José L. Avalos‬

Multichromatic Dynamic Control of Multi-Membered Microbial Consortia Compositions for Chemical Production

This paper develops a light-controlled microbial consortium system to dynamically adjust population composition and boost chemical production.

Robust Multiplicative Control in Chemical Reaction Networks Extended Version

This paper develops a control framework for chemical reaction networks to robustly track multiplicative combinations of species concentrations and validates it with simulations.

Heterologous iron-sulfur cluster biogenesis and delivery for cytosolic isobutanol and isopentanol production in Saccharomyces cerevisiae

This study enhances cytosolic isobutanol and isopentanol production in yeast by introducing prokaryotic iron-sulfur cluster biosynthesis genes and accessory proteins.

Noise analysis of derivative-action biomolecular topologies

This study analyzes noise in biomolecular topologies that implement derivative-action signal differentiation, showing that noise amplification can be avoided.

Enhanced GPP synthesis by Erg20p-peptide fusions and biomolecular condensates boosts monoterpene production in yeast

The paper enhances monoterpene production in yeast by using Erg20p-peptide fusions and biomolecular condensates to increase GPP synthesis over FPP synthesis.

Spatial organization of enzymes and cofactors in synthetic membrane-associated condensates (sMACs)

The paper demonstrates that synthetic membrane-associated condensates (sMACs) can be engineered to enhance metabolic functions by creating localized redox microenvironments through cofactor partitioning.

Balancing doses of EL222 and light improves optogenetic induction of protein production in Komagataella phaffii

This study improves optogenetic control of protein production in K. phaffii by balancing EL222 and light doses, enhancing tunability and flexibility compared to methanol-based induction.

Biochemical implementation of acceleration sensing and PIDA control (Extended Version)

This paper designs a PIDA control scheme as a chemical reaction network to improve dynamic performance and steady-state tracking in biochemical systems.

HP1-enhanced chromatin compaction stabilizes a synthetic metabolic circuit in yeast

This paper shows that expressing HP1 homologues in yeast increases chromatin compaction, reducing mutation and recombination rates, and improving the stability of synthetic metabolic circuits.

AC-BioSD : A biomolecular signal differentiator module with enhanced performance (extended version)

The paper introduces AC-BioSD, a biomolecular signal differentiator with improved performance in signal differentiation and noise attenuation.

High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates

The paper introduces an open-source device for high-throughput optogenetic experiments in microwell plates, enabling automated stimulation, spectroscopy, and feedback control in E. coli.

A Modular Design for Synthetic Membraneless Organelles Enables Compositional and Functional Control

This paper introduces a modular framework for synthetic membraneless organelles that enables compositional and functional control through decoupled cluster formation and protein recruitment.

Optogenetic Amplification Circuits for Light-Induced Metabolic Control

The paper introduces OptoAMP circuits that amplify light-induced transcriptional responses in microbial metabolism, improving control over metabolic pathways in fermentations.

Optogenetic lac operon to control chemical and protein production in Escherichia coli with light

This paper develops OptoLAC circuits to control gene expression in E. coli using blue light, improving metabolic engineering and protein production compared to IPTG induction.