2024
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.
2019
Lane, Stephan et al. “Xylose Assimilation Enhances the Production of Isobutanol in Engineered Saccharomyces Cerevisiae.” Biotechnology and Bioengineering 2019.
Lovelett, Robert, José L. Avalos, and IoannisG. Kevrekidis. “Partial Observations and Conservation Laws: Grey-Box Modeling in Biotechnology and Optogenetics.” Industrial & Engineering Chemistry Research (2019): n. pag. Print.
Kuroda, Kouichi et al. “Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast.” Cell Systems (2019): n. pag. Print.
Zhang, Yanfei et al. “Xylose Utilization Stimulates Mitochondrial Production of Isobutanol and 2-Methyl-1-Butanol in Saccharomyces Cerevisiae.” Biotechnology for Biofuels (2019): n. pag. Print.
Zhao, Evan M. et al. “Light-Based Control of Metabolic Flux through Assembly of Synthetic Organelles.” Nature Chemical Biology (2019): n. pag.
2018
Bracha, Dan et al. “Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds.” Cell 175.6 (2018): 1467–1480.
Lalwani, Makoto A., Evan M. Zhao, and José L. Avalos. “Current and Future Modalities of Dynamic Control in Metabolic Engineering.” Current Opinion in Biotechnology (2018): n. pag.