Embedded Files
Preprints
Alexis E., Espinel-Ríos, S., Laurenti L., Cardelli L., Kevrekidis, I.G., Rowley C.W., Avalos J.L., 2026. Noise analysis of derivative-action biomolecular topologies. bioRxiv: https://doi.org/10.64898/2026.05.06.723344.
Espinel-Ríos, S., 2025. Switching-time bioprocess control with pulse-width-modulated optogenetics. arXiv: https://doi.org/10.48550/arXiv.2511.22893. Accepted at the 23rd IFAC World Congress to be held in Busan, Republic of Korea (August 23-28, 2026).
Peer-reviewed journal articles
Espinel-Ríos, S., Walser, R., Zhang, D., 2026. Reinforcement learning for robust dynamic metabolic control. Biotechnology and Bioengineering. https://doi.org/10.1002/bit.70077
Espinel-Ríos, S., Avalos, J.L., Chanona, E.A. del R., Zhang, D., 2025. Reinforcement learning for efficient and robust multi-setpoint and multi-trajectory tracking in bioprocesses. Computers & Chemical Engineering. https://doi.org/10.1016/j.compchemeng.2025.109297
Hoffman, S.M., Espinel‐Ríos, S., Kwartler, S.K., Lalwani, M.A., Avalos, J.L., 2025. Balancing doses of EL222 and light improves optogenetic induction of protein production in Komagataella phaffii. Biotechnology and Bioengineering. https://doi.org/10.1002/bit.29027
Espinel-Ríos, S., 2025. Biotechnology systems engineering: preparing the next generation of bioengineers. Frontiers in Systems Biology. https://doi.org/10.3389/fsysb.2025.1583534
Alexis, E., Espinel-Ríos, S., Kevrekidis, I.G., Avalos, J.L., 2025. Biochemical implementation of acceleration sensing and PIDA control. npj Systems Biology and Applications. https://doi.org/10.1038/s41540-025-00514-0
Espinel-Ríos, S., Montaño López, J., Avalos, J.L., 2025. Omics-driven hybrid dynamic modeling of bioprocesses with uncertainty estimation. Biochemical Engineering Journal. https://doi.org/10.1016/j.bej.2025.109637
Pennington, O., Espinel Ríos, S., Sebastian, M.T., Dickson, A., Zhang, D., 2024. A multiscale hybrid modelling methodology for cell cultures enabled by enzyme-constrained dynamic metabolic flux analysis under uncertainty. Metabolic Engineering. https://doi.org/10.1016/j.ymben.2024.10.013
Espinel-Ríos, S., Avalos, J.L., 2024. Hybrid physics-informed metabolic cybergenetics: process rates augmented with machine-learning surrogates informed by flux balance analysis. Industrial & Engineering Chemistry Research. https://doi.org/10.1021/acs.iecr.4c00001
Espinel-Ríos, S., Behrendt, G., Bauer, J., Morabito, B., Pohlodek, J., Schütze, A., Findeisen, R., Bettenbrock, K., Klamt, S., 2024. Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. Process Biochemistry. https://doi.org/10.1016/j.procbio.2024.04.032
Espinel‐Ríos, S., Morabito, B., Pohlodek, J., Bettenbrock, K., Klamt, S., Findeisen, R., 2023. Toward a modeling, optimization, and predictive control framework for fed‐batch metabolic cybergenetics. Biotechnology and Bioengineering. https://doi.org/10.1002/bit.28575
Boecker, S., Espinel-Ríos, S., Bettenbrock, K., Klamt, S., 2022. Enabling anaerobic growth of Escherichia coli on glycerol in defined minimal medium using acetate as redox sink. Metabolic Engineering. https://doi.org/10.1016/j.ymben.2022.05.006
Espinel‐Ríos, S., Bettenbrock, K., Klamt, S., Findeisen, R., 2022. Maximizing batch fermentation efficiency by constrained model‐based optimization and predictive control of adenosine triphosphate turnover. AIChE Journal. https://doi.org/10.1002/aic.17555
Espinel-Ríos, S., Ruiz-Espinoza, J.E., 2018. Production of 1,3-propanediol from crude glycerol: bioprocess design and profitability analysis. Revista Mexicana de Ingeniería Química. https://doi.org/10.24275/uam/izt/dcbi/revmexingquim/2019v18n3/espinel
Espinel-Ríos, S., Palmerín-Carreño, D.M., Hernández-Orihuela, A.L., Martínez-Antonio, A., 2018. A Plackett-Burman design for substituting MRS medium components with avocado seed hydrolysate for growth and lactic acid production by Lactobacillus sp. Revista Mexicana de Ingeniería Química. https://doi.org/10.24275/uam/izt/dcbi/revmexingquim/2019v18n1/espinel
Gao, W., Tabil, L.G., Dumonceaux, T., Espinel Ríos, S., Zhao, R., 2017. Optimization of biological pretreatment to enhance the quality of wheat straw pellets. Biomass and Bioenergy. https://doi.org/10.1016/j.biombioe.2016.12.012
Peer-reviewed conference articles
Espinel-Ríos, S., Mo, J.Q., Zhang, D., del Rio-Chanona, E.A., Avalos, J.L., 2024. Enhancing reinforcement learning for population setpoint tracking in co-cultures. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2025.07.122
Espinel-Ríos, S., Avalos, J.L., 2024. Linking intra- and extra-cellular metabolic domains via neural-network surrogates for dynamic metabolic control. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2024.10.020
Pennington, O., Espinel-Ríos, S., Sebastian, M.T., Dickson, A., Zhang, D., 2024. Dynamic multiscale hybrid modelling of a CHO cell system for recombinant protein production. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2024.08.326
Espinel-Ríos, S., Kok, R., Klamt, S., Avalos, J.L., Findeisen, R., 2023. Batch-to-batch optimization with model adaptation leveraging Gaussian processes: the case of optogenetically assisted microbial consortia. IEEE Xplore. https://doi.org/10.23919/iccas59377.2023.10316811
Espinel-Ríos, S., Bettenbrock, K., Klamt, S., Avalos, J.L., Findeisen, R., 2023. Machine learning-supported cybergenetic modeling, optimization and control for synthetic microbial communities. Computer Aided Process Engineering. https://doi.org/10.1016/b978-0-443-15274-0.50413-3
Espinel-Ríos, S., Slaviero, G., Bettenbrock, K., Klamt, S., Findeisen, R., 2023. Monitoring intracellular metabolite concentrations by moving horizon estimation based on kinetic modeling. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2023.10.968
Espinel-Ríos, S., Huber, N., Alcalá-Orozco, E.A., Morabito, B., Rexer, T.F.T., Reichl, U., Klamt, S., Findeisen, R., 2022. Cell-free biosynthesis meets dynamic optimization and control: a fed-batch framework. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2023.01.021
Espinel-Ríos, S., Morabito, B., Pohlodek, J., Bettenbrock, K., Klamt, S., Findeisen, R., 2022. Optimal control and dynamic modulation of the ATPase gene expression for enforced ATP wasting in batch fermentations. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2022.07.440
Espinel-Ríos, S., Morabito, B., Bettenbrock, K., Klamt, S., Findeisen, R., 2022. Soft sensor for monitoring dynamic changes in cell composition. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2023.01.022
Morabito, B., Pohlodek, J., Kranert, L., Espinel-Ríos, S., Findeisen, R., 2022. Efficient and simple Gaussian process supported stochastic model predictive control for bioreactors using HILO-MPC. IFAC-PapersOnLine. https://doi.org/10.1016/j.ifacol.2022.07.562
Patents
Avalos, J. L., Hoffman, S. M., Espinel-Ríos, S., 2025. Optogenetic production of recombinant protein in Pichia pastoris. https://patents.google.com/patent/WO2025240129A2/en
Martínez-Antonio, A., Minchaca-Acosta, A. Z., Hernández-Orihuela, A. L., Rosales-Colunga, L. M., Estévez-Palmas, J. M., Espinel-Ríos, S., 2016. Culture medium derived from avocado seed material. https://patents.google.com/patent/WO2016079568A1/en
Conference abstracts
Jaewan J., Emmanouil A., Espinel-Rios, S., Avalos, J., 2025. Dynamic control of co-culture population using optogenetics. Metabolic Engineering 16, AIChE. https://aiche.confex.com/aiche/me16/meetingapp.cgi/Paper/710565
Avalos, J.L., Hoffman, S.M., Espinel‐Ríos, S., Lalwani, M., 2024. Optogenetic control of protein production in Pichia pastoris replaces methanol induction with light. Biochemical and Molecular Engineering XXIII. https://dc.engconfintl.org/biochem_xxiii/100/
Gao, W., Tabil, L.G., Zhao, R., Espinel Ríos, S., Dumonceaux, T., 2016. Enhancing the physical quality of barley straw pellets by optimizing biological pretreatment. ASABE International Meeting. American Society of Agricultural and Biological Engineers. https://doi.org/10.13031/aim.20162447920
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