Karsten Zengler

11 papers Journal 11

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers. PLoS Comput. Biol. Diego Tec-Campos, Juan D. Tibocha-Bonilla, Celina Jiang, Anurag Passi, Deepan Thiruppathy, Cristal Zuñiga, Camila Posadas, Alejandro Zepeda, Karsten Zengler
2024	J	`jnl`	A Domain Decomposition Method for Solution of a PDE-Constrained Generalized Nash Equilibrium Model of Biofilm Community Metabolism. SIAM J. Appl. Math. Isaac Klapper, Daniel B. Szyld, Xinli Yu, Karsten Zengler, Tianyu Zhang, Cristal Zuñiga
2023	J	`jnl`	Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R. PLoS Comput. Biol. Maxwell Neal, Deepan Thiruppathy, Karsten Zengler
2023	J	`jnl`	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. PLoS Comput. Biol. Diego Tec-Campos, Camila Posadas, Juan D. Tibocha-Bonilla, Deepan Thiruppathy, Nathan Glonek, Cristal Zuñiga, Alejandro Zepeda, Karsten Zengler
2022	J	`jnl`	ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization. BMC Bioinform. Gustavo Tamasco, Manish Kumar, Karsten Zengler, Rafael Silva-Rocha, Ricardo Roberto da Silva
2022	J	`jnl`	Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. PLoS Comput. Biol. Gabriela Canto-Encalada, Diego Tec-Campos, Juan D. Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, Cristal Zuñiga
2019	J	`jnl`	A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput. Biol. Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared Broddrick, Karsten Zengler, Bernhard O. Palsson
2019	J	`jnl`	Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLoS Comput. Biol. 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
2014	J	`jnl`	Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in PLoS Comput. Biol. Adam M. Feist, Harish Nagarajan, Amelia-Elena Rotaru, Pier-Luc Tremblay, Tian Zhang, Kelly P. Nevin, Derek R. Lovley, Karsten Zengler
2014	J	`jnl`	Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. BMC Syst. Biol. Joanne K. Liu, Edward J. O'Brien, Joshua A. Lerman, Karsten Zengler, Bernhard O. Palsson, Adam M. Feist
2011	J	`jnl`	A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 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, Kathleen Marchal, Monica L. Mo, Emre Özdemir, Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Sara Sigurbjörnsdóttir, Jonas Steinmann, Suresh Sudarsan, Neil Swainston, Inge M. Thijs, Karsten Zengler, Bernhard O. Palsson, Joshua N. Adkins, Dirk Bumann