Wegner S, Barocio-Galindo R, Avalos J. The bright frontiers of microbial metabolic optogenetics. Curr Opin Chem Biol. 2022;71:102207. PMID: 36103753

Hoffman S, Lalwani M, Avalos J. Light-Controlled Fermentations for Microbial Chemical and Protein Production. J Vis Exp. 2022;(181). PMID: 35404352

Hoffman S, Tang A, Avalos J. Optogenetics Illuminates Applications in Microbial Engineering. Annu Rev Chem Biomol Eng. 2022;13:373–403. PMID: 35320696

Zhang Y, Cortez J, Hammer S, Carrasco-López C, Echauri S, Wiggins J, Wang W, Avalos J. Biosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol production. Nat Commun. 2022;13(1):270. PMCID: PMC8755756

Wegner S, Chen J-M, Ip S, Zhang Y, Dugar D, Avalos J. Engineering acetyl-CoA supply and ERG9 repression to enhance mevalonate production in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol. 2021;48(9-10). PMCID: PMC8788843

Lalwani M, Kawabe H, Mays R, Hoffman S, Avalos J. Optogenetic Control of Microbial Consortia Populations for Chemical Production. ACS Synth Biol. 2021;10(8):2015–2029. PMID: 34351122

Lalwani M, Zhao E, Wegner S, Avalos J. The Inducible Q System Enables Simultaneous Optogenetic Amplification and Inversion in for Bidirectional Control of Gene Expression. ACS Synth Biol. 2021;10(8):2060–2075. PMID: 34346207

López J, Duran L, Avalos J. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol. 2022;20(1):35–48. PMCID: 5812522

Hoffman S, Alvarez M, Alfassi G, Rein D, Garcia-Echauri S, Cohen Y, Avalos J. Cellulosic biofuel production using emulsified simultaneous saccharification and fermentation (eSSF) with conventional and thermotolerant yeasts. Biotechnol Biofuels. 2021;14(1):157. PMCID: PMC8285809

Zhao E, Lalwani M, Chen J-M, Orillac P, Toettcher J, Avalos J. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol. 2021;10(5):1143–1154. PMCID: PMC8721662

Zhao E, Lalwani M, Lovelett R, García-Echauri S, Hoffman S, Gonzalez C, Toettcher J, Kevrekidis I, Avalos J. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol. 2020;9(12):3254–3266. PMID: 33232598

Carrasco-López C, García-Echauri S, Kichuk T, Avalos J. Optogenetics and biosensors set the stage for metabolic cybergenetics. Curr Opin Biotechnol. 2020;65:296–309. PMID: 32932048

Lalwani M, Ip S, Carrasco-López C, Day C, Zhao E, Kawabe H, Avalos J. Optogenetic control of the lac operon for bacterial chemical and protein production. Nat Chem Biol. 2021;17(1):71–79. PMCID: 5876151

Carrasco-López C, Zhao E, Gil A, Alam N, Toettcher J, Avalos J. Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold. Nat Commun. 2020;11(1):4045. PMCID: PMC7427095

Gil A, Carrasco-López C, Zhu L, Zhao E, Ravindran P, Wilson M, Goglia A, Avalos J, Toettcher J. Optogenetic control of protein binding using light-switchable nanobodies. Nat Commun. 2020;11(1):4044. PMCID: PMC7426870

Kichuk T, Carrasco-López C, Avalos J. Lights up on organelles: Optogenetic tools to control subcellular structure and organization. WIREs Mech Dis. 2021;13(1):e1500. PMID: 32715616

Duran L, López J, Avalos J. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res. 2020;20(6). PMID: 32592388

Hammer S, Avalos J. Corrigendum to "Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis" [Metab. Eng. 44 (2017) 302-312]. Metab Eng. 2020;61:438. PMID: 32417202

Hammer S, Zhang Y, Avalos J. Mitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in . ACS Synth Biol. 2020;9(3):546–555. PMID: 32049515

Lane S, Zhang Y, Yun E, Ziolkowski L, Zhang G, Jin Y-S, Avalos J. Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae. Biotechnol Bioeng. 2020;117(2):372–381. PMID: 31631318

Kuroda K, Hammer S, Watanabe Y, López J, Fink G, Stephanopoulos G, Ueda M, Avalos J. Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast. Cell Syst. 2019;9(6):534–547.e5. PMID: 31734159

Zhang Y, Lane S, Chen J-M, Hammer S, Luttinger J, Yang L, Jin Y-S, Avalos J. Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in . Biotechnol Biofuels. 2019;12:223. PMCID: PMC6753614

Zhao E, Suek N, Wilson M, Dine E, Pannucci N, Gitai Z, Avalos J, Toettcher J. Light-based control of metabolic flux through assembly of synthetic organelles. Nat Chem Biol. 2019;15(6):589–597. PMCID: PMC6755918

Bracha D, Walls M, Wei M-T, Zhu L, Kurian M, Avalos J, Toettcher J, Brangwynne C. Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. Cell. 2018;175(6):1467–1480.e13. PMCID: PMC6724719

Alper H, Avalos J. Metabolic pathway engineering. Synth Syst Biotechnol. 2018;3(1):1–2. PMCID: PMC5884275

Hammer S, Avalos J. Metabolic engineering: Biosensors get the green light. Nat Chem Biol. 2016;12(11):894–895. PMID: 27755525

Zhang Y, Avalos J. Traditional and novel tools to probe the mitochondrial metabolism in health and disease. Wiley Interdiscip Rev Syst Biol Med. 2017;9(2). PMID: 28067471

Hammer S, Avalos J. Harnessing yeast organelles for metabolic engineering. Nat Chem Biol. 2017;13(8):823–832. PMID: 28853733

Hammer S, Avalos J. Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis. Metab Eng. 2017;44:302–312. PMID: 29037781

Zhao E, Zhang Y, Mehl J, Park H, Lalwani M, Toettcher J, Avalos J. Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature. 2018;555(7698):683–687. PMCID: PMC5876151

Lalwani M, Zhao E, Avalos J. Current and future modalities of dynamic control in metabolic engineering. Curr Opin Biotechnol. 2018;52:56–65. PMID: 29574344

Avalos J, Bever K, Wolberger C. Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme. Mol Cell. 2005;17(6):855–68. PMID: 15780941

Cosgrove M, Bever K, Avalos J, Muhammad S, Zhang X, Wolberger C. The structural basis of sirtuin substrate affinity. Biochemistry. 2006;45(24):7511–21. PMID: 16768447

Hoff K, Avalos J, Sens K, Wolberger C. Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide. Structure. 2006;14(8):1231–40. PMID: 16905097

Tao X, Avalos J, Chen J, MacKinnon R. Crystal structure of the eukaryotic strong inward-rectifier K+ channel Kir2.2 at 3.1 A resolution. Science. 2009;326(5960):1668–74. PMCID: PMC2819303

Avalos J, Fink G, Stephanopoulos G. Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol. 2013;31(4):335–41. PMCID: PMC3659820