COBRA 2015 Program

Detailed Program  

Wednesday, September 16
11:15-13:15 Registration
13:15-13:30 Opening Remarks
13:30-18:00 Session 1: Biotechnology Applications

Chair: Markus J. Herrgård, Technical University of Denmark
13:30-14:00 Vassily Hatzimanikatis, EPFL

The Contribution of COBRA to the Design of Synthetic Pathways
14:00-14:30 Lucía Agudo, Centro de Investigaciones Biológicas

Genome-Scale Metabolic Reconstruction and Analysis of Azoarcus Sp. Cib, a Model Bacterium in Anaerobic Degradation of Aromatic Compounds
14:30-15:00 Isabel Rocha, MIT Portugal

Reconciling Experimental Data With in Silico Predictions In Metabolic Engineering Applications
15:00-15:30 Zhuo Wang, Shanghai Jiao Tong University

Integrative Model of Regulation and Metabolism Improves Growth Phenotype Prediction in Saccharomyces Cerevisiae
15:30-16:00 Coffee Break

Keynote: Bernhard Palsson, UCSD

Genome-Scale Models Can Compute Proteome Allocation

17:00-17:30 Averina Nicolae, Luxembourg Centre for Systems Biomedicine

Elementary Flux Analysis and Non-Stationary 13C Fluxomics Combine to Characterise Cytosol-Mitochondria Compartmentalisation in the CHO-K1 Cell Line

Steffen Klamt, Max Planck Institute for Dynamics of Complex Technical Systems

Structural Requirements for the Feasibility of Growth-Coupled Product Synthesis in Microbial Strains

18:00-20:00 Welcome Reception and Poster Session I
Thursday, September 17

Keynote: Jens Nielsen, Chalmers University

Metabolism of the Gut Microbiome: New Insights Through Genome-Scale Metabolic Modeling

10:00-13:00 Session 2: Omics and Phenotype Data Integration

Chair: Nathan D. Price, Institute for Systems Biology
10:00-10:30 Uwe Sauer, ETH Zurich

Extending Metabolic Networks by in vitro Metabolomics

Aleksej Zelezniak, Francis Crick Institute and University of Cambridge

Missing Links in the Genotype-Phenotype Path: Metabolic Network Connectivity Together with Protein Levels As Predictors of Metabolite Changes

11:00-11:30 Coffee Break
11:30-12:00 Aarash Bordbar, Sinopia Biosciences

Integration of Quantitative Endometabolomics with Genome-Scale Models to Bypass the Steady-State Assumption

Balazs Papp, Biological Research Centre of the Hungarian Academy of Sciences

The Dynamic Environment Model for the Origin of Complex Metabolic Innovations

12:30-12:45 Elad Noor, Institute of Molecular Systems Biology

The Enzyme Cost of Metabolic Pathway Fluxes
12:45-13:00 Joana Xavier, University of Minho

Universally Essential Cofactors in Prokaryotes
13:00-14:00 Lunch
14:00-17:00 Session 3: Biomedical Applications

Chair: Ines Thiele, University of Luxembourg Luxembourg
14:00-14:30 Eytan Ruppin, University of Maryland and Tel Aviv University

The Computational Study of Cancer Metabolism: Some Recent Results and Pending Challenges
14:30-15:00 Alexei Vazquez, Beatson Institute for Cancer Research

Quantification of Folate Metabolism Using Transient Metabolic Flux Analysis
15:00-15:30 Stefania Magnusdottir, University of Luxembourg

Data-Driven Refinement of 321 Metabolic Reconstructions Representing the Human Gut Microbiota
15:30-16:00 Thomas Sauter, University of Luxembourg

Integrated Metabolic Modelling Reveals Cell-Type Specific Epigenetic Control Points of the Macrophage Metabolic Network
16:00-16:30 Coffee Break
16:30-17:00 Wenzhong Xiao, Mass General Hospital/ Harvard Medical School

Personalized Quantitative Metabolic Modeling in the Study of Metabolic Dysfunction after Severe Injury
17:00-22:00 Heidelberg City Tour and Dinner
Friday, September 18
9:00-13:00 Session 4: Models and Algorithms

Chair: Tomer Shlomi, Computer Science, Technion IIT, Haifa Israel
9:00-9:30 Jennifer Reed, University of Wisconsin

Application of Algorithms to Identify and Produce Precursors to Commercial Chemicals
9:30-10:00 David Heckmann, Heinrich Heine University

Combining Kinetic and Constraint-Based Models to Predict Evolution of a Complex Photosynthetic Trait
10:00-10:30 Matthew Biggs, University of Virginia

Metabolic Network-Guided Binning of Metagenomic Sequence Fragments
10:30-11:00 Coffee Break
11:00-11:30 Michael Balber, Technion IIT

Constraint-Based Isotope Tracing (CBIT): Inferring Flux Constraints from Isotopic Tracing Data

Costas Maranas, Penn State

Designing Optimal and Thermodynamically Feasible Overall Stoichiometric Bioconversions

12:00-12:30 Elizabeth Brunk, UCSD

Systems Biology of the Structural Proteome
12:30-13:30 Lunch
13:30-15:00 Poster Session II
15:30-17:30 Session 5: Multiscale Modelling

Chair: Kiran Patil, EMBL
15:30-16:00 Ines Thiele, University of Luxembourg

A Computational Modeling Approach Elucidate Metabolic Interactions between the Gut Microbiota Community and Their Impact on Host Metabolism
16:00-16:30 Peter Karp, SRI International

Modeling Microbial Communities with Metaflux
16:30-17:00 Daniel Segre, Boston University

Spatio-Temporal Modeling of Metabolism in Microbial Communities
17:00-17:30 Kai Zhuang, Technical University of Denmark

Multi-Scale Exploration of the "Metabolism" of a Bio-Based Economy
17:30-18:00 Poster Awards and Closing Remarks