5th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018)

Session: Poster Session

Presentations

06:00 PM

A Multiobjective Strain Design Platform for Modular Cell Engineering
Cong Trinh, Sergio Garcia
Genome Scale Metabolic Analysis of the Lactobacillus Genus with a Focus on Probiotic Strains
Thomas J. Moutinho, Benjamin C. Neubert, Jason A. Papin
Identification and Analysis of Bacterial Genomic Metabolic Signatures in the Department of Energy's Systems Biology Knowledgebase
Matthew DeJongh, Megan Grimes, Lauren Satkiewicz, Nathan Tintle, Aaron Best
Representation of ME-Models in Sbml
Marc Alexander Voigt, Colton J. Lloyd, Laurence Yang, Zachary A. King, Oliver Kohlbacher, Kay Nieselt, Andreas Dräger
Probabilistic Metabolic Network Reconstruction: A Modular Approach to Integrate Omics Data and Represent Uncertainty
David Bernstein, Shany Ofaim, Luca Zoccarato, Daniel Sher, Daniel Segrè
Modeling of Potentially Virulence-Associated Metabolic Pathways in Pseudomonas Aeruginosa PA14 Including Experimental Verification
Alina Renz, Erwin Bohn, Monika Schütz, Andreas Dräger
Miren: An Optimization Tool for Data-Driven Discovery of Global Regulatory Phenomena Used to Elucidate the Heat Stress Response Mechanism in Rice Seed
Mohammad Mazharul Islam, Jaspreet Sandhu, Harkamal Walia, Rajib Saha
Erythrodb: A Multi-Omic Visual Knowledge Base for the Human Red Blood Cell
James T. Yurkovich, Bernhard O. Palsson
Fine Tuning Thresholds to Facilitate Integration of Transcriptomics Data
Song-Min Schinn, Austin Chiang, Chintan Joshi, Anne Richelle, Nathan Lewis
Implementation and Application of a New Combined Stoichiometric and Thermodynamic Flux Balance Analysis
Simeon Leupold, Bastian Niebel, Matthias Heinemann
Comparative Genomics and Network Modeling of Parasites
Maureen A. Carey, Jason A. Papin, Jennifer L. Guler, Ana Untariou, Michal Stolarczyk, Gregory L. Medlock
Template of Metabolic Reprogramming in Cancer and Healthy Cells for Inferring Oncogenes
Feng-Sheng Wang, Wu-Hsiung Wu, Fan-Yu Li, Yi-Chen Shu, Jin-Mei Lai, Peter Mu-Hsin Chang, Chi-Ying F. Huang5
Reconciling Barseq Datasets for Z. Mobilis Using a Genome-Scale Metabolic Model
Dylan Courtney, Shu Pan, Jennifer Reed, Wai Kit Ong
Bayesian Inference of Metabolic Kinetics from Genome-Scale Multiomics Data
Peter C. St. John, Jonathan Strutz, Yannick J. Bomble
Metabolic Network Reconstruction of Treponema Pallidum Spp. Pallidum
Silvia Morini, Isabella Casini, Thomas M. Hamm, Kay Nieselt, Andreas Dräger
Development of an Accelerated Workflow for Parameterizing Kinetic Models of Metabolism
Saratram Gopalakrishnan, Satyakam Dash, Costas D. Maranas
Optfill: A Novel Optimization-Based Tool to Automate the Gapfilling of Genome-Scale Metabolic Models
Wheaton Schroeder, Rajib Saha
Untangling Dynamic Protein Behaviour with Rule-Based Modelling and Sensitivity Analysis
Robin Denhardt-Eriksson
A Systematic Assessment of Current Genome-Scale Metabolic Reconstruction Tools
Sebastián N. Mendoza, Brett G. Olivier, Bas Teusink, Douwe Molenaar
Metabolic Network Reconstruction for the Pan-Genome: A Scalable Method to Get High-Quality Metabolic Models across the Tree of Life
Kevin Correia, Radhakrishnan Mahadevan
Elementary Mass Action Stoichiometric Simulation Models Predict Non-Negligible Concentrations of Enzyme-Bound Metabolites
Marta R. A. Matos, Daniel C. Zielinski, Lars K. Nielsen, Nikolaus Sonnenschein
Constraint-Based Modeling Reveals the Distinct Metabolic Potential in Gut Microbiomes of Inflammatory Bowel Disease Patients with Dysbiosis
Almut Heinken, Laurent Heirendt, Federico Baldini, Ines Thiele, Ronan M.T. Fleming
Selective Metabolic Vulnerabilities in Multiple Myeloma
Luis Vitores Valcárcel, Iñigo Apaolaza, Xabier Agirre, Felipe Prosper, Francisco J. Planes, Raquel Ordoñez, Cem Meydan, Ari Melnick
Metabolic Supply and Demand Constrain Optimal Regulatory Strategies: Structural Evidence from the E coli Small Molecule Regulatory Network
Christian Euler, Radhakrishna Mahadevan
Modelling of Cell Metabolism to Reduce the Lactate Generation in CHO Cell Cultures
Iván Martínez-Monge, Svetlana Volkova, Igor Marín de Mas, Hooman Hefzi, Pere Comas, Nathan Lewis, Martí Lecina, Jordi Joan Cairó, Lars Keld Nielsen
Leveraging a Clostridium Difficile Genre and Metagenomics to Identify Candidate Probiotic Bacterial Strains
Matthew Jenior, Jason Papin
Tailoring a Metabolic Model for CHO Cell-Line By Integrating Data-Inferred Metabolic Activities
Song-Min Schinn, Wei Wei, Yifeng Xu, Carly Morrison, Lin Zhang, Nathan Lewis
Essential Metabolism for a Minimal Cell - Poster
Marian Breuer
Enzyme Multicollinearity in Genome-Scale Metabolic Models Revealed By an Efficient Coupling Algorithm
Paul A. Jensen, Dikshant Pradhan
A Multi-Omics Investigation Unveiling the Tiered Regulation of Breast Cancer Cell Metabolism
Rotem Katzir
Sbmltools: A Sbml Integration Tool for Kbase
Filipe Liu, José P. Faria, Qizhi Zhang, Miguel Rocha, Isabel Rocha, Christopher S. Henry
Kinetic Model of Clostridium Beijerinckii Based on Phenotypic States Superposition
Marcelo Rivas-Astroza, Ivan Paredes, German Aroca, Raul Conejeros
Gapseq: A Novel Approach for in silico Prediction and Analysis of Bacterial Metabolic Pathways and Genome-Scale Networks
Christoph Kaleta, Johannes Zimmermann, Silvio Waschina
Predicting Shifts in Cardiomyocyte Metabolism during Heart Failure
Bonnie Dougherty, Kristopher Rawls, Glynis Kolling, Vinnakota Kalyan, Venkat Pannala, Anders Wallqvist, Jason A. Papin
Utilizing RNA-Seq Data in Bayesian Estimation of Gene Activity States
Eldon Sorensen, Jaden Boehme, Angela Gasdaska, Matthew DeJongh, Aaron Best, William Lindsey, Nathan Tintle
Implementing and Evaluating a Gaussian Mixture Framework for Identifying Gene Function from Tnseq Data
Kevin Li, Rachel Chen, William Lindsey, Aaron Best, Matthew DeJongh, Christopher S. Henry, Nathan Tintle
Developing and Evaluating Integrated Metabolic Regulatory Models for Microbial Life
Nathan Tintle, Matthew DeJongh, Aaron Best, William Lindsey, Molly Creagar, Craig Disselkoen, Ruby Fore, Derek Friend, Thomas Kamp, Christopher S. Henry
Model-Guided Engineering of Cyanobacteria for Improved Biofuel Production
Hugh M. Purdy, Jennifer L. Reed
Developement and Application of Constraint-Based Modeling Methods to Study Vulnerabilities Associated to Lipid Metabolism in Prostate Cancer
Igor Marín de Mas, Esther Aguilar, Carmen Bedia, Timothy M. Thomson, Romà Tauler, Balazs Papp, Marta Cascante, Lars K. Nielsen
MLProScape: Machine Learning (ML) Based Method for Engineering Enzymes Faster By Modeling Protein Fitness Landscape (ProScape)
Sanjan T.P. Gupta, Evan Glasgow, Brian G. Fox, Parmeswaran Ramanathan, Jennifer Reed
Multiple Reconstructions of P. Putida for Metabolic Engineering Applications
Joshua Mueller
System-Level Examination of Metabolism in Rhizosphere Grown Burkholderiales
Ali Navid, Jennifer Pett-Ridge, Evan Star, Jillian F. Banfield, Mary Firestone, Erin Nuccio
The Strain Optimization API: A Flexible Strain Design Formalism for an Automated High-Throughput Industrial Pipeline
Chiam Yu Ng
Computational Modeling of Ostrecoccus Tauri Central Metabolism Based on Statistical Thermodynamics
Neeraj Kumar, William R. Cannon, James E. Evans, Jeremy D. Zucker
Towards a Genome-Wide Transport Systems Encoding Genes Tracker
Oscar Dias, Davide Lagoa, Eugénio Ferreira
A Computational Knowledge-Base Elucidates the Response of Staphylococcus Aureus to Different Media Types
Bernhard O. Palsson, Yara Seif, Jon Monk, Nathan Mih, Saugat Poudel, Jared T. Broddrick, Cristal Zuniga P, Hannah Tsunemoto, Karsten Zengler
Models Constrained with Transcriptomics or Proteomics Data Generate Discordant Predictions
Maureen A. Carey, Ana Untariou, Jason A. Papin
Medusa: A Software Package for Construction and Analysis of Ensembles of Metabolic Networks
Gregory L. Medlock, Jason A. Papin
Towards a Metabolic and Expression Model of the Metabolically Versatile Bacterium Rhodopseudomonas Palustris
Adil Alsiyabi, Cheryl Immethun, Rajib Saha
A Metabolic Reconstruction of Lactobacillus Reuteri and Analysis of Its Potential As a Cell Factory
Thordis Kristjansdottir, Elleke F. Bosma, Filipe Branco dos Santos, Emre Özdemir, Alex Toftgaard Nielsen, Steinn Gudmundsson