analyse the in vivo response of the chassis when hostingour synthetic constructs in plasmids
P1.08Biological 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 

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