Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations by Yoon-Mi Choi, Dong-Hyuk Choi, Yi Qing Lee, Lokanand Koduru, Nathan E. Lewis, Meiyappan Lakshmanan, Dong-Yup Lee

Subjects: “…Flux balance analysis (FBA)…”
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Assumptions on decision making and environment can yield multiple steady states in microbial community models by Axel Theorell, Jörg Stelling

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Methods for integration of transcriptomic data in genome-scale metabolic models by Min Kyung Kim, Desmond S. Lun

Subjects: “…Flux balance analysis…”
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Predicting microbial interactions with approaches based on flux balance analysis: an evaluation by Clémence Joseph, Haris Zafeiropoulos, Kristel Bernaerts, Karoline Faust

Subjects: “…Flux balance analysis…”
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A Topological Characterization of Medium-Dependent Essential Metabolic Reactions by Nikolaus Sonnenschein, Carsten Marr, Marc-Thorsten Hütt

Subjects: “…flux-balance analysis…”
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A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota by David M. Versluis, Ruud Schoemaker, Ellen Looijesteijn, Daniël Muysken, Prescilla V. Jeurink, Marcel Paques, Jan M. W. Geurts, Roeland M. H. Merks

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Time-Optimal Adaptation in Metabolic Network Models by Markus A. Köbis, Alexander Bockmayr, Ralf Steuer

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Emergent cooperation in microbial metabolism by Edwin H Wintermute, Pamela A Silver

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MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota by Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio

Subjects: “…flux balance analysis…”
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MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota by Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio

Subjects: “…flux balance analysis…”
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Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells by Bruno G. Galuzzi, Marco Vanoni, Chiara Damiani

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LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism by Robert A. Dromms, Justin Y. Lee, Mark P. Styczynski

Subjects: “…Flux balance analysis…”
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Integrating Spectral Sensing and Systems Biology for Precision Viticulture: Effects of Shade Nets on Grapevine Leaves by Renan Tosin, Igor Portis, Leandro Rodrigues, Igor Gonçalves, Catarina Barbosa, Jorge Teixeira, Rafael J. Mendes, Filipe Santos, Conceição Santos, Rui Martins, Mário Cunha

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Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome by Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike K Aurich, Ronan MT Fleming

Subjects: “…flux balance analysis…”
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Reconstruction and flux‐balance analysis of the Plasmodium falciparum metabolic network by Germán Plata, Tzu‐Lin Hsiao, Kellen L Olszewski, Manuel Llinás, Dennis Vitkup

Subjects: “…flux‐balance analysis…”
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Evaluation of reaction gap-filling accuracy by randomization by Mario Latendresse, Peter D. Karp

Subjects: “…Flux balance analysis…”
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A Novel Methodology to Estimate Metabolic Flux Distributions in Constraint-Based Models by Francesco Alessandro Massucci, Isaac Pérez Castillo, Andrea De Martino, Francesc Font-Clos

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RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms by Leanne S. Whitmore, Bernard Nguyen, Ali Pinar, Anthe George, Corey M. Hudson

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Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets by David M Curran, Alexandra Grote, Nirvana Nursimulu, Adam Geber, Dennis Voronin, Drew R Jones, Elodie Ghedin, John Parkinson

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Metabolic reconstruction identifies strain‐specific regulation of virulence in Toxoplasma gondii by Carl Song, Melissa A Chiasson, Nirvana Nursimulu, Stacy S Hung, James Wasmuth, Michael E Grigg, John Parkinson

Subjects: “…flux balance analysis…”
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