2025
Tang, Allison Y. et al. “Anti-Pdc1p Nanobody As a Genetically Encoded Inhibitor of Ethanol Production Enables Dual Transcriptional and Post-Translational Controls of Yeast Fermentations.” (2025): n. pag.
Lee, Dongheon et al. “Principles of Metabolic Pathway Control by Biomolecular Condensates in Cells.” (2025): n. pag.
González, Lidice et al. “HP1-Enhanced Chromatin Compaction Stabilizes a Synthetic Metabolic Circuit in Yeast.” bioRxiv (2025): n. pag.
Kichuk, Therese, and José L. Avalos. “Shape Matters: The Utility and Analysis of Altered Yeast Mitochondrial Morphology in Health, Disease, and Biotechnology.” (2025): n. pag.
Espinel-Ríos, Sebastián, José Montaño López, and José L Avalos. “Omics-Driven Hybrid Dynamic Modeling of Bioprocesses With Uncertainty Estimation.” (2025): n. pag.
Hoffman, Shannon M. et al. “Balancing Doses of EL222 and Light Improves Optogenetic Induction of Protein Production in Komagataella Phaffii.” bioRxiv (2025): n. pag.
2024
Wegner, Scott A., Hahn Kim, and José L. Avalos. “Optogenetic Screening of MCT1 Activity Implicates a Cluster of Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) As Inhibitors of Lactate Transport.” PLOS ONE (2024): n. pag.
Lee, Dongheon et al. “Principles of Metabolic Pathway Control By Biomolecular Condensates in Cells.” (2024): n. pag.
Siu, Ka-Hei, and Jose Avalos. “Engineering Cellular Processes through Synthetic Membrane-Associated Biomolecular Condensates.” (2024): n. pag.
Tang, Allison, and José Avalos. “Optogenetic Control of Enzyme Degradation for Metabolic Pathway Tunability.” (2024): n. pag.
Espinel-Ríos, Sebastián et al. “Enhancing Reinforcement Learning for Population Setpoint Tracking in Co-Cultures.” (2024): n. pag.
Tang, Allison Y et al. “Light-Induced Nanobody-Mediated Targeted Protein Degradation for Metabolic Flux Control.” (2024): n. pag.
Espinel-Ríos, Sebastián, José Montaño López, and José L Avalos. “Omics-Driven Hybrid Dynamic Modeling of Bioprocesses With Uncertainty Estimation.” arXiv (2024): n. pag.
Wegner, Scott A, and José L Avalos. “Mevalonate Secretion Is Not Mediated by a Singular Non-Essential Transporter in Saccharomyces Cerevisiae..” Biotechnology Notes (2024): n. pag. Print.
Alexis, Emmanouil et al. “Biochemical Implementation of Acceleration Sensing and PIDA Control.” bioRxiv (2024): n. pag.
Alexis, Emmanouil et al. “AC-BioSD: A Biomolecular Signal Differentiator Module With Enhanced Performance.” IEEE Control Systems Letters (2024): n. pag.
Espinel-Ríos, Sebastián, and José L Avalos. “Hybrid Physics-Informed Metabolic Cybergenetics: Process Rates Augmented With Machine-Learning Surrogates Informed by Flux Balance Analysis.” Industrial & Engineering Chemistry Research (2024): n. pag.
Rana, Ushnish et al. “Asymmetric Oligomerization State and Sequence Patterning Can Tune Multiphase Condensate Miscibility.” Nature Chemistry (2024): n. pag.
Alexis, Emmanouil et al. “AC-BioSD : A Biomolecular Signal Differentiator Module With Enhanced Performance.” bioRxiv (2024): n. pag.
Kichuk, Therese et al. “Using MitER for 3D Analysis of Mitochondrial Morphology and ER Contacts.” Cell Reports Methods (2024): n. pag.
Espinel-Ríos, Sebastián, and José L Avalos. “Hybrid Physics-Informed Metabolic Cybergenetics: Process Rates Augmented With Machine-Learning Surrogates Informed by Flux Balance Analysis.” arXiv (2024): n. pag.
2023
Malani, Saurabh et al. “Some of the Variables, Some of the Parameters, Some of the Times, With Some Physics Known: Identification With Partial Information.” arXiv (2023): n. pag.
Espinel-Ríos, Sebastián, and José L Avalos. “Linking Intra-and Extra-Cellular Metabolic Domains via Neural-Network Surrogates for Dynamic Metabolic Control.” arXiv (2023): n. pag.
Walls, Mackenzie T et al. “A Modular Design for Synthetic Membraneless Organelles Enables Compositional and Functional Control.” bioRxiv (2023): n. pag.
Rana, Ushnish et al. “Oligomerization and Sequence Patterning Can Tune Multiphasic Condensate Miscibility.” Biophysical Journal (2023): n. pag.
Espinel-Ríos, Sebastián et al. “Machine Learning-Supported Cybergenetic Modeling, Optimization and Control for Synthetic Microbial Communities.” Computer Aided Chemical Engineering (2023): n. pag.
2022
Benman, William et al. “High-Throughput Feedback-Enabled Optogenetic Stimulation and Spectroscopy in Microwell Plates.” bioRxiv (2022): n. pag.
Malani, Saurabh et al. “Some of the Variables, Some of the Times, With Some Things Known: Identification With Partial Information.” 2022 AIChE Annual Meeting (2022): n. pag.
Zhang, Jie, Jay D Keasling, and Jose Avalos. “Engineered Yeast Brews Precursors of Anticancer Drug Vinblastine.” NATURE (2022): n. pag.
Hoffman, Shannon M, Allison Y Tang, and José L Avalos. “Optogenetics Illuminates Applications in Microbial Engineering.” Annual Review of Chemical and Biomolecular Engineering (2022): n. pag.
Hoffman, Shannon M., Makoto A. Lalwani, and Jose L. Avalos. “Light-Controlled Fermentations for Microbial Chemical and Protein Production.” Journal of Visualized Experiments (2022): n. pag.
Zhang, Yanfei et al. “Biosensor for Branched-Chain Amino Acid Metabolism in Yeast and Applications in Isobutanol and Isopentanol Production.” Nature Communications (2022): n. pag.
López, José Montaño, Lisset Duran, and José L. Avalos. “Physiological Limitations and Opportunities in Microbial Metabolic Engineering.” Nature Reviews Microbiology (2022): n. pag.
2021
Jack, Joshua et al. “Anode Co-Valorization for Scalable and Sustainable Electrolysis.” Green Chemistry (2021): n. pag.
Wegner, Scott A. et al. “Engineering Acetyl-CoA Supply and ERG9 Repression to Enhance Mevalonate Production in Saccharomyces Cerevisiae.” Journal of Industrial Microbiology and Biotechnology (2021): n. pag. Print.
Lalwani, Makoto A. et al. “Optogenetic Control of Microbial Consortia Populations for Chemical Production.” ACS Synthetic Biology (2021): n. pag.
Lalwani, Makoto A. et al. “The Neurospora Crassa Inducible Q System Enables Simultaneous Optogenetic Amplification and Inversion in Saccharomyces Cerevisiae for Bidirectional Control of Gene Expression.” ACS Synthetic Biology (2021): n. pag.
Hoffman, Shannon M. et al. “Cellulosic Biofuel Production Using Emulsified Simultaneous Saccharification and Fermentation (eSSF) With Conventional and Thermotolerant Yeasts.” Biotechnology for Biofuels (2021): n. pag.
Lovelett, Robert J. et al. “Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications.” ACS Synthetic Biology 10.2 (2021): 219–227.
Zhao, Evan M. et al. “Optogenetic Amplification Circuits for Light-Induced Metabolic Control.” ACS Synthetic Biology (2021): n. pag.
Kichuk, Therese C., César Carrasco‐López, and José L. Avalos. “Lights up on Organelles: Optogenetic Tools to Control Subcellular Structure and Organization.” WIREs Systems Biology and Medicine (2021): n. pag.
Lalwani, Makoto A. et al. “Optogenetic Control of the Lac Operon for Bacterial Chemical and Protein Production.” Nature Chemical Biology (2021): n. pag.
2020
Zhao, Evan M. et al. “Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering.” ACS Synthetic Biology 9.12 (2020): 3254–3266.
Carrasco-López, César et al. “Optogenetics and Biosensors Set the Stage for Metabolic Cybergenetics.” Current Opinion in Biotechnology 65 (2020): n. pag.
Carrasco-López, César et al. “Development of Light-Responsive Protein Binding in the Monobody Non-Immunoglobulin Scaffold.” Nature Communications 11.1 (2020): 1–13.
López, José Montaño, and José L. Avalos. “Genetically Engineered Yeast Makes Medicinal Plant Products.” Nature (2020): n. pag.
Duran, Lisset, José Montaño López, and José L. Avalos. “¡Viva La Mitochondria!: Harnessing Yeast Mitochondria for Chemical Production.” FEMS Yeast Research 20.6 (2020): n. pag.
Zhang, Yanfei et al. “Genetically Encoded Biosensors for Branched-Chain Amino Acid Metabolism to Monitor Mitochondrial and Cytosolic Production of Isobutanol and Isopentanol in Yeast.” bioRxiv (2020): n. pag.
Hammer, Sarah K., Yanfei Zhang, and José L. Avalos. “Mitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in Saccharomyces Cerevisiae.” ACS Synthetic Biology (2020): n. pag.
Gil, Agnieszka A. et al. “Optogenetic Control of Protein Binding Using Light-Switchable Nanobodies.” Nature Communications 11.1 (2020): 1–12.