Poster Session II

Friday, September 18, 2015: 1:30 PM
Crowne Plaza Heidelberg City Centre
Description:
Poster Session II


Redgem: A Novel Approach for Systematic Reduction of Genome-Scale Models
Meric Ataman

Systems Biology of a Complete, Defined Gut Microbiome
Greg Medlock, Matthew Biggs, Glynis Kolling, Mikko Arvas, Jonathan Swann and Jason Papin

A Reconciled Genome-Scale MODEL of the Malaria Parasite Plasmodium Falciparum – Reconstruction and Thermodynamics-Based Flux Balance Analysis
Anush Chiappino Pepe

ATM-FBA: Automatic Thresholding to Minimize Deviation Between Flux State and Gene Expression State
Abdelmoneim Amer Desouki, Gabriel Gelius-Dietrich and Martin J. Lercher

Constraint-Based Analysis of Genetic Variation Effects in Escherichia coli after Adaptive Laboratory Evolution
Kristian Jensen, João G.R. Cardoso, Markus J. Herrgård, Mikael R. Andersen and Nikolaus Sonnenschein

ME 2.0: A Computational Framework for Constructing and Simulating Genome-Scale Models of Metabolism and Expression
Ali Ebrahim, Colton J. Lloyd, Laurence Yang and Bernhard O. Palsson

A Study of Dynamic Responses of E. coli Metabolism upon Large Perturbations Using Large-Scale Kinetic Models
Milenko Tokic, Geogios Fengos, Ljubisa Miskovic and Vassily Hatzimanikatis

Model-Driven Design and Analysis of Synthetic Auxotrophs and Their Predicted Metabolite Cross-Feeding in Co-Culture
Colton J. Lloyd, Zachary A. King, Edward J. OBrien and Adam M. Feist

Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories
João G.R. Cardoso, Kristian Jensen, Emre Özdemir, Markus J. Herrgård and Nikolaus Sonnenschein

A Novel Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Large-Scale and Genome-Scale Metabolic Networks
Stefano Andreozzi, Ljubisa Miskovic and Vassily Hatzimanikatis

Identification of Potential Cancer Therapy Target Genes through Synthetic Interaction Analyses
Bushra Dohai, Amphun Chaiboonchoe, Rediet Demissie, Ibrahim Chehade, Basel Khraiwesh, Rana Al Assah and Kourosh Salehi-Ashtiani

Integrating Expression Profiles into a Constraint Based Model to Infer the Carbon Source of a Micro-Organism
Rainer König, Franziska Hörhold, Joao Saraiva and Marcus Oswald

Metabolic Network Percolation Provides Insight into Microbial Fastidiousness
David Bernstein and Daniel Segrè

Robust Prediction of Minimal Medium Composition Using Sparse Optimization
Fatima Monteiro, Tangi Migot, Hoai Minh Le, Edinson Lucumi Moreno, Ines Thiele, Thomas Hankemeier and Ronan Fleming

Exploring in silico Metabolic Phenotypes with a Genome-Scale Model of Mycobacterium Tuberculosis
Victor A. Lopez-Agudelo, Howard Ramirez-Malule, Silvia Ochoa, Luis F. Barrera, Andres Baena and Rigoberto Rios

Generation and Use of a Genome-Scale Model to Describe Metabolic Shift in CHO Cells
Natalia E. Jiménez, Nicolas Loira and Ziomara P. Gerdtzen

Improving Metabolite Annotation through a New Generation of Parsing Tools for Genome-Scale Modeling
Dimitra Lappa, Benjamín J. Sánchez and Jens Nielsen

Investigating the Warburg Effect Using a Core Metabolic Network with Kinetic Parameters
Avlant Nilsson, Adil Mardinoglu and Jens Nielsen

Study on How Underlying Uncertainty in the Flux Values Affects Metabolic Control Analysis of Optimally Grown E. coli
Tuure Hameri, Geogios Fengos, Meric Ataman, Ljubisa Miskovic and Vassily Hatzimanikatis

Biochemical Systems Analysis of the Epithelial to Mesenchymal Transition
Óttar Rolfsson, Neha Rohatgi, Sonal Kumari, Magnus K. Magnussson, Thorarinn Gudjonsson, Steinn Gudmundsson and Skarphéðinn Halldórsson

Genome-Scale Reconstruction of C. Elegans Metabolism and Its Application to Age Research
Juliane Gebauer and Christoph Kaleta

Impact of Dietary Carbohydrate: Lipid Ratio on Metabolism in Murine Small Intestinal Epithelial Cells
Neeraj Sinha, Maria Suarez Diez, Evert Van Schothorst and Guido Hooiveld

A Refined Genome-Scale Reconstruction of Chlamydomonas Metabolism
Saheed Imam, Sascha Schäuble, Jake Valenzuela, Adrián L. G. de Lomana, Warren Carter, Nathan D. Price and Nitin Baliga

A Generalized Framework for Targeted 13C Metabolic Flux Ratio Analysis
Maria Kogadeeva, Uwe Sauer and Nicola Zamboni

Systematic Analysis of the Metabolic Interactions in a Model Gut Microbiota Community and Its Impact on Host Metabolism
Almut Heinken and Ines Thiele

Parameterizing Genome-Scale Models Using Proteomic Data Enables Prediction of Gene Expression
Ali Ebrahim, Edward J. O'Brien, Donghyuk Kim, Joshua A. Lerman, Aarash Bordbar, Adam M. Feist and Bernhard O. Palsson

Integrating Transcriptomic Data with Thermodynamically Consistent Metabolic Models
Daniel F. Hernandez Gardiol, Vikash Pandey and Vassily Hatzimanikatis

Study of the Effects of Alternative Fluxes on the Metabolic Control Analysis of Optimally Grown E. coli
Geogios Fengos, Daniel Hernandez, Tuure Hameri, Meric Ataman, Ljubisa Miskovic and Vassily Hatzimanikatis

The Severity of an Enzyme Mutation Strongly Influences Pleiotropy, Often Mediated through Currency Metabolite Production
Deya Alzoubi and Martin J. Lercher

Generation of a Genome-Scale Metabolic Model of Ustilago Maydis, Causative Agent of Corn Smut
Christian Lieven, Thiemo Zambanini, Nick Wierckx and Lars M. Blank

The Landscape of Metabolic Interactions in Human Gut Ecosystem
Boyang JI and Jens Nielsen

Reconstruction of a Context-Specific Metabolic Model of Epithelial to Mesenchymal Transition
Neha Rohatgi, Steinn Gudmundsson, Skarphéðinn Halldórsson and Óttar Rolfsson

Expanding a Yeast Genome Scale Model to Account for Enzymatic Limitations
Benjamín J. Sánchez, Cheng Zhang, Petri-Jaan Lahtvee and Jens Nielsen

Deciphering the Restriction and the Mobilisation of Phenotypic Robustness By the Virulence Regulatory Network in the Plant Pathogen Ralstonia Solanacearum Using Hybrid Genome-Scale Modelling
Rémi Peyraud, Ludovic Cottret, Lucas Marmiesse, Jerome Gouzy and Stephane Genin

Prediction of a Shared Enzymatic Machinery Between Parkinson's Disease Selectively Vulnerable Neurons
Miguel A.P. Oliveira, Longfei Mao and Ronan M.T. Fleming

Charting Metabolic Interactions in Microbial Communities
Aleksej Zelezniak, Sergej Andrejev, Olga Ponomarova, Daniel R. Mende, Peer Bork and Kiran Patil

Globalfit: Refining Metabolic Networks By Simultaneously Matching Growth and Non-Growth Data Sets
Daniel Hartleb and Martin J. Lercher

Identifying Engineering Targets from Transcriptomic Data Using Genome-Scale Metabolic Model
Minsuk Kim, Jeong Sang Yi and Byung-Gee Kim

Yeastscent – Exploring the Volatile Metabolite Space of Saccharomyces Cerevisiae
Birgitta E. Ebert, Christoph Halbfeld and Lars M. Blank

Enhanced Metabolic Discovery Using Enzyme Family Inference and Approximate Bayesian Computation
William A. Bryant, John W. Pinney and Michael J.E. Sternberg

Evaluation of Metabolic Engineering Strategies for Production of a Large Panel of Chemicals
Anne Sofie L. Hansen, MIguel A. Campodonico, Markus J. Herrgård and Nikolaus Sonnenschein

Integration of Rnaseq Data in iFA762 Model Provides Insight into the Ectoines Metabolism of the Halophilic Bacteria Chromohalobacter Salexigens
Francine Piubeli, Montserrat Argandoña, Manuel Salvador, Carmen Vargas and Joaquín Nieto

In silico Analysis and Model-Driven Optimization of the Biodesulfurization Process in Pseudomonas Putida
Igor Martinez, José Luis García, Juan Nogales and Eduardo Díaz

Harnessing the Landscape of Cultivable Bacterial Growth for Predicting New Organism-Growth Media Pairings
Raphy Zarecki, Matthew A. Oberhardt, Sabine Gronow, Elke Lang, Hans-Peter Klenk, Uri Gophna and Eytan Ruppin

Constrains-Based De-Composition of the Metabolic Robustness in Bacteria
Juan Nogales, Steinn Gudmundsson, Juan Luis Ramos, Eduardo Díaz and Bernhard Palsson

Integration of Transcriptomic Data and Metabolic Models for Expression-Informed Flux-Balance Analysis
Matthew DeJongh, Aaron Best, Nathan Tintle and Christopher S. Henry

Genome-Scale Model Driven Characterization of the Effect of Single Nucleotide Polymorphisms on Erythrocyte Metabolism
Nathan Mih, Elizabeth Brunk, Aarash Bordbar and Bernhard O. Palsson

Genome-Scale Model for a Marine Diatom with Distinct Evolutionary Footprint
Jennifer Levering, Jared T. Broddrick, Alessandra A. Gallina, Christopher L. Dupont, Andrew E. Allen, Bernhard Ø. Palsson and Karsten Zengler

A Novel Reconstruction Pipeline for Genome-Based Network Models Using High Quality Reference Networks
Patrick Schlossbauer, Joachim W. Schmid, Michael Rempel, Dirk Mueller, Sophia Bongard and Klaus Mauch

Assessing the Reliability of Genome-Scale Metabolic Models in the Prediction of Gene Knockout Phenotypes
Helder Lopes, Paulo Maia, Kiran Patil and Isabel Rocha

Comparing Knockout Strategies from in silico Rational Strain Design Tools
Vítor Vieira, Paulo Maia, Miguel Rocha and Isabel Rocha

Using Genome-Scale Metabolic Modeling to Compare Serotypes of the Foodborne Pathogen Listeria Monocytogenes
David Baumler and Zachary Metz

A Bi-Level Integration Algorithm for Simultaneous Modeling of Multiple Cells
Elham Taheri, Ehsan Motamedian and Fatemeh Bagheri

System-Level Analysis of Phototrophic Metabolism in Rhodopseudomonas Palustris Reveals That Proton Metabolism Affects Metabolic Efficiency and Hydrogen Production
Ali Navid, Yongqin Jiao and Jennifer Pett-Ridge

Reconstruction of Metabolic Models and Prediction of Flux Profile for Complex Electrosynthetic Microbial Community Based on Metatranscriptome Data
Janaka N. Edirisinghe, Chris Marshall, Pamela Weisenhorn, Hal May, Jack Gilbert and Christopher S. Henry

Impact of Diet on Growth and Maintenance of Adipocytes, Myocytes and Hepatocytes in Infants
Partho Sarathi Sen, Adil Mardinoglu and Jens Nielsen

Do Genome-Scale Models Need Exact Solvers or Clearer Standards?
Ali Ebrahim

The Metabolomics Toolbox (MetTB): Analysis of Extracellular Metabolomic Data in the Context of the Metabolic Model
Maike K. Aurich and Ines Thiele

Reconstruction of Regulatory Network Models and Reconciliation with Gene Expression Data
José P. Faria, Ross Overbeek, Ronald C. Taylor, Neal Conrad, Veronika Vonstein, Svetlana Gerdes, Anne Goelzer, Vincent Fromion, Miguel Rocha, Isabel Rocha and Christopher S. Henry

Modelseed 2.0: A Next Generation Resource for Automated Model Reconstruction, Comparison, and Analysis
Neal Conrad, Janaka N. Edirisinghe, José P. Faria, Sam Seaver, Michael Mundy, Nicholas Chia and Christopher S. Henry

Modelling Growth of Mycobacterium Tuberculosis Under Low-Iron Conditions
Andre Voigt and Eivind Almaas

Multi-Scale Model of the Gastrointestinal Tract
Marouen BEN Guebila

Bacarena: Individual Based Metabolic Analysis of Cellular Communities in Their Environments
Eugen Bauer

A Genome-Scale Metabolic Network Reconstruction of the Thermophilic Bacterium Rhodothermus Marinus DSM 4252
Steinn Gudmundsson, Þórdís Kristjánsdóttir, Snædís Björnsdóttir, Edda Olgudóttir, Birkir Reynisson, Ólafur Fridjónsson, Gudmundur Hreggvigsson and Sigurdur Brynjolfsson

Towards a Genome-Scale Metabolic Model of the Streptococcus Pneumoniae R6 Avirulent Strain
Oscar Dias, João Saraiva, Eugénio Ferreira and Isabel Rocha

Global Characterization of in Vivo Enzyme Catalytic Rates and Their Correspondence to in Vitro Kcat Measurements
Dan Davidi, Arren Bar-Even, Wolfram Liebermeister, Avi Flamholz, Katja Tummler, Miki Goldenfeld, Tomer Shlomi, Dan Tawfik, Elad Noor and Ron Milo

Virtual Metabolic Human: a comprehensive metabolic resource of human, human associated microbes and disease
Alberto Noronha, Ana Correia, Yohan Jarosz, Hulda Haraldsdottir, Piotr Gawron, Eugen Bauer, Almut Heinken, Stefania Magnusdottir, Swagatika Sahoo, Reinhard Schneider, Ronan Mt Fleming and Ines Thiele

Conditions for duality between fluxes and concentrationsin biochemical networks
Ronan Fleming, Ines Thiele and Nikos Vlassis

Metabolic Network-Guided Binning of Metagenomic Sequence Fragments - Poster
Matthew Biggs and Jason A. Papin

Modeling the Secondary Metabolism of the Penicillium Genus
Jens Christian Nielsen, Sylvain Prigent, Sietske Grijseels, Mhairi Workman and Jens Nielsen

Reconciled Rat and Human Metabolic Reconstructions for Comparative Toxicogenomics Analyses
Edik Blais, Kristopher Rawls, Zhuo Li, Glynis Kolling, Ping Ye, Ander Wallqvist and Jason A. Papin
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