Publications

2024

A. Aksenov, A., Blacutt, A., Ginnan, N., Rolshausen, P.E., V. Melnik, A., Lotfi, A., C. Gentry, E., Ramasamy, M., Zuniga, C., Zengler, K. and Mandadi, K.K. (2024). Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus. Scientific Reports, 14(1), 20306.

Briones-Báez, M. F., Aguilera-Vázquez, L., Rangel-Valdez, N., Zuniga, C., Martínez-Salazar, A. L., & Gomez-Santillan, C. (2024). Pitfalls in Metaheuristics Solving Stoichiometric-Based Optimization Models for Metabolic Networks. Algorithms, 17(8), 336.

Kumar, M., Tibocha-Bonilla, J.D., Füssy, Z., Lieng, C., Schwenck, S.M., Levesque, A.V., Al-Bassam, M.M., Passi, A., Neal, M., Zuniga, C. and Kaiyom, F., 2024. Mixotrophic growth of a ubiquitous marine diatom. Science Advances, 10(29), p.eado2623.

Lyu, X., Nuhu, M., Candry, P., Wolfanger, J., Betenbaugh, M., Saldivar, A., Zuniga, C., Wang, Y. and Shrestha, S. (2024). Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass. Journal of Industrial Microbiology and Biotechnology, p.kuae025.

Thumsi, A., Martínez, D., Swaminathan, S.J., Esrafili, A., Suresh, A.P., Jaggarapu, M.M.C., Lintecum, K., Halim, M., Mantri, S.V., Sleiman, Y. and Appel, N. (2024). Inverse‐Vaccines for Rheumatoid Arthritis Re‐establish Metabolic and Immunological Homeostasis in Joint Tissues. Advanced Healthcare Materials, p.2303995.

Klapper, I., Szyld, D. B., Yu, X., Zengler, K., Zhang, T., & Zuniga, C. (2024). A domain decomposition method for solution of a PDE-constrained generalized Nash equilibrium model of biofilm community metabolism. SIAM Journal on Applied Mathematics, 84(1), 97-113.

Focil, C., Canto-Encalada, G., Campos, D. T., Zuniga, C., & Zepeda, A. (2024). Applying genome-scale metabolic modeling tools to understand microbial communities in wastewater treatment. In Development in Waste Water Treatment Research and Processes (pp. 297-332). Elsevier.

Saldivar, A., Ruiz-Ruiz, P., Revah, S., & Zuniga, C. (2024). Genome-scale flux balance analysis reveals redox trade-offs in the metabolism of the thermoacidophile Methylacidiphilum fumariolicum under auto-, hetero-and methanotrophic conditions. Frontiers in Systems Biology, 4, 1291612.

2023

Canto-Encalada, G., Armstrong, J., Focil-Espinosa, C., Adekunle-Fiyin, A., Peeler, I., Gebbie, W.R., Nunez-Garcia, J., Saldivar, A., Martinez, D. and Zuniga, C. (2023). Ten quick tips for accurate reconstruction of prokaryotic and eukaryotic genome-scale Metabolic Models. Preprints.

Wang, B., Zuniga, C., Guarnieri, M. T., Zengler, K., Betenbaugh, M., & Young, J. D. (2023). Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis. Metabolic Engineering. 80 (12-24)

Tec-Campos, D., Posadas, C., Tibocha-Bonilla, J. D., Thiruppathy, D., Glonek, N., Zuñiga, C., … & Zengler, K. (2023). 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 Computational Biology, 19(8), e1011371.

Tibocha‐Bonilla, J. D., Kumar, M., Zengler, K., & Zuniga, C. (2023). Integrating Metabolic Modeling and High‐Throughput Data to Characterize Diatoms Metabolism. The Mathematical Biology of Diatoms, 165-191.

Bremer, E., Calteu, A., Danchin, A., Harwood, C., Helmann, D., Medigue, C., Palsson, B., Sekowska, A., Vallenet, D., Zuniga A., Zuniga, C. A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century. Microbial Biotechnology. 1-29.

Li, C. T., Eng, R., Zuniga, C., Huang, K. W., Chen, Y., Zengler, K., & Betenbaugh, M. J. (2023). Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control. npj Systems Biology and Applications, 9(1), 7.

2022

Tibocha-Bonilla, J. D., Zuniga, C., Lekbua, A., Lloyd, C., Rychel, K., Short, K., & Zengler, K. (2022). Predicting stress response and improved protein overproduction in Bacillus subtilis. npj Systems Biology and Applications, 8(1), 1-12.

Zuniga A., Westin C., Smith C., Souza C., Zamora R., Zuniga C. (2022). Ten simple rules for easily establishing your first professional social media page for job hunting Preprint Concept Paper.

Klapper, I., Szyld, D. B., Yu, Y., Zengler, K., Zhang, T., & Zuniga, C.(2022). A domain decomposition method for solution of a PDE-constrained generalized Nash equilibrium model of biofilm community metabolism.

Briones-Baez, M. F., Aguilera-Vazquez, L., Rangel-Valdez, N., Martinez-Salazar, A. L., Zuñiga, C. (2022). Multi-Objective Optimization of Microalgae Metabolism: An Evolutive Algorithm Based on FBA. Metabolites, 12(7), 603.

Kumar, M., Zuniga, C., Tibocha-Bonilla, J. D., Smith, S. R., Coker, J., Allen, A. E., Zengler, K. (2022). Constraint-based modeling of diatoms metabolism and quantitative biology approaches. In The Molecular Life of Diatoms (pp. 775-808). Springer, Cham.

Canto-Encalada, G., Tec-Campos, D., Tibocha-Bonilla, J. D., Zengler, K., Zepeda, A., Zuñiga, C. (2022). Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. PLOS Computational Biology, 18(2), e1009828.

Passi, A., Tibocha-Bonilla, J. D., Kumar, M., Tec-Campos, D., Zengler, K., Zuniga, C. (2022): Genome-scale metabolic modeling enables in-depth understanding of big data. Metabolites 12.1 14.

2021

Norena-Caro, D. A., Zuniga, C., Pete, A. J., Saemundsson, S. A., Donaldson, M. R., Adams, A. J., … & Benton, M. G. (2021). Analysis of the cyanobacterial amino acid metabolism with a precise genome-scale metabolic reconstruction of Anabaena sp. UTEX 2576. Biochemical Engineering Journal, 171, 108008.

Zuniga, C. … & Guarnieri, M. T. (2021). Biotechnology for secure biocontainment designs in an emerging bioeconomy. Current Opinion in Biotechnology, 71, 25-31.

Li, C. T., Trigani, K., Zuñiga, C., Eng, R., Chen, E., Zengler, K., Betenbaugh, M. J. (2021). Examining the impact of carbon dioxide levels and modulation of resulting hydrogen peroxide in Chlorella vulgaris. Algal Research, 60, 102492.

Marotz, C., Zuniga, C., Zaramela, L., Knight, R., & Zengler, K. (2021). Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics. In The Oral Microbiome (pp. 87-92). Humana, New York, NY.

Zuniga, C., Tibocha-Bonilla, J. D., Betenbaugh, M. J. (2021). Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities. Current Opinion in Biotechnology, 71, 91-97.

Zaramela, L., Moyne, O., Kumar, M., Zuniga, C., Tibocha-Bonilla J., Zengler, K (2021) The sum is greater than the parts: Exploiting microbial communities to achieve complex functions. Current Opinion in Biotechnology. 67:149–157

2020

Zuñiga, C., Peacock, B., Liang, B., McCollum, B., Irigoyen, S.,…, Zengler, K (2020) Linking metabolic phenotypes to pathogenic traits among “Candidatus Liberibacter asiaticus” and its hosts. npj Systems Biology and Applications 6 (1), 1-12.

Tibocha-Bonilla, J., Kumar, M., Richelle, A., Godoy-Silva, R., Zengler, K., Zuniga, C. (2020) Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes. npj Systems Biology and Applications. 6,1-9.

Zuñiga, C., Li, T., Guarnieri, M., Jenkins, J., Li, C., Bingol, K., Kim, K., Zengler, K (2020) Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. Nature communications 11 (1), 1-13.

Tec-Campos, D., Zuñiga, C., Passi, A., Del Toro, J., Tibocha-Bonilla, J., Zepeda, A., Zengler, K (2020) Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ. Metabolic engineering communications, 11.

Li, T., Jiang, L., Hu, Y., Paul, J. T., Zuniga, C., Zengler, K., & Betenbaugh, M. J. (2020). Creating a synthetic lichen: Mutualistic co-culture of fungi and extracellular polysaccharide-secreting cyanobacterium Nostoc PCC 7413. Algal Research, 45, 101755.

2019

Li, C-T., Yelsky, J., Chen, Y., Zuniga, C., Eng, R., Jiang, L., Shapiro, A., Huang, K-W., Zengler, K., Betenbaugh, M. (2019) Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity. npj Systems Biology and Applications. 5(1), 1-11.

Zuniga, C., Li, C-T., Yu, G., Al-Bassam, M., Li, T-T., Jiang, L., Zaramela, L., Guarnieri, M., Betenbaugh, M., Zengler, K. (2019) Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities. Nature Microbiology. 4(12), 2184-2191.

Seif, Y., Monk, J., Mih, N., Broddrick, J., Tsunemoto, H., Poudel, S., Zuniga, C., Zengler, K., Palsson, B. (2019) A computational knowledge-base elucidates the metabolic response of Staphylococcus aureus to different media types. Plos Computational Biology. 1-27.

Rule, A., Birmingham, A., Zuniga, C., Altintas, I., Huang, S., Knight, R., Moshiri, N., Nguyen, M.H., Rosenthal, S.R., Pérez, F., Rose, P. (2019) Ten simple rules for reproducible research in Jupyter Notebooks. Plos Computational Biology. 15(7).

Zaramela, L., Martino, C., Alisson-Silva, F., Rees, S., Diaz, S., Chuzel, L., Ganatra, M., Taron, C., Secrest, P., Zuniga, C., Huang, J., Siegel, D., Chang, G., Varki, A., Zengler, K. (2019) Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates. Nature Microbiology. 122(96), 1-8.

2018

Tibocha-Bonilla, J., Zuniga, C., Zengler, K. (2018) Advances in metabolic modeling of oleaginous microalgae. Biotechnology for Biofuels. 11, 241.

Muñoz, R., Soto, C., Zuniga, C., Revah, S (2018) A systematic comparison of two empirical gas-liquid mass transfer determination methodologies to characterize methane biodegradation in stirred tank bioreactors. Journal of environmental management, 217, 247-252

Marotz, C. A., Sanders, J. G., Zuniga, C., Zaramela, L. S., Knight, R., Zengler, K. (2018) Improving saliva shotgun metagenomics by chemical host DNA depletion. Microbiome, 6(1), 42.

Al-Bassam, M., Kim, J., Zaramela, L., Kellman, B., Zuniga, C., Wozniak, J., Gonzalez, D., Zengler, K. (2018) Optimization of carbon and energy utilization through differential translational efficiency. Nature communications. 9, 4474.

2017

Zuniga, C., Zaramela, L., Zengler, K. (2017) Elucidation of complexity and prediction of interactions in microbial communities. Microbial Biotechnology. 10(6):1500-1522.

Zuniga, C., Levering, J., Antoniewicz, M., Guarnieri, M., Betenbaugh, M., Zengler, K. (2017) Predicting dynamic metabolic demands in the photosynthetic eukaryote Chlorella vulgaris. Plant Physiology. 176, pp. 1–13. 

Steffani-Vallejo, J.L., Zuniga, C., Cruz-Morales, P., Lozano, L., Morales, M., Licona-Cassani, C., Revah, S., Utrilla, J. (2017) Draft genome sequence of Sphingobacterium sp. CZ-UAM, isolated from a methanotrophic consortium. Genome Announcements. 5: e00792-17.

2016

Zuniga, C., Li, C. T., Huelsman, T., Levering, J., Zielinski, D. C., McConnell, B. O, Betenbaugh, M. J. Zengler, K. (2016) Genome-scale metabolic model for the green alga Chlorella vulgaris UTEX 395 accurately predicts phenotypes under autotrophic, heterotrophic, and mixotrophic growth conditions. Plant Physiology, pp-00593.

2015

Tan, J., Zuniga, C., Zengler, K. (2015) Unraveling interactions in microbial communities – from co-cultures to microbiomes. Journal of Microbiology. 53 (5), 295-305.

2013

Zuniga, C., Morales, M., S., Revah, S. (2013) Polyhydroxyalkanoates accumulation by Methylobacterium organophilum CZ-2 during methane degradation using citrate or propionate as cosubstrates. Bioresour. Technol. 129, 686-689.

Zuniga, C., Morales, M., S., Revah S. (2013) Methane elimination and synthesis of PHAs by Methylobacterium organophilum CZ-2 using cosubstrates. Proceedings of the 5th IWA Conference on Odors and Air Emissions Jointly held with the 10th Conference on Biofiltration for Air Pollution Control, USA

2011

Zuniga, C., Morales, M., Le Borgne, S., Revah, S. (2011) Production of poly-β-hydroxybutyrate (PHB) by Methylobacterium organophilum isolated from a methanotrophic consortium in a two-phase partition bioreactor. J. Hazard. Mat. 190, 876-882.

2010

Zuniga, C., Morales, M., S., Revah (2010) Methane elimination and synthesis of poly-β-hydroxybutyrate, Proceedings of the 9th Conference of Biofiltration for Air Pollution Control, USA.