July 19-20, 2007 - Vienna, Austria
Hall F1, Austria Vienna Center
A satellite of ISMB'07 (www.iscb.org/ismbeccb2007/)
The 8th BioPathways meeting is organized by the BioPathways Consortium (www.biopathways.org ), an open forum aimed at fostering computational approaches to the modeling, reconstruction, analysis and simulation of biological networks. Previous BioPathways meeting have focused on a variety of themes, such as computational reconstruction of molecular networks, pathway evolution, integration of models and experiments, models and ontologies for pathways, metabolic pathways on modeling of interactions and regulation on a systems scale. Our special focus this year will be on computational methods for Synthetic Biology. Synthetic Biology addresses the design and fabrication of biological components and systems that do not exist in the natural world as well as the re-design and fabrication of already existing biological systems. Whereas many of the computational methods developed in order to model and analyze natural systems are relevant to the modeling of synthetic living systems, there is also an acute need for new computational methods in order to support the rational design goals and the abstraction/modularity/assembly approach of synthetic biology.
The meeting will include 3 other plenary sessions, touching on the full spectrum of pathways and networks-related themes.
Day I –
July 19 th
7:30 – 8:45 |
Registration |
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9:00-9:10 |
Vincent Schachter |
Opening remarks |
Session 1: Computational
Methods and Infrastructure for Synthetic Biology |
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9:10-09:30 |
Vitor Martins dos Santos, Helmholtz Center for Infection Research, Braunschweig |
EMERGENCE: a Foundation for Synthetic Biology in Europe |
9:30-10:00 |
Alfonso Valencia, CNIO, Madrid |
Bioinformatics tools to help in the design of biological systems |
10:00-10:30 |
Jörg Stelling, ETH, Zürich |
Formal tools for Model-Based Synthetic Biology |
10:30-11:00 |
Coffee Break |
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11:00-11:30 |
Randy Rettberg, MIT, Cambridge |
The MIT registry of parts and devices |
11:30-12:00 |
Alfonso Jaramillo, Ecole Polytechnique, Paris |
Model-based design of genetic circuitry |
12:00-13:00 |
Lunch |
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Session 2: Network Reconstruction & Analysis (part
1) |
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13:00-13:45 |
Florence d’Alche-Buc, University of Evry |
Supervised Inference of Protein-Protein Interaction Networks |
13:45-14:30 |
Jason Ernst, Carnegie Mellon University |
Reconstructing Dynamic Regulatory Maps |
14:30-14:50 |
Tijana Milenkovic and Natasa Przulj, Irvine, University of California |
Uncovering Biological Network Function via Graphlet Degree Signatures |
14:50-15:10 |
Kam Dahlquist, Loyola Marymount University |
Mathematical Modeling of the Transcriptional Network Controlling the Environmental Stress Response in Saccharomyces cerevisiae |
Session 3: Databases & Software
Tools |
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15:10-15:30 |
Ozgun Babur, Bilkent University |
PATIKAweb Components for Microarray Data Analysis & Advanced Graph-Theoretic Querying |
15:30-16:00 |
Coffee Break |
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16:00-16:20 |
Richard Adams, University of Edinburgh |
The Edinburgh Pathway Editor |
16:20-16:40 |
Esther Schmidt, EBI, Cambridge |
Reactome - a knowledgebase of biological pathways |
16:40-17:20 |
Eric Neumann, Teranode Corp. |
A Genome - Phenome Integrated Approach for Mining Disease-Causal Genes using Semantic Web |
Round Table Discussion |
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17:20-18:30 |
IT Infrastructure & Computational Methods for Systems and Synthetic Biology |
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Day II – July 20th
Session 4 : Network Reconstruction &
Analysis (part 2) |
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9:00-9:45 |
Peter Karp, SRI International |
Gene Regulation in EcoCyc and Pathway Tools |
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9:45-10:30 |
Jerzy Tiuryn, University of Warsaw |
Identification of functional modules from ancestral protein-protein interactions |
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10:30-11:00 |
Coffee Break |
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11:00-11:20 |
Rainer Koenig, DFKZ, Heidelberg |
Using gene expression data and network topology to detect substantial pathways, clusters and switches |
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11:20-11:40 |
Hanif Khalak |
Microarray-based Class Modeling and
Prediction using Set-Enrichment |
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11:40-12:00 |
Sol Efroni, NIH/NCI |
Identification of Key Processes underlying Cancer Phenotypes using Biologic Pathway Analysis |
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12:00-13:00 |
Lunch |
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13:00-13:45 |
Eytan Ruppin, Tel-Aviv University |
Genome Scale Studies of Robustness and Annotation of the Yeast Metabolic Network |
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13:45-14:30 |
Fengzhu Sun, University of Southern California |
Network motif identification in stochastic networks |
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Session 5: Evolution of pathways and networks |
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14:30-15:15 |
Simon Lovell |
Protein-protein interactions and their networks: can they tell us about biology? |
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15:15-15:35 |
Natalia Maltsev |
Co-evolutionary analysis of Metabolic Pathways and Enzymes in PUMA2 and Chisel systems |
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15:35-16:00 |
Coffee Break |
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16:00-16:45 |
Toni Gabaldón |
Evolution of metabolic systems: insights from comparative genomics |
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16:45-17:30 |
Philip Kim |
Relating three-dimensional structures to protein networks provides evolutionary insights |
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Round Table Discussion |
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17:30-18:30 |
Network Reconstruction and Evolution |
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End of meeting |
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