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

Session: Poster Session

Presentations

06:00 PM

Predicted Responses of a Large-Scale Pseudomonas Putida KT2440 Kinetic Metabolic Model to Several Single-Gene Knockouts Are Consistent with Experimental Observations
Milenko Tokic, Ljubisa Miskovic, Vassily Hatzimanikatis
Development of an Accelerated Workflow for Parameterizing Kinetic Models of Metabolism
Saratram Gopalakrishnan, Satyakam Dash, Costas D. Maranas
Mighty Morphing Metabolic Models: Leveraging Manual Curations for Automatic Metabolic Reconstruction of Clades
Evangelos Simeonidis, Brendan King, Matthew A. Richards, Nathan D. Price
Metabolic Network Reconstruction of Treponema Pallidum Spp. Pallidum
Silvia Morini, Isabella Casini, Thomas M. Hamm, Kay Nieselt, Andreas Dräger
Thermodynamics As an Optimization Goal for Metabolism: Prediction of Metabolite Levels, Rate Constants and Post-Translational Regulation
Jeremy D. Zucker, William R. Cannon, Douglas J. Baxter, Neeraj Kumar, Jay C. Dunlap, Jennifer M. Hurley, Scott E. Baker
A Multiobjective Strain Design Platform for Modular Cell Engineering
Cong Trinh, Sergio Garcia
Genome Scale Metabolic Modeling and Analysis of Clostridium Difficile
Charles J. Norsigian, Bernhard Ø. Palsson, Jonathan M. Monk
Reconciling Barseq Datasets for Z. Mobilis Using a Genome-Scale Metabolic Model
Dylan Courtney, Shu Pan, Jennifer Reed, Wai Kit Ong
Laboratory Evolution Reveals a Two-Dimensional Rate-Yield Tradeoff in Microbial Metabolism
Zachary A. King, Chuankai Cheng
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
Constructing a High Quality Genome-Scale Metabolic Network for Streptomyces Lividans TK24
Justien Ghesquière, Kjerstin De Winter, Kenneth Simoens, Tobias Busche, Christian Rückert, Tomer Shlomi, Jörn Kalinowski, Kristel Bernaerts, Wouter Daniels, Bart Lievens
Comparative Genomics and Network Modeling of Parasites
Maureen A. Carey, Jason A. Papin, Jennifer L. Guler, Ana Untariou, Michal Stolarczyk, Gregory L. Medlock
Multiomics Integration for Prediction of Complex Metabolic Phenotypes
Aleksej Zelezniak
Implementation and Application of a New Combined Stoichiometric and Thermodynamic Flux Balance Analysis
Simeon Leupold, Bastian Niebel, Matthias Heinemann
Construction of a Dynamic Flux Balance Analysis Model for Streptococcus Gordonii
Kjerstin De Winter, Kristel Bernaerts, Steffen Waldherr, Wim Teughels
Fine Tuning Thresholds to Facilitate Integration of Transcriptomics Data
Song-Min Schinn, Austin Chiang, Chintan Joshi, Anne Richelle, Nathan Lewis
Mgpipe: A Toolbox for Investigating Metagenomics Data through Personalized Microbiota Metabolic Models
Ines Thiele, Federico Baldini, Almut Heinken, Ronan M.T. Fleming, Laurent Heirendt
Erythrodb: A Multi-Omic Visual Knowledge Base for the Human Red Blood Cell
James T. Yurkovich, Bernhard O. Palsson
Computational Pathway Design for Funneling Lignin Intermediates to Aromatic Products
Lin Wang, Gregg Beckham, Costas D. Maranas
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
COBRA.jl - Gearing up for the huge scale
Laurent Heirendt, Sylvain Arreckx, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M.T. Fleming
Modeling of Potentially Virulence-Associated Metabolic Pathways in Pseudomonas Aeruginosa PA14 Including Experimental Verification
Alina Renz, Erwin Bohn, Monika Schütz, Andreas Dräger
Genome-Scale Metabolic Modeling of Actinomycetes for Secondary Metabolites Production
Omkar Mohite, Tilmann Weber, Hyun Uk Kim, Sang Yup Lee
Probabilistic Metabolic Network Reconstruction: A Modular Approach to Integrate Omics Data and Represent Uncertainty
David Bernstein, Shany Ofaim, Luca Zoccarato, Daniel Sher, Daniel Segrè
Systematic Reduction of Genome-Scale Models for the Study of Metabolic Phenotypes of Human Cells
Maria Masid, Meriç Ataman, Vassily Hatzimanikatis
Representation of ME-Models in Sbml
Marc Alexander Voigt, Colton J. Lloyd, Laurence Yang, Zachary A. King, Oliver Kohlbacher, Kay Nieselt, Andreas Dräger
A Distance Measure for Heterogeneity Using Genome Scale Metabolic Networks
Andrea Cabbia, Peter A. J. Hilbers, Natal A. W. van Riel
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
Etfl: A Formulation of ME-Models Accounting for Expression and Thermodynamics in Constraint-Based Models
Pierre Salvy, Vassily Hatzimanikatis
Genome Scale Metabolic Analysis of the Lactobacillus Genus with a Focus on Probiotic Strains
Thomas J. Moutinho, Benjamin C. Neubert, Jason A. Papin
Genome-Scale Metabolic Reconstructions for Phylogeny?
Christian Schulz, Eivind Almaas
Bayesian Inference of Metabolic Kinetics from Genome-Scale Multiomics Data
Peter C. St. John, Jonathan Strutz, Yannick J. Bomble
Determination of CHO Biomass Composition
Diana Szeliova, David Ruckerbauer, Michael Hanscho, Sarah Galleguillos, Nicole Borth, Stephan Hann
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
Identification of the Enzymes Responsible for Diverse Phenotypic States of Yeast Lipid Metabolism Using Comprehensive Mechanistic Models
Sophia Tsouka, Vassily Hatzimanikatis
Towards a Metabolic and Expression Model of the Metabolically Versatile Bacterium Rhodopseudomonas Palustris
Adil Alsiyabi, Cheryl Immethun, Rajib Saha
Cobrapy: A Solid Foundation for a Diverse Python Metabolic Modeling Community
Moritz E. Beber, João G.R. Cardoso, Christian Diener, Mátyás Fodor, Ali Kaafarani, Zachary A. King, Matthias König, Svetlana Kutuzova, Christian Lieven, Alba Lopez, Michael Mundy, Vivek Rai, Henning Redestig, Nikolaus Sonnenschein, Peter C. St. John, Sascha Steinbiß
Medusa: A Software Package for Construction and Analysis of Ensembles of Metabolic Networks
Gregory L. Medlock, Jason A. Papin
Bofdat: Generating Biomass Objective Function for Constraint-Based Metabolic Models from Experimental Data
Jean-Christophe Lachance
Models Constrained with Transcriptomics or Proteomics Data Generate Discordant Predictions
Maureen A. Carey, Ana Untariou, Jason A. Papin
Metabolic Analysis of Nitrogen Fixation in the Soybean Micro-Symbiont Sinorhizobium Fredii Using Constraint-Based Modeling
Carolina A. Contador, Qianwen Wang, Siu Hung Joshua Chan, Hon-Ming Lam
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
Describing the Glucose-Lactate Consumption Rate during Expansion and Osteogenic Differentiation of Human Bone Marrow Derived Mesenchymal Stem Cells: A Premise for Building a Systems Biology Model of Osteogenesis Using Metabolomics Analysis
Þóra B. Sigmarsdóttir, Olafur Sigurjonsson, Sarah McGarrity, Óttar Rolfsson
Towards a Genome-Wide Transport Systems Encoding Genes Tracker
Oscar Dias, Davide Lagoa, Eugénio Ferreira
A Deep Dive into False Positive Gene Essentiality Predictions with Modeling and Multi-Omics Analysis
Adam M. Feist
Computational Modeling of Ostrecoccus Tauri Central Metabolism Based on Statistical Thermodynamics
Neeraj Kumar, William R. Cannon, James E. Evans, Jeremy D. Zucker
Metabolic Chaos during Microbial Stress Responses
Paul A. Jensen
The Strain Optimization API: A Flexible Strain Design Formalism for an Automated High-Throughput Industrial Pipeline
Chiam Yu Ng
Elucidating the Metabolic Rewiring of Pluripotent Stem Cells during Differentiation into Adult Progenitors Using an Updated and Enzyme-Constrained Human Genome-Scale Model
Dong-Yup Lee, Meiyappan Lakshmanan, Lokanand Koduru
System-Level Examination of Metabolism in Rhizosphere Grown Burkholderiales
Ali Navid, Jennifer Pett-Ridge, Evan Star, Jillian F. Banfield, Mary Firestone, Erin Nuccio