COBRA 2018 Program

Schedule is subject to change. Last updated September 26, 2018


Sunday October 14th, Day 1
12:00 PM to 1:00 PM REGISTRATION
1:00 PM to 1:15 PM WELCOMING REMARKS
1:15 PM to 3:00 PM SESSION 1: NEW FRONTIERS I
1:15 PM to 1:45 PM

INVITED SPEAKER: Developing a seamless pipeline from 13C labeling data to kinetic models with a genome-wide coverage

Costas Maranas, The Pennsylvania State University

1:45 PM to 2:15 PM

INVITED SPEAKER:

Vassily Hatzimanikatis, Ecole Polytechnique Federale de Lausanne (EPFL)

2:15 PM to 2:30 PM

Machine Learning for Uncertainty Reduction in Biochemical Kinetic Models

Ljubisa Miskovic, Ecole Polytechnique Federale de Lausanne (EPFL)

2:30 PM to 2:45 PM

Expanding Metabolic Models to Three Dimensions

Elizabeth Brunk, University of California San Diego

2:45 PM to 3:00 PM

Key Decisions for the Development of the Next-Generation of Context-Specific Models

Anne Richelle, University of California San Diego

3:00 PM to 3:30 PM BREAK
3:30 PM to 5:15 PM SESSION 1: NEW FRONTIERS II
3:30 PM to 4:00 PM

INVITED SPEAKER: Metabolic Coordination through Metabolite-Protein Interactions

Uwe Sauer, Eidgenössische Technische Hochschule (ETH) Zürich

4:00 PM to 4:30 PM

INVITED SPEAKER: An Upper Limit in Gibbs Energy Dissipation Governs Cellular Metabolism

Matthias Heinemann, University of Groningen

4:30 PM to 4:45 PM

Compass: FBA-Powered Modeling of Single-Cell RNA-Seq Characterizes Cell-to-Cell Metabolic Heterogeneity and Reveals Novel Therapeutic Targets in Autoimmunity

Allon Wagner, University of California Berkeley

4:45 PM to 5:00 PM

Metabolic Model-Based Evaluation of Microbiome-Metabolome Association Studies

Cecilia Noecker, University of Washington

5:00 PM to 5:15 PM

Yeast-GEM: Reviving the Consensus Genome-Scale Model of S. Cerevisiae As a Standard in the Community

Benjamín J. Sánchez, Chalmers University of Technology

5:15 PM to 6:00 PM BREAK/POSTER SET-UP
6:00 PM to 7:00 PM POSTER RECEPTION
7:00 PM to 8:00 PM DINNER
   
Monday October 15th, Day 2
8:00 AM to 11:00 AM REGISTRATION
8:45 AM to 9:00 AM OPENING REMARKS
9:00 AM to 10:30 AM SESSION 2: APPLICATIONS IN MEDICINE I
9:00 AM to 9:30 AM

INVITED SPEAKER: Urea cycle dysregulation, emerging pyrimidines mutation bias and enhanced response to immunotherapy in cancer

Eytan Ruppin, Cancer Data Science Lab, National Cancer Institute

9:30 AM to 9:45 AM

Modeling Physiological Responses to Stress: Metabolism of Fasting and Acetaminophen-Induced Liver Damage in the Laboratory Rat

Anders Wallqvist, U.S. Army Medical Research and Materiel Command

9:45 AM to 10:00 AM

Differential Metabolic Functionality in Antibiotic-Resistant Pseudomonas aeruginosa Revealed with an Integrated Computational and Experimental Approach

Laura J. Dunphy, University of Virginia

10:00 AM to 10:15 AM

Model-Based Prediction of Functional SNPs Suggests Factors for Metabolic Diversity and Drug Resistance across Human-Associated Mycobacterium Tuberculosis

Ove Øyås, Eidgenössische Technische Hochschule (ETH) Zürich

10:15 AM to 10:30 AM

Synthetic Lethality in Cancer Research Via Genetic Minimal Cut Sets -

Francisco J. Planes, TECNUN, University of Navarra

10:30 AM to 11:00 AM BREAK
11:00 AM to 11:30 AM

INVITED SPEAKER: COBRA Distinguished Young Investigator Award Winner

Pathogen Metabolism and Antibiotic Resistance

Sriram ChandrasekeranUniversity of Michigan

11:30 AM to 12:15 PM SESSION 2: APPLICATIONS IN MEDICINE II
11:30 AM to 11:45 AM

Identifying and Targeting Key Cellular Mechanisms for Proliferation in Malaria Parasites: A Combined Experimental and Computational Strategy

Anush Chiappino-Pepe, Swiss Federal Institute of Technology (EPFL)

11:45 AM to 12:00 PM

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

Gregory L. Medlock, University of Virginia

12:00 PM to 12:15 PM

Understanding the Role of Bile Acids in Alzheimer's Disease

Priyanka Baloni, Institute for Systems Biology

12:15 PM to 2:30 PM LUNCH on your own at Pike Place Market
2:30 PM to 3:45 PM SESSION 3: MULTI-SCALE MODELING I
2:30 PM to 3:00 PM

INVITED SPEAKER: Towards a more complete view of a cell's functions through genome scale models of metabolism, protein synthesis, post-translational modification, and secretion

Nathan Lewis, University of California San Diego

3:00 PM to 3:15 PM

Deciphering the Mechanisms Underlying Nutrient Exchange in Insect-Microbe Symbioses

Nana Ankrah, Cornell University

3:15 PM to 3:30 PM

Incorporation of Dynamic pH into an Integrative Model of a Nitrification Microcosm Co-Culture of Nitrosomonas Europaea and Nitrobacter Winogradskyi

Frank Chaplen, Oregon State University

3:30 PM to 3:45 PM

Dynamic Side of the Warburg Effect: Glycolytic Intermediate Storage in Tumor Cells to Buffer Fluctuating Glucose and O2 Supply

Johannes H.G.M. van Beek, Vrije University Medical Center, Amsterdam

3:45 PM to 4:15 PM BREAK
4:15 PM to 5:15 PM SESSION 3: MULTI-SCALE MODELING II
4:15 PM to 4:45 PM

INVITED SPEAKER: New Directions for Cobra

Bernhard Palsson, University of California San Diego; Novo Nordisk Center for Biosustainability, Denmark

4:45 PM to 5:00 PM

Toward a Proteome-Complete Model of the Human Red Blood Cell

James T. Yurkovich, University of California, San Diego

5:00 PM to 5:15 PM

Koptic: A Novel Approach for in silico Prediction of Enzyme Kinetics and Regulation

Wheaton Schroeder, University of Nebraska - Lincoln

5:15 PM to 6:15 PM The Future of COBRA Discussion Panel
   
Tuesday October 16th, Day 3
8:00 AM to 11:00 AM REGISTRATION
8:45 AM to 9:00 AM OPENING REMARKS
9:00 AM to 10:00 AM SESSION 4: APPLICATIONS IN METABOLIC ENGINEERING I
9:00 AM to 9:30 AM

INVITED SPEAKER: Systems Biology of Yeast Metabolism

Jens Nielsen, Chalmers University of Technology

9:30 AM to 9:45 AM

Experimental Design for Parameter Estimation in Kinetic Models of Metabolism

Christian Euler, University of Toronto

9:45 AM to 10:00 AM

Essential Metabolism for a Minimal Cell

Marian Breuer, University of Illinois at Urbana-Champaign

10:00 AM to 10:30 AM BREAK
10:30 AM to 11:15 AM SESSION 4: APPLICATIONS IN METABOLIC ENGINEERING II
10:30 AM to 10:45 AM

Characterization and Design of Phase Spaces and Yield Spaces in Genome-Scale Metabolic Models

Jürgen Zanghellini, Austrian Centre of Industrial Biotechnology, University of Natural Resources and Life Sciences

10:45 AM to 11:00 AM

DD-Decaf: Data-Driven Design of Cell Factories and Communities

Nikolaus Sonnenschein, Technical University of Denmark

11:00 AM to 11:15 AM

Dynamic Enzyme-Cost Flux Balance Analysis (deFBA) Modelling for an Industrially Relevant Methanotroph Methylomicrobium Buryatense

Kobe De Becker, KU Leuven

11:15 AM to 12:15 PM Community standards and resources Discussion Panel
12:15 PM to 1:30 PM LUNCH
1:30 PM to 3:30 PM SESSION 5: METHODS AND SOFTWARE I
1:30 PM to 2:00 PM

INIVITED SPEAKER: Data Fusion Based on Coupled Matrix and Tensor Factorizations

Evrim Acar, Unversity of Copenhagen

2:00 PM to 2:30 PM

INVITED SPEAKER: COBRA and Machine Learning Approaches for Engineering Microbial Biocatalysts

Jennifer Reed, University of Wisconsin-Madison

2:30 PM to 2:45 PM

How Accurate Is Automated Gap Filling of Metabolic Models?

Peter Karp, SRI International

2:45 PM to 3:00 PM

Bridging the Gap between Structural Systems Biology and Constraint-Based Modeling: Tools for Defining the Functional Structural Proteome and Extracting Genome-Scale Structural Information for Metabolic and Macromolecular Expression Models

Edward Catoiu, University of California, San Diego

3:00 PM to 3:15 PM

Scalable Tools for Analyzing Steady-State Microbial Communities Using Standardized Genome-Scale Metabolic Models Siu Hung

Joshua Chan, Colorado State University

3:15 PM to 3:30 PM

Genome-Scale Metabolic Model Embedding for Fed-Batch Optimal Feed Policy Determination

Raul ConejerosPontificia Universidad Catolica de Valparaiso

3:30 PM to 4:00 PM BREAK
4:00 PM to 5:45 PM SESSION 5: METHODS AND SOFTWARE II
4:00 PM to 4:30 PM

INVITED SPEAKER: Memote: A Community Driven Effort Towards a Standardized Genome-Scale Metabolic Model Test Suite

Christian Lieven, Technical University of Denmark

4:30 PM to 4:45 PM

An Ecology of Modeling Methods, Data, and Tools to Decipher Functional Delegation and Species Interactions within a Microbiome

Christopher S. Henry, Argonne National Laboratory

4:45 PM to 5:00 PM

Thermodynamic Topology of Metabolite Networks Elucidates Regulatory Responses to Genetic and Environmental Perturbations

Tolutola Oyetunde, Washington University in St. Louis

5:00 PM to 5:15 PM

Dynamic FBA with Global Constraints on Cellular Protein Fraction

Eivind Almaas, Norwegian University of Science and Technology 

5:15 PM to 5:30 PM

Incorporating Flux Sampling into a Minimal Assumption Dynamic Flux Balance Analysis Algorithm

St. Elmo Wilken, University of California, Santa Barbara

5:30 PM to 5:45 PM

Creation and Analysis of Biochemical Constraint-Based Models: The Cobra Toolbox v3.0

Ronan M.T. Fleming, Leiden University

5:45 PM to 6:00 PM COBRA AWARDS
6:00 PM to 6:15 PM CLOSING REMARKS