Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R. by Maxwell Neal, Deepan Thiruppathy, Karsten Zengler

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Pan-genome-scale metabolic modeling of Bacillus subtilis reveals functionally distinct groups by Maxwell Neal, William Brakewood, Michael Betenbaugh, Karsten Zengler

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Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry by Kateryna Zhalnina, Karsten Zengler, Dianne Newman, Trent R. Northen

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synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing by Livia S. Zaramela, Megan Tjuanta, Oriane Moyne, Maxwell Neal, Karsten Zengler

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Microbiome Signatures in a Fast- and Slow-Progressing Gastric Cancer Murine Model and Their Contribution to Gastric Carcinogenesis by Prerna Bali, Joanna Coker, Ivonne Lozano-Pope, Karsten Zengler, Marygorret Obonyo

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Advances in metabolic modeling of oleaginous microalgae by Juan D. Tibocha-Bonilla, Cristal Zuñiga, Rubén D. Godoy-Silva, Karsten Zengler

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Deciphering metabolic differentiation during Bacillus subtilis sporulation by Juan D. Tibocha-Bonilla, Jelani Lyda, Eammon Riley, Kit Pogliano, Karsten Zengler

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Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO₂ Levels by Jennifer Levering, Christopher L. Dupont, Andrew E. Allen, Bernhard O. Palsson, Karsten Zengler

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ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization by Gustavo Tamasco, Manish Kumar, Karsten Zengler, Rafael Silva-Rocha, Ricardo Roberto da Silva

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Improving saliva shotgun metagenomics by chemical host DNA depletion by Clarisse A. Marotz, Jon G. Sanders, Cristal Zuniga, Livia S. Zaramela, Rob Knight, Karsten Zengler

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Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers by Deepan Thiruppathy, Oriane Moyne, Clarisse Marotz, Michael Williams, Perris Navarro, Livia Zaramela, Karsten Zengler

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Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load by Clarisse Marotz, James T. Morton, Perris Navarro, Joanna Coker, Pedro Belda-Ferre, Rob Knight, Karsten Zengler

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A streamlined ribosome profiling protocol for the characterization of microorganisms by Haythem Latif, Richard Szubin, Justin Tan, Elizabeth Brunk, Anna Lechner, Karsten Zengler, Bernhard O. Palsson

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Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data by Anurag Passi, Juan D. Tibocha-Bonilla, Manish Kumar, Diego Tec-Campos, Karsten Zengler, Cristal Zuniga

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Establishing microbial composition measurement standards with reference frames by James T. Morton, Clarisse Marotz, Alex Washburne, Justin Silverman, Livia S. Zaramela, Anna Edlund, Karsten Zengler, Rob Knight

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Predicting stress response and improved protein overproduction in Bacillus subtilis by Juan D. Tibocha-Bonilla, Cristal Zuñiga, Asama Lekbua, Colton Lloyd, Kevin Rychel, Katie Short, Karsten Zengler

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A Novel Sparse Compositional Technique Reveals Microbial Perturbations by Cameron Martino, James T. Morton, Clarisse A. Marotz, Luke R. Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler

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A Novel Sparse Compositional Technique Reveals Microbial Perturbations by Cameron Martino, James T. Morton, Clarisse A. Marotz, Luke R. Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler

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Determining the control circuitry of redox metabolism at the genome-scale. by Stephen Federowicz, Donghyuk Kim, Ali Ebrahim, Joshua Lerman, Harish Nagarajan, Byung-kwan Cho, Karsten Zengler, Bernhard Palsson

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Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control by Chien-Ting Li, Richard Eng, Cristal Zuniga, Kai-Wen Huang, Yiqun Chen, Karsten Zengler, Michael J. Betenbaugh

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