A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Ines Thiele; Daniel R. Hyduke; Benjamin Steeb; Guy Fankam; Douglas K. Allen; Susanna Bazzani; Pep Charusanti; Feng-Chi Chen; Ronan M. T. Fleming; Chao A. Hsiung; Sigrid C. J. De Keersmaecker; Yu-Chieh Liao; et al. (BMC Syst. Biol., 2011)

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. - Joanne K. Liu; Edward J. O'Brien; Joshua A. Lerman; Karsten Zengler; Bernhard O. Palsson; Adam M. Feist (BMC Syst. Biol., 2014)

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens. - Adam M. Feist; Harish Nagarajan; Amelia-Elena Rotaru; Pier-Luc Tremblay; Tian Zhang 004; Kelly P. Nevin; Derek R. Lovley; Karsten Zengler (PLoS Comput. Biol., 2014)

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. - Joanne K. Liu; Colton J. Lloyd; Mahmoud M. Al-Bassam; Ali Ebrahim; Ji-Nu Kim; Connor A. Olson; Alexander Aksenov; Pieter C. Dorrestein; Karsten Zengler (PLoS Comput. Biol., 2019)

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. - Yara Seif; Jonathan M. Monk; Nathan Mih; Hannah Tsunemoto; Saugat Poudel; Cristal Zuñiga; Jared Broddrick; Karsten Zengler; Bernhard O. Palsson (PLoS Comput. Biol., 2019)

ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization. - Gustavo Tamasco; Manish Kumar; Karsten Zengler; Rafael Silva-Rocha; Ricardo Roberto da Silva (BMC Bioinform., 2022)

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. - Gabriela Canto-Encalada; Diego Tec-Campos; Juan D. Tibocha-Bonilla; Karsten Zengler; Alejandro Zepeda; Cristal Zuñiga (PLoS Comput. Biol., 2022)

The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions. - Diego Tec-Campos; Camila Posadas; Juan D. Tibocha-Bonilla; Deepan Thiruppathy; Nathan Glonek; Cristal Zuñiga; Alejandro Zepeda; Karsten Zengler (PLoS Comput. Biol., 2023)

Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R. - Maxwell Neal; Deepan Thiruppathy; Karsten Zengler (PLoS Comput. Biol., 2023)

A Domain Decomposition Method for Solution of a PDE-Constrained Generalized Nash Equilibrium Model of Biofilm Community Metabolism. - Isaac Klapper; Daniel B. Szyld; Xinli Yu; Karsten Zengler; Tianyu Zhang; Cristal Zuñiga (SIAM J. Appl. Math., 2024)

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers. - Diego Tec-Campos; Juan D. Tibocha-Bonilla; Celina Jiang; Anurag Passi; Deepan Thiruppathy; Cristal Zuñiga; Camila Posadas; Alejandro Zepeda; Karsten Zengler (PLoS Comput. Biol., 2025)