Technical Program for COBRA 2024 | AIChE

Technical Program for COBRA 2024 

All times listed in PST




Start End Duration Event
Day 1 - Thursday, October 24
8:00 AM 9:00 AM 1:00 Registration (Open all day)
9:00 AM 9:10 AM 0:10 Chair's Introduction - Bernhard Palsson
Session 1: Human Health
9:10 AM 9:45 AM 0:35

Keynote: Adil Mardinoglu, KTH Royal Institute of Technology: 

Enabling Precision Medicine Using Multiomics and Systems Biology 

9:45 AM 10:05 AM 0:20

Bram Nap, University of Galway:"We Are What We Eat: A Nutrition Toolbox Permits in silico Analysis and Optimization of Personalized Diets through Metabolic Modeling"

10:05 AM 10:25 AM 0:20 Sunayana Malla, University of Nebraska-Lincoln: Dissecting Metabolic Landscape of Alveolar Macrophage
10:25 AM 10:45 AM 0:20 Coffee Break
10:45 AM 11:20 AM 0:35 Invited Speaker: Anu Raghunathan, NCL India
11:20 AM 11:40 AM 0:20

Christopher S. Henry, Argonne National Laboratory: Understanding Uncertainty in Model Reconstruction to Produce Insights into Metabolic Progression in the Gut Microbiome

11:40 AM 12:00 PM 0:20

Igor Marín de Mas, Copenhagen University Hospital: Algorithm-Aided Protocol for Constructing Highly Curated Genome-Scale Models of Human Metabolism

12:00 PM 1:30 PM 1:30 Lunch
Session 2: Chronic Diseases
1:30 PM 2:05 PM 0:35 Keynote: Ronan Fleming, University of Galway:

Variational Kinetic Modelling of Inherited Metabolic Diseases
2:05 PM 2:25 PM 0:20

Tahereh Razmpour, University of Nebraska-Lincoln: "Integrating Transcriptomics Data, Genome-Scale Metabolic Modeling, and Machine Learning to Elucidate Metabolic Vulnerabilities and Biomarkers in Pancreatic Cancer"

2:25 PM 2:45 PM 0:20 Tim Hensen, University of Galway: In silico Modelling Links Microbiome-Derived Metabolites to Risk Factors for Alzheimer's Disease
2:45 PM 3:05 PM 0:20 Coffee Break
3:05 PM 3:40 PM 0:35 Invited Speaker: Lutfu Safak Yilmaz, University of Massachusetts Chan Medical School
3:40 PM 4:10 PM 0:20

Amit Ghosh, Indian Institute of Technology Kharagpur: Genome Scale-Differential Flux Analysis to Understand Metabolic Deregulation in Lung Cell Post Sars-Cov2 Infection

4:10 PM 4:30 PM 0:20

Daniel Fässler, University Medicine Greifswald: Integrating Genome-Wide Statistical Screenings and Constraint-Based Modeling to Understand Gene-Metabolite Relations Via Microbiome-Personalized Whole Body Models

5:00 PM 7:00 PM 2:00 Reception




Day 2 - Friday, October 25
8:00 AM 9:00 AM 1:00 Registration (Open all day)
9:00 AM 9:10 AM 0:10 Chair's Summary of Previous Day
Session 3: Microbial Communities
9:10 AM 9:45 AM 0:35 Keynote: Sean Gibbons, Institute of Systems Biology
9:45 AM 10:05 AM 0:20 Helen Scott, Boston University - "A Model-Based Approach to Understanding Microbial Carbon Use Efficiency"
10:05 AM 10:25 AM 0:20 Juan Bonilla, UCSD - "Metabolism and Gene Expression Models Unravel the Effect of Diet and Metabolic Dysbiosis of the Gut Microbiome on Disease"
10:25 AM 10:45 AM 0:20 Coffee Break
10:45 AM 11:05 AM 0:20

Nantia Leonidou, Institute for Bioinformatics and Medical Informatics (IBMI) - "Integrative Metabolic Modeling: From Human Nasal Microbiome to Antiviral Target Prediction in the Respiratory Tract"

11:05 AM 11:25 AM 0:20 Parsa Ghadermazi, Colorado State University - "Predicting Microbial Interactions Using a Novel Reinforcement Learning Algorithm"
11:25 AM 11:45 AM 0:20

Gracelyn Richmond, Albert Einstein College of Medicine - "An Integrative in vitro and in silico Platform for Studying Microbial Community Metabolic Dynamics"

12:00 PM 1:30 PM 1:30 Lunch
Session 4: Microbial Pathogens
1:30 PM 2:05 PM 0:35

Keynote: Paul Jensen, University of Michigan:

Integrating Cobra Models with Closed-Loop Autonomous Experiments

2:05 PM 2:25 PM 0:20 Nabia Shahreen, U of Nebraska-Lincoln - "Metabolic Adaptations and Overflow Metabolism in Staphylococcus Aureus and Neisseria Gonorrhea"
2:25 PM 2:45 PM 0:20

Denis Joly, Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL) - "Less Is More: Efficient Modelling of Cell-Cell Metabolic Interactions Via Minimal Operational Physiological Units (MOPhUs)"

2:45 PM 3:05 PM 0:20 Coffee Break
3:05 PM 3:25 PM 0:20

Janaka N. Edirisinghe, Argonne National Laboratory - "Bridging the Gap: Integrating Diverse Fungal Models and Energy Biosynthesis Strategies for Enhanced Understanding of Microbial Ecophysiology"

3:25 PM 3:45 PM 0:20

Kalani Paranagama, School of Translational Medicine, Monash University - "Metabolic Diversity of Klebsiella Pneumoniae and Association with Ecological Niche"

3:45 PM 4:05 PM 0:20 Emma Glass, University of Virginia - "Evolution Shapes Metabolic Function and Niche-Specific Antimicrobial Targets in Pathobionts
5:00 PM 7:00 PM 2:00 Poster Session




Day 3 - Saturday, October 26
8:00 AM 9:00 AM 1:00 Registration (Open all day)
9:00 AM 9:10 AM 0:10 Chair's Summary of Previous Day
Session 5: Biomanufacturing
9:10 AM 9:45 AM 0:35 Keynote: Huimin Zhao, University of Illinois Urbana-Champaign

Exploring a Data-driven Research Paradigm for Synthetic Biology 
9:45 AM 10:05 AM 0:20 Harish Nagarajan, Genomatica - "Data-driven design and development of commercial and scalable cell factories"
10:05 AM 10:25 AM 0:20 Aziz Ben Ammar, RWTH Aachen University - Building a Sustainable Protein Factory: A Genome-Scale Model of Xanthobacter Sp. SoF1
10:25 AM 10:45 AM 0:20 Coffee Break
10:45 AM 11:05 AM 0:20

Samira van den Bogaard, RWTH Aachen University - Learning More from Data: Extending Metabolic Models with Concepts of Resource Allocation on the Protein and Transcript Level

11:05 AM 11:25 AM 0:20

Benjamin Strain, Imperial College London - Integrating Industry Leading Datasets with Genome Scale Metabolic Models to Direct Chinese Hamster Ovary (CHO) Cell Metabolic Engineering.

11:25 AM 11:45 AM 0:20 Daniel Zielinski, University of California - The Metabolic Potential of Soluble Quinone-Mediated Extracellular Electron Transfer
11:45 AM 1:15 PM 1:30 Lunch
Session 6: Biosustainability
1:15 PM 1:50 PM 0:35 Keynote Speaker: BK Cho, KAIST
1:50 PM 2:10 PM 0:20 Sophie Zhu, University College London - Modelling of Microbial Communities with Non-Model Organisms for Bioprocess Development
2:10 PM 2:30 PM 0:20

Evangelia Vayena, Swiss Federal Institute of Technology (EPFL) - In silico Functional Comparison of the Leaf Microbiome By Reducing Metabolic Complexity

2:30 PM 2:50 PM 0:20 Coffee Break
2:50 PM 3:10 PM 0:20

Ljubisa Miskovic, Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL) - Generative Machine Learning for High-Throughput Dynamic Studies of Metabolism

3:10 PM 3:30 PM 0:20 Parizad Babaei, Novonesis - Sustainable Production of Nutritious Protein from CO2 using Fungal Cell Factories
3:30 PM 3:50 PM 0:20

Rana A. Barghout, University of Toronto - Kingems: Advancing Enzyme-Constrained Genome-Scale Models with Deep Learning Predicted Kinetic Parameters

3:50 PM 4:10 PM 0:20 Ending Remarks