1.Hu M, Dinh H, Shen Y, Suthers P, Foster C, Call C, Ye X, Pratas J, Fatma Z, Zhao H, Rabinowitz J, Maranas C. Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. Metab Eng. 2023;76:1–17. PMID: 36603705 Reference Link
1.Xiao T, Khan A, Shen Y, Chen L, Rabinowitz J. Glucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeast. Nat Chem Biol. 2022;18(12):1380–1387. PMCID: 1082793 Reference Link
1.Hoffman S, Lalwani M, Avalos J. Light-Controlled Fermentations for Microbial Chemical and Protein Production. J Vis Exp. 2022;(181). PMID: 35404352 Reference Link
1.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 Reference Link
1.Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella A, Shen Y, Cowan A, McReynolds M, Kennedy B, Lato A, Campagna S, Singh M, Rabinowitz J. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods. 2021;18(11):1377–1385. PMCID: PMC8733904 Reference Link
1.Nofal M, Wang T, Yang L, Jankowski C, Li S, Han S, Parsons L, Frese A, Gitai Z, Anthony T, Wühr M, Sabatini D, Rabinowitz J. GCN2 adapts protein synthesis to scavenging-dependent growth. Cell Syst. 2022;13(2):158–172.e9. PMCID: PMC8961722 Reference Link
1.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 Reference Link
1.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 Reference Link
1.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 Reference Link
1.Arita Y, Kim G, Li Z, Friesen H, Turco G, Wang R, Climie D, Usaj M, Hotz M, Stoops E, Baryshnikova A, Boone C, Botstein D, Andrews B, McIsaac S. A genome-scale yeast library with inducible expression of individual genes. Mol Syst Biol. 2021;17(6):e10207. PMCID: PMC8182650 Reference Link
1.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 Reference Link
1.Valastyan J, Kraml C, Pelczer I, Ferrante T, Bassler B. Saccharomyces cerevisiae Requires To Produce 4-Hydroxy-5-Methylfuran-3(2H)-One, a Mimic of the Bacterial Quorum-Sensing Autoinducer AI-2. mBio. 2021;12(2). PMCID: PMC8092285 Reference Link
1.Lovelett R, Zhao E, Lalwani M, Toettcher J, Kevrekidis I, Avalos J. Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications. ACS Synth Biol. 2021;10(2):219–227. PMID: 33492138 Reference Link
1.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 Reference Link
1.Wong S, Hepowit N, Port S, Yau R, Peng Y, Azad N, Habib A, Harpaz N, Schuldiner M, Hughson F, MacGurn J, Weisman L. Cargo Release from Myosin V Requires the Convergence of Parallel Pathways that Phosphorylate and Ubiquitylate the Cargo Adaptor. Curr Biol. 2020;30(22):4399–4412.e7. PMCID: PMC8025699 Reference Link
1.Luongo T, Eller J, Lu M-J, Niere M, Raith F, Perry C, Bornstein M, Oliphint P, Wang L, McReynolds M, Migaud M, Rabinowitz J, Johnson B, Johnsson K, Ziegler M, Cambronne X, Baur J. SLC25A51 is a mammalian mitochondrial NAD transporter. Nature. 2020;588(7836):174–179. PMCID: PMC7718333 Reference Link
1.Green R, Wang L, Hart S, Lu W, Skelding D, Burton J, Mi H, Capel A, Chen H, Lin A, Subramaniam A, Rabinowitz J, Shou W. Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect. PLoS Biol. 2020;18(8):e3000757. PMCID: PMC7470746 Reference Link
1.Duran L, López J, Avalos J. ¡Viva la mitochondria!: harnessing yeast mitochondria for chemical production. FEMS Yeast Res. 2020;20(6). PMID: 32592388 Reference Link
1.Murawska M, Schauer T, Matsuda A, Wilson M, Pysik T, Wojcik F, Muir T, Hiraoka Y, Straub T, Ladurner A. The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions. Mol Cell. 2020;77(3):501–513.e7. PMCID: PMC7007867 Reference Link
1.Gibney P, Chen A, Schieler A, Chen J, Xu Y, Hendrickson D, McIsaac S, Rabinowitz J, Botstein D. A tps1Δ persister-like state in Saccharomyces cerevisiae is regulated by MKT1. PLoS One. 2020;15(5):e0233779. PMCID: PMC7259636 Reference Link
1.Travis S, DAmico K, Yu I-M, McMahon C, Hamid S, Ramirez-Arellano G, Jeffrey P, Hughson F. Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1. J Biol Chem. 2020;295(30):10125–10135. PMCID: PMC7383367 Reference Link
1.Dao H, Dul B, Dann G, Liszczak G, Muir T. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Nat Chem Biol. 2020;16(2):134–142. PMCID: PMC6982587 Reference Link
1.Garcia D, Leach R, Wadsworth G, Choudhary K, Li H, Aviran S, Kim H, Zakian V. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun. 2020;11(1):2173. PMCID: PMC7195438 Reference Link
1.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 Reference Link
1.Park J-D, Moon K, Miller C, Rose J, Xu F, Ebmeier C, Jacobsen J, Mao D, Old W, DeShazer D, Seyedsayamdost M. Thailandenes, Cryptic Polyene Natural Products Isolated from Using Phenotype-Guided Transposon Mutagenesis. ACS Chem Biol. 2020;15(5):1195–1203. PMCID: PMC9106368 Reference Link
1.Travis S, Kokona B, Fairman R, Hughson F. Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering. Proc Natl Acad Sci U S A. 2019;116(48):24031–24040. PMCID: PMC6883825 Reference Link
1.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 Reference Link
1.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 Reference Link
1.Chen C-F, Pohl T, Chan A, Slocum J, Zakian V. Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding. Genetics. 2019;213(2):465–479. PMCID: PMC6781895 Reference Link
1.Chen X, Robinson D, Storey J. The functional false discovery rate with applications to genomics. Biostatistics. 2021;22(1):68–81. PMCID: PMC7846131 Reference Link
1.Pohl T, Zakian V. Pif1 family DNA helicases: A helpmate to RNase H?. DNA Repair (Amst). 2019;84:102633. PMCID: PMC6901714 Reference Link
1.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 Reference Link
1.Hall A, Rose M. Cell fusion in yeast is negatively regulated by components of the cell wall integrity pathway. Mol Biol Cell. 2019;30(4):441–452. PMCID: PMC6594448 Reference Link
1.Allard C, Decker F, Weiner O, Toettcher J, Graziano B. A size-invariant bud-duration timer enables robustness in yeast cell size control. PLoS One. 2018;13(12):e0209301. PMCID: PMC6303054 Reference Link
1.Tye B, Commins N, Ryazanova L, Wühr M, Springer M, Pincus D, Churchman S. Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. Elife. 2019;8. PMCID: PMC6453566 Reference Link
1.Chen C-F, Pohl T, Pott S, Zakian V. Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation in . Genetics. 2019;211(1):105–119. PMCID: PMC6325707 Reference Link
1.Jeon J, McGinty R, Muir T, Kim J-A, Kim J. Crosstalk among Set1 complex subunits involved in H2B ubiquitylation-dependent H3K4 methylation. Nucleic Acids Res. 2018;46(21):11129–11143. PMCID: PMC6265457 Reference Link
1.Xu Y-F, Lu W, Chen J, Johnson S, Gibney P, Thomas D, Brown G, May A, Campagna S, Yakunin A, Botstein D, Rabinowitz J. Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase. ACS Chem Biol. 2018;13(10):3011–3020. PMCID: PMC6466636 Reference Link
1.Geronimo C, Singh S, Galletto R, Zakian V. The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity. Nucleic Acids Res. 2018;46(16):8357–8370. PMCID: PMC6144861 Reference Link
1.Hammer S, Avalos J. Harnessing yeast organelles for metabolic engineering. Nat Chem Biol. 2017;13(8):823–832. PMID: 28853733 Reference Link
1.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 Reference Link
1.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 Reference Link
1.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 Reference Link
1.Gibney P, Schieler A, Chen J, Bacha-Hummel J, Botstein M, Volpe M, Silverman S, Xu Y, Bennett B, Rabinowitz J, Botstein D. Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast. Mol Biol Cell. 2018;29(8):897–910. PMCID: PMC5896929 Reference Link
1.Smith J, Hall A, Rose M. Membrane curvature directs the localization of Cdc42p to novel foci required for cell-cell fusion. J Cell Biol. 2017;216(12):3971–3980. PMCID: PMC5716282 Reference Link
1.Melloy P, Rose M. Influence of the bud neck on nuclear envelope fission in Saccharomyces cerevisiae. Exp Cell Res. 2017;358(2):390–396. PMCID: PMC6067115 Reference Link
1.Choi J, Rajagopal A, Xu Y-F, Rabinowitz J, O’Shea E. A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae. PLoS One. 2017;12(5):e0176085. PMCID: PMC5435139 Reference Link
1.Geronimo C, Zakian V. Getting it done at the ends: Pif1 family DNA helicases and telomeres. DNA Repair (Amst). 2016;44:151–158. PMCID: PMC5441554 Reference Link
1.Tran P, Pohl T, Chen C-F, Chan A, Pott S, Zakian V. PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes. Nat Commun. 2017;8:15025. PMCID: PMC5413955 Reference Link
1.Park J, Rubin S, Xu Y-F, Amador-Noguez D, Fan J, Shlomi T, Rabinowitz J. Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat Chem Biol. 2016;12(7):482–9. PMCID: PMC4912430 Reference Link