Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R.

by Maxwell Neal, Deepan Thiruppathy, Karsten Zengler
Published 2023-10-01

Elucidation of complexity and prediction of interactions in microbial communities

by Cristal Zuñiga, Livia Zaramela, Karsten Zengler
Published 2017-11-01

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
Published 2018-09-01

Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health

by Joanna K Coker, Oriane Moyne, Dmitry A. Rodionov, Karsten Zengler
Published 2021-01-01

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
Published 2022-12-01

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
Published 2021-01-01

Advances in metabolic modeling of oleaginous microalgae

by Juan D. Tibocha-Bonilla, Cristal Zuñiga, Rubén D. Godoy-Silva, Karsten Zengler
Published 2018-09-01

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
Published 2022-11-01

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
Published 2017-02-01

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
Published 2018-02-01

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
Published 2021-12-01

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
Published 2015-06-01

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
Published 2021-02-01

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds.

by Gabriela Canto-Encalada, Diego Tec-Campos, Juan D Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, Cristal Zuñiga
Published 2022-02-01

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
Published 2019-02-01

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
Published 2022-12-01

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
Published 2019-06-01

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.

by Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, Jose Utrilla, Karsten Zengler, Bernhard O Palsson
Published 2018-01-01

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
Published 2023-03-01

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
Published 2014-04-01