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

Session: Poster Session

Presentations

06:00 PM

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, Christopher S. Henry
Multiple Reconstructions of P. Putida for Metabolic Engineering Applications
Joshua Mueller
Genome Scale Metabolic Model Assisted Strain Designs for Itaconic Acid Production in Yeast
Zheng Zhao, Eric M. Young, Bianca Gielesen, Liang Wu, Ben Gordon, Johannes A. Roubos, Christopher A. Voigt
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
Genome-Scale Constraint-Based Metabolic Modeling and Analysis of Cryptoccocus Curvatus
Nhung Pham, Maria Suarez-Diez, Peter J Schaap, Vitor A. P. Martins Dos Santos, Maarten Reijnders, Bart Nijsse
Leveraging a Clostridium Difficile Genre and Metagenomics to Identify Candidate Probiotic Bacterial Strains
Matthew Jenior, Jason Papin
Identifying Orphan Enzymes in Pseudomonas Putida Using Cobra-Based Methods
Brandon Phan, Christine Vera Colon, Nathaniel Bennett, Shu Pan, Jennifer L. Reed
Model-Guided Engineering of Cyanobacteria for Improved Biofuel Production
Hugh M. Purdy, Jennifer L. Reed
Exploring the Metabolic Role of Multidrug-Resistance Efflux Pumps in Salmonella Typhimurium
Sean G. Mack, Daniel J. Dwyer, Xuan Wang-Kan, Laura J. V. Piddock
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
The genetic basis for adaptation of model-designed syntrophic co-cultures
Colton J. Lloyd, Ali Ebrahim, Zachary A. King, Laurence Yang, Edward J. O'Brien, Joanne Liu, Edward Catoiu, Bernhard O. Palsson
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
Genome-Scale Flux Elucidation in the Fast-Growing Cyanobacterium Synechococcus Elongatus Utex 2973
Costas D. Maranas, John I Hendry, Saratram Gopalakrishnan, Himadri B. Pakrasi, Yinjie J. Tang
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
A Machine Learning-Empowered Kinetic Reconstruction of E. coli Metabolism
Daniel C. Zielinski, Bernhard O. Palsson
Predicting Shifts in Cardiomyocyte Metabolism during Heart Failure
Bonnie Dougherty, Kristopher Rawls, Glynis Kolling, Vinnakota Kalyan, Venkat Pannala, Anders Wallqvist, Jason A. Papin
Effective Visualization for Investigating Elementary Flux Modes in Genome-Scale Metabolic Models
Chaitra Sarathy, Michael Lenz, Martina Kutmon, Chris T. Evelo, Ilja C.W. Arts
Gapseq: A Novel Approach for in silico Prediction and Analysis of Bacterial Metabolic Pathways and Genome-Scale Networks
Christoph Kaleta, Johannes Zimmermann, Silvio Waschina
Genome-Scale Metabolic Model of Chromochloris, an Emerging Model Organism for Sustainable Fuel Production
Alexander Metcalf, Nanette Boyle
Kinetic Model of Clostridium Beijerinckii Based on Phenotypic States Superposition
Marcelo Rivas-Astroza, Ivan Paredes, German Aroca, Raul Conejeros
Systems Approaches to Identify Metabolite Signatures in Placental Development
Nathan D. Price, Priyanka Baloni, Alison Paquette, Heather Brockway, Yoel Sadovsky, Louis Muglia
Sbmltools: A Sbml Integration Tool for Kbase
Filipe Liu, José P. Faria, Qizhi Zhang, Miguel Rocha, Isabel Rocha, Christopher S. Henry
Sammi: An Interactive, Semi-Automated Tool for the Illustration and Visualization of Metabolic Networks
Andre Schultz, Rehan Akbani
A Multi-Omics Investigation Unveiling the Tiered Regulation of Breast Cancer Cell Metabolism
Rotem Katzir
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, Jonathan R. Karr, Andrew Sundstrom
Enzyme Multicollinearity in Genome-Scale Metabolic Models Revealed By an Efficient Coupling Algorithm
Paul A. Jensen, Dikshant Pradhan
Metabolic Modeling of a Model Diatom
Manish Kumar, Shawn W. Polson, Lisa Zeigler Allen, Karsten Zengler
Essential Metabolism for a Minimal Cell - Poster
Marian Breuer
Automated Reconstruction, Evaluation and Comparison of Diverse Genome Scale Fungal Models
Janaka N Edirisinghe, José P. Faria, Filipe Liu, Sara Calhoun, Igor Grigoriev, Christopher S. Henry
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
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, Lars K, Nielsen
Dynamic FBA with Time-Course Transcriptomics
Snorre Sulheim, Eivind Almaas, Alexander Wentzel
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
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
Genetic Optimization Algorithm for Metabolic Engineering Revisited
Tobias B. Alter, Lars M. Blank, Birgitta E. Ebert
Metabolic Supply and Demand Constrain Optimal Regulatory Strategies: Structural Evidence from the E coli Small Molecule Regulatory Network
Christian Euler, Radhakrishna Mahadevan
Grid-Based Computational Methods for the Design of Constraint-Based Parsimonious Chemical Reaction Networks to Simulate Metabolite Production: Gridprod
Takeyuki Tamura
Selective Metabolic Vulnerabilities in Multiple Myeloma
Luis Vitores Valcárcel, Iñigo Apaolaza, Xabier Agirre, Felipe Prosper, Francisco J. Planes, Raquel Ordoñez, Cem Meydan, Ari Melnick
Characterizing and Ranking Computed Metabolic Engineering Strategies
Philipp Schneider, Steffen Klamt
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
Deconvoluting Independent Regulatory Signals in the Escherichia coli Transcriptome
Anand Sastry, Bernhard O. Palsson, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu, Donghyuk Kim, Kumari Sonal Choudhary, Laurence Yang, Zachary A. King
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
New Methods to Constrain Genome Scale Models with Stable Isotope Labeling Data
Tyler Backman, David E. Ando, Jay D. Keasling, Hector Garcia Martin
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
Constraint-Based Modeling of Allelic Variation Mechanistically Links Genome-Wide Associations
Erol Kavvas
A Systematic Assessment of Current Genome-Scale Metabolic Reconstruction Tools
Sebastián N. Mendoza, Brett G. Olivier, Bas Teusink, Douwe Molenaar
An Integrated COBRA-PBPK Model to Study Interactions between the Gut Microbiome and the Brain in Autism
Meghana Palukuri, Shruti Shivakumar, Swagatika Sahoo, Raghunathan Rengaswamy
Untangling Dynamic Protein Behaviour with Rule-Based Modelling and Sensitivity Analysis
Robin Denhardt-Eriksson
Exploring Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors
Ljubisa Miskovic, Milenko Tokic, Noushin Hadadi, Meric Ataman, Dário Neves, Birgitta E. Ebert, Lars M. Blank, Vassily Hatzimanikatis
Optfill: A Novel Optimization-Based Tool to Automate the Gapfilling of Genome-Scale Metabolic Models
Wheaton Schroeder, Rajib Saha