Session: Poster Session (Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018))

Towards a Metabolic and Expression Model of the Metabolically Versatile Bacterium Rhodopseudomonas Palustris
Adil Alsiyabi, Cheryl Immethun and Rajib Saha

Genetic Optimization Algorithm for Metabolic Engineering Revisited
Tobias B. Alter, Lars M. Blank and Birgitta E. Ebert

New Methods to Constrain Genome Scale Models with Stable Isotope Labeling Data
Tyler Backman, David E. Ando, Jay D. Keasling and Hector Garcia Martin

Mgpipe: A Toolbox for Investigating Metagenomics Data through Personalized Microbiota Metabolic Models
Federico Baldini, Almut Heinken, Laurent Heirendt, Ronan M.T. Fleming and Ines Thiele

Systems Approaches to Identify Metabolite Signatures in Placental Development
Priyanka Baloni, Alison Paquette, Heather Brockway, Yoel Sadovsky, Louis Muglia and Nathan D. Price

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 and Sascha Steinbiß

Probabilistic Metabolic Network Reconstruction: A Modular Approach to Integrate Omics Data and Represent Uncertainty
David Bernstein, Shany Ofaim, Luca Zoccarato, Daniel Sher and Daniel Segrè

Essential Metabolism for a Minimal Cell - Poster
Marian Breuer

A Distance Measure for Heterogeneity Using Genome Scale Metabolic Networks
Andrea Cabbia, Peter A. J. Hilbers and Natal A. W. van Riel

Thermodynamics As an Optimization Goal for Metabolism: Prediction of Metabolite Levels, Rate Constants and Post-Translational Regulation
William R. Cannon, Jeremy D. Zucker, Douglas J. Baxter, Neeraj Kumar, Jennifer M. Hurley, Scott E. Baker and Jay C. Dunlap

Comparative Genomics and Network Modeling of Parasites
Maureen A. Carey, Michal Stolarczyk, Ana Untariou, Gregory L. Medlock, Jennifer L. Guler and Jason A. Papin

Models Constrained with Transcriptomics or Proteomics Data Generate Discordant Predictions
Maureen A. Carey, Ana Untariou and Jason A. Papin

Toward a Whole-Cell Model of Human Embryonic Stem Cells: A Composable Model of Metabolism Built on a Scalable Framework for Integrating Multiple Pathway Submodels
Yin Hoon Chew, Andrew Sundstrom and Jonathan R. Karr

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 and Hon-Ming Lam

Metabolic Network Reconstruction for the Pan-Genome: A Scalable Method to Get High-Quality Metabolic Models across the Tree of Life
Kevin Correia and Radhakrishnan Mahadevan

Reconciling Barseq Datasets for Z. Mobilis Using a Genome-Scale Metabolic Model
Dylan Courtney, Wai Kit Ong, Shu Pan and Jennifer Reed

Developing and Evaluating Integrated Metabolic Regulatory Models for Microbial Life
Molly Creagar, Thomas Kamp, Ruby Fore, Derek Friend, Craig Disselkoen, Christopher S. Henry, Matthew DeJongh, Aaron Best, William Lindsey and Nathan Tintle

Constructing a High Quality Genome-Scale Metabolic Network for Streptomyces Lividans TK24
Wouter Daniels, Kjerstin De Winter, Justien Ghesquière, Kenneth Simoens, Tobias Busche, Christian Rückert, Bart Lievens, Tomer Shlomi, Jörn Kalinowski and Kristel Bernaerts

Construction of a Dynamic Flux Balance Analysis Model for Streptococcus Gordonii
Kjerstin De Winter, Wim Teughels, Steffen Waldherr and Kristel Bernaerts

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 and Aaron Best

Untangling Dynamic Protein Behaviour with Rule-Based Modelling and Sensitivity Analysis
Robin Denhardt-Eriksson

Towards a Genome-Wide Transport Systems Encoding Genes Tracker
Davide Lagoa, Eugénio Ferreira and Oscar Dias

Predicting Shifts in Cardiomyocyte Metabolism during Heart Failure
Bonnie Dougherty, Kristopher Rawls, Glynis Kolling, Vinnakota Kalyan, Venkat Pannala, Anders Wallqvist and Jason A. Papin

Metabolic Network Reconstruction of Treponema Pallidum Spp. Pallidum
Silvia Morini, Isabella Casini, Thomas M. Hamm, Kay Nieselt and Andreas Dräger

Modeling of Potentially Virulence-Associated Metabolic Pathways in Pseudomonas Aeruginosa PA14 Including Experimental Verification
Alina Renz, Erwin Bohn, Monika Schütz and Andreas Dräger

Representation of ME-Models in Sbml
Marc Alexander Voigt, Colton J. Lloyd, Laurence Yang, Zachary A. King, Oliver Kohlbacher, Kay Nieselt and Andreas Dräger

Automated Reconstruction, Evaluation and Comparison of Diverse Genome Scale Fungal Models
Janaka N Edirisinghe, José P. Faria, Sara Calhoun, Filipe Liu, Igor Grigoriev and Christopher S. Henry

Metabolic Supply and Demand Constrain Optimal Regulatory Strategies: Structural Evidence from the E coli Small Molecule Regulatory Network
Christian Euler and Radhakrishna Mahadevan

Improving High Throughput Genome-Scale Metabolic Model Reconstruction and Validation with Tnseq Data Using Modelseed 2
José P. Faria, Janaka N Edirisinghe, Filipe Liu, Samuel M.D. Seaver, James G. Jeffryes, Qizh Zhang, Pamela Weisenhorn, Boris Sadkhin, Nidhi Gupta, Tian Gu and Christopher S. Henry

A Deep Dive into False Positive Gene Essentiality Predictions with Modeling and Multi-Omics Analysis
Adam M. Feist

A Multiobjective Strain Design Platform for Modular Cell Engineering
Sergio Garcia and Cong T. Trinh

Development of an Accelerated Workflow for Parameterizing Kinetic Models of Metabolism
Satyakam Dash, Saratram Gopalakrishnan and Costas D. Maranas

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 and Jennifer Reed

Constraint-Based Modeling Reveals the Distinct Metabolic Potential in Gut Microbiomes of Inflammatory Bowel Disease Patients with Dysbiosis
Almut Heinken, Laurent Heirendt, Federico Baldini, Ronan M.T. Fleming and Ines Thiele

COBRA.jl - Gearing up for the huge scale
Laurent Heirendt, Sylvain Arreckx, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele and Ronan M.T. Fleming

Genome-Scale Flux Elucidation in the Fast-Growing Cyanobacterium Synechococcus Elongatus Utex 2973
John I Hendry, Saratram Gopalakrishnan, Himadri B. Pakrasi, Yinjie J. Tang and 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 and Rajib Saha

Metabolic Chaos during Microbial Stress Responses
Paul A. Jensen

Leveraging a Clostridium Difficile Genre and Metagenomics to Identify Candidate Probiotic Bacterial Strains
Matthew Jenior and Jason Papin

Fine Tuning Thresholds to Facilitate Integration of Transcriptomics Data
Chintan Joshi, Song-Min Schinn, Austin Chiang, Anne Richelle and Nathan Lewis

A Multi-Omics Investigation Unveiling the Tiered Regulation of Breast Cancer Cell Metabolism
Rotem Katzir

Constraint-Based Modeling of Allelic Variation Mechanistically Links Genome-Wide Associations
Erol Kavvas

Laboratory Evolution Reveals a Two-Dimensional Rate-Yield Tradeoff in Microbial Metabolism
Zachary A. King and Chuankai Cheng

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 and Steinn Gudmundsson

Metabolic Modeling of a Model Diatom
Manish Kumar, Shawn W. Polson, Lisa Zeigler Allen and Karsten Zengler

Computational Modeling of Ostrecoccus Tauri Central Metabolism Based on Statistical Thermodynamics
Neeraj Kumar, William R. Cannon, James E. Evans and Jeremy D. Zucker

Bofdat: Generating Biomass Objective Function for Constraint-Based Metabolic Models from Experimental Data
Jean-Christophe Lachance

Elucidating the Metabolic Rewiring of Pluripotent Stem Cells during Differentiation into Adult Progenitors Using an Updated and Enzyme-Constrained Human Genome-Scale Model
Meiyappan Lakshmanan, Dong-Yup Lee and Lokanand Koduru

Implementation and Application of a New Combined Stoichiometric and Thermodynamic Flux Balance Analysis
Simeon Leupold, Bastian Niebel and Matthias Heinemann

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 and Nathan Tintle

Sbmltools: A Sbml Integration Tool for Kbase
Filipe Liu, José P. Faria, Qizhi Zhang, Miguel Rocha, Isabel Rocha and Christopher S. Henry

The genetic basis for adaptation of model-designed syntrophic co-cultures
Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O'Brien, Joanne Liu and Bernhard O. Palsson

Exploring the Metabolic Role of Multidrug-Resistance Efflux Pumps in Salmonella Typhimurium
Sean G. Mack, Xuan Wang-Kan, Laura J. V. Piddock and Daniel J. Dwyer

Thermodynamic Metabolic Flux Analysis with Consistent Handling of Errors in the Estimates from the Component Contribution Method
Vishnuvardhan Mahamkali, Kaspar Valgepea, Tim McCubbin, Esteban Marcellin and Lars K, Nielsen

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 and Lars K. Nielsen

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 and Lars Keld Nielsen

Systematic Reduction of Genome-Scale Models for the Study of Metabolic Phenotypes of Human Cells
Maria Masid, Meriç Ataman and Vassily Hatzimanikatis

Elementary Mass Action Stoichiometric Simulation Models Predict Non-Negligible Concentrations of Enzyme-Bound Metabolites
Marta R. A. Matos, Daniel C. Zielinski, Lars K. Nielsen and Nikolaus Sonnenschein

Medusa: A Software Package for Construction and Analysis of Ensembles of Metabolic Networks
Gregory L. Medlock and Jason A. Papin

A Systematic Assessment of Current Genome-Scale Metabolic Reconstruction Tools
Sebastián N. Mendoza, Brett G. Olivier, Douwe Molenaar and Bas Teusink

Genome-Scale Metabolic Model ofÂ Chromochloris, an Emerging Model Organism for Sustainable Fuel Production
Alexander Metcalf and Nanette R. Boyle

Exploring Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors
Milenko Tokic, Noushin Hadadi, Meric Ataman, Dário Neves, Birgitta E. Ebert, Lars M. Blank, Ljubisa Miskovic and Vassily Hatzimanikatis

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 and Vassily Hatzimanikatis

Genome-Scale Metabolic Modeling of Actinomycetes for Secondary Metabolites Production
Omkar Mohite, Tilmann Weber, Hyun Uk Kim and Sang Yup Lee

Genome Scale Metabolic Analysis of the Lactobacillus Genus with a Focus on Probiotic Strains
Thomas J. Moutinho Jr., Benjamin C. Neubert and Jason A. Papin

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 and Erin Nuccio

The Strain Optimization API: A Flexible Strain Design Formalism for an Automated High-Throughput Industrial Pipeline
Chiam Yu Ng

Genome Scale Metabolic Modeling and Analysis of Clostridium Difficile
Charles J. Norsigian, Bernhard Ø. Palsson and Jonathan M. Monk

An Integrated COBRA-PBPK Model to Study Interactions between the Gut Microbiome and the Brain in Autism
Meghana Palukuri, Shruti Shivakumar, Swagatika Sahoo and Raghunathan Rengaswamy

Genome-Scale Constraint-Based Metabolic Modeling and Analysis of Cryptoccocus Curvatus
Nhung Pham, Maarten Reijnders, Maria Suarez-Diez, Bart Nijsse, Peter J Schaap and Vitor A. P. Martins Dos Santos

Identifying Orphan Enzymes in Pseudomonas Putida Using Cobra-Based Methods
Brandon Phan, Shu Pan, Christine Vera Colon, Nathaniel Bennett and Jennifer L. Reed

Enzyme Multicollinearity in Genome-Scale Metabolic Models Revealed By an Efficient Coupling Algorithm
Dikshant Pradhan and Paul A. Jensen

Model-Guided Engineering of Cyanobacteria for Improved Biofuel Production
Hugh M. Purdy and Jennifer L. Reed

Kinetic Model of Clostridium Beijerinckii Based on Phenotypic States Superposition
Marcelo Rivas-Astroza, Ivan Paredes, German Aroca and Raul Conejeros

Etfl: A Formulation of ME-Models Accounting for Expression and Thermodynamics in Constraint-Based Models
Pierre Salvy and Vassily Hatzimanikatis

Deconvoluting Independent Regulatory Signals in the Escherichia coli Transcriptome
Anand Sastry, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu, Donghyuk Kim, Kumari Sonal Choudhary, Laurence Yang, Zachary A. King and Bernhard O. Palsson

Effective Visualization for Investigating Elementary Flux Modes in Genome-Scale Metabolic Models
Chaitra Sarathy, Michael Lenz, Martina Kutmon, Chris T. Evelo and Ilja C.W. Arts

Characterizing and Ranking Computed Metabolic Engineering Strategies
Philipp Schneider and Steffen Klamt

Optfill: A Novel Optimization-Based Tool to Automate the Gapfilling of Genome-Scale Metabolic Models
Wheaton Schroeder and Rajib Saha

Sammi: An Interactive, Semi-Automated Tool for the Illustration and Visualization of Metabolic Networks
Andre Schultz and Rehan Akbani

Genome-Scale Metabolic Reconstructions for Phylogeny?
Christian Schulz and Eivind Almaas

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 and 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, Sarah McGarrity, Óttar Rolfsson and Olafur Sigurjonsson

Mighty Morphing Metabolic Models: Leveraging Manual Curations for Automatic Metabolic Reconstruction of Clades
Evangelos Simeonidis, Brendan King, Matthew A. Richards and Nathan D. Price

Utilizing RNA-Seq Data in Bayesian Estimation of Gene Activity States
Eldon Sorensen, Jaden Boehme, Angela Gasdaska, Matthew DeJongh, Aaron Best, William Lindsey and Nathan Tintle

Bayesian Inference of Metabolic Kinetics from Genome-Scale Multiomics Data
Peter C. St. John, Jonathan Strutz and Yannick J. Bomble

Dynamic FBA with Time-Course Transcriptomics
Snorre Sulheim, Alexander Wentzel and Eivind Almaas

Determination of CHO Biomass Composition
Diana Szeliova, David Ruckerbauer, Sarah Galleguillos, Stephan Hann, Michael Hanscho and Nicole Borth

Grid-Based Computational Methods for the Design of Constraint-Based Parsimonious Chemical Reaction Networks to Simulate Metabolite Production: Gridprod
Takeyuki Tamura

Identification of the Enzymes Responsible for Diverse Phenotypic States of Yeast Lipid Metabolism Using Comprehensive Mechanistic Models
Sophia Tsouka and Vassily Hatzimanikatis

Selective Metabolic Vulnerabilities in Multiple Myeloma
Luis Vitores Valcárcel, Raquel Ordoñez, Cem Meydan, Iñigo Apaolaza, Ari Melnick, Xabier Agirre, Felipe Prosper and Francisco J. Planes

Computational Pathway Design for Funneling Lignin Intermediates to Aromatic Products
Lin Wang, Gregg T. Beckham and Costas D. Maranas

Template of Metabolic Reprogramming in Cancer and Healthy Cells for Inferring Oncogenes
Wu-Hsiung Wu, Fan-Yu Li, Yi-Chen Shu, Jin-Mei Lai, Peter Mu-Hsin Chang, Chi-Ying F. Huang5 and Feng-Sheng Wang

Gapseq: A Novel Approach for in silico Prediction and Analysis of Bacterial Metabolic Pathways and Genome-Scale Networks
Johannes Zimmermann, Christoph Kaleta and Silvio Waschina

Erythrodb: A Multi-Omic Visual Knowledge Base for the Human Red Blood Cell
James T. Yurkovich and Bernhard O. Palsson

Multiomics Integration for Prediction of Complex Metabolic Phenotypes
Aleksej Zelezniak

Genome Scale Metabolic Model Assisted Strain Designs for Itaconic Acid Production in Yeast
Eric M. Young, Zheng Zhao, Bianca Gielesen, Liang Wu, Ben Gordon, Johannes A. Roubos and Christopher A. Voigt

A Machine Learning-Empowered Kinetic Reconstruction of E. coli Metabolism
Daniel C. Zielinski and Bernhard O. Palsson

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 and Nathan Lewis