COBRA 2018 Program

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

Costas Maranas, The Pennsylvania State University

INVITED SPEAKER:

Vassily Hatzimanikatis, Ecole Polytechnique Federale de Lausanne (EPFL)

Machine Learning for Uncertainty Reduction in Biochemical Kinetic Models

Ljubisa Miskovic, Ecole Polytechnique Federale de Lausanne (EPFL)

Expanding Metabolic Models to Three Dimensions

Elizabeth Brunk, University of California San Diego

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

Anne Richelle, University of California San Diego

INVITED SPEAKER: Metabolic Coordination through Metabolite-Protein Interactions

Uwe Sauer, Eidgenössische Technische Hochschule (ETH) Zürich

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

Matthias Heinemann, University of Groningen

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

Metabolic Model-Based Evaluation of Microbiome-Metabolome Association Studies

Cecilia Noecker, University of Washington

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

Benjamín J. Sánchez, Chalmers University of Technology

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

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

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

Laura J. Dunphy, University of Virginia

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

Synthetic Lethality in Cancer Research Via Genetic Minimal Cut Sets -

Francisco J. Planes, TECNUN, University of Navarra

INVITED SPEAKER: COBRA Distinguished Young Investigator Award Winner

Pathogen Metabolism and Antibiotic Resistance

Sriram Chandrasekeran, University of Michigan

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)

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

Gregory L. Medlock, University of Virginia

Understanding the Role of Bile Acids in Alzheimer's Disease

Priyanka Baloni, Institute for Systems Biology

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

Deciphering the Mechanisms Underlying Nutrient Exchange in Insect-Microbe Symbioses

Nana Ankrah, Cornell University

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

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

INVITED SPEAKER: New Directions for Cobra

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

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

James T. Yurkovich, University of California, San Diego

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

Wheaton Schroeder, University of Nebraska - Lincoln

INVITED SPEAKER: Systems Biology of Yeast Metabolism

Jens Nielsen, Chalmers University of Technology

Experimental Design for Parameter Estimation in Kinetic Models of Metabolism

Christian Euler, University of Toronto

Essential Metabolism for a Minimal Cell

Marian Breuer, University of Illinois at Urbana-Champaign

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

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

Nikolaus Sonnenschein, Technical University of Denmark

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

Kobe De Becker, KU Leuven

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

Evrim Acar, Unversity of Copenhagen

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

Jennifer Reed, University of Wisconsin-Madison

How Accurate Is Automated Gap Filling of Metabolic Models?

Peter Karp, SRI International

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

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

Joshua Chan, Colorado State University

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

Raul Conejeros, Pontificia Universidad Catolica de Valparaiso

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

Christian Lieven, Technical University of Denmark

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

Christopher S. Henry, Argonne National Laboratory

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

Tolutola Oyetunde, Washington University in St. Louis

Dynamic FBA with Global Constraints on Cellular Protein Fraction

Eivind Almaas, Norwegian University of Science and Technology 

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

St. Elmo Wilken, University of California, Santa Barbara

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

Ronan M.T. Fleming, Leiden University