Publications

2024

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.

2022

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.
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.
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.
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

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.

2017

Hammer, Sarah K., and José L. Avalos. “Uncovering the Role of Branched-Chain Amino Acid Transaminases in Saccharomyces Cerevisiae Isobutanol Biosynthesis.” Metabolic Engineering (2017): -.
Hammer, Sarah K., and José L. Avalos. “Harnessing Yeast Organelles for Metabolic Engineering.” Nature Chemical Biology (2017): 823–832.
Zhang, Yanfei, and José L. Avalos. “Traditional and Novel Tools to Probe the Mitochondrial Metabolism in Health and Disease.” Wiley Interdisciplinary Reviews: Systems Biology and Medicine 9.2 (2017): n. pag.
Adesina, Oluwakemi et al. “Embracing Biological Solutions to the Sustainable Energy Challenge.” Chem 2.1 (2017): 20–51.

2016

Hammer, Sarah K., and Jose L. Avalos. “Metabolic Engineering: Biosensors Get the Green Light.” Nat Chem Biol 2016: 894–895.

2013

Avalos, Jose L., Gerald R. Fink, and Gregory Stephanopoulos. “Compartmentalization of Metabolic Pathways in Yeast Mitochondria Improves the Production of Branched-Chain Alcohols.” Nature Biotechnology 31 (2013): 335–341.

2006

Cosgrove, M. S. et al. “The Structural Basis of Sirtuin Substrate Affinity.” Biochemistry 45 (2006): 7511–7521.