McFann S, Shvartsman S, Toettcher J. Putting in the Erk: Growth factor signaling and mesoderm morphogenesis. Curr Top Dev Biol. 2022;149:263–310. PMID: 35606058

McNamara H, Ramm B, Toettcher J. Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. Semin Cell Dev Biol. 2023;141:33–42. PMID: 35484026

Singh A, Wu P, Ryabichko S, Raimundo J, Swan M, Wieschaus E, Gregor T, Toettcher J. Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. Cell Rep. 2022;38(12):110543. PMCID: PMC9019726

Palmer M, Nerger B, Goodwin K, Sudhakar A, Lemke S, Ravindran P, Toettcher J, Košmrlj A, Nelson C. Stress ball morphogenesis: How the lizard builds its lung. Sci Adv. 2021;7(52):eabk0161. PMCID: PMC8694616

Farahani P, Lemke S, Dine E, Uribe G, Toettcher J, Nelson C. Substratum stiffness regulates Erk signaling dynamics through receptor-level control. Cell Rep. 2021;37(13):110181. PMCID: PMC8756379

Ravindran P, McFann S, Thornton R, Toettcher J. A synthetic gene circuit for imaging-free detection of signaling pulses. Cell Syst. 2022;13(2):131–142.e13. PMCID: PMC8857027

Verma A, Jena S, Isakov D, Aoki K, Toettcher J, Engelhardt B. A self-exciting point process to study multicellular spatial signaling patterns. Proc Natl Acad Sci U S A. 2021;118(32). PMCID: PMC8364135

Dine E, Reed E, Toettcher J. Positive feedback between the T cell kinase Zap70 and its substrate LAT acts as a clustering-dependent signaling switch. Cell Rep. 2021;35(12):109280. PMCID: PMC8292983

McFann S, Dutta S, Toettcher J, Shvartsman S. Temporal integration of inductive cues on the way to gastrulation. Proc Natl Acad Sci U S A. 2021;118(23). PMCID: PMC8201965

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

Farahani P, Reed E, Underhill E, Aoki K, Toettcher J. Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems. Annu Rev Biomed Eng. 2021;23:61–87. PMID: 33722063

Murugan A, Husain K, Rust M, Hepler C, Bass J, Pietsch J, Swain P, Jena S, Toettcher J, Chakraborty A, Sprenger K, Mora T, Walczak A, Rivoire O, Wang S, Wood K, Skanata A, Kussell E, Ranganathan R, Shih H-Y, Goldenfeld N. Roadmap on biology in time varying environments. Phys Biol. 2021;18(4). PMCID: PMC8652373

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

Golonka D, Fischbach P, Jena S, Kleeberg J, Essen L-O, Toettcher J, Zurbriggen M, Möglich A. Publisher Correction: Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors. Commun Biol. 2019;2(1):475. PMID: 33323941

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

Ravindran P, Wilson M, Jena S, Toettcher J. Engineering combinatorial and dynamic decoders using synthetic immediate-early genes. Commun Biol. 2020;3(1):436. PMCID: PMC7426417

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

Johnson H, Djabrayan N, Shvartsman S, Toettcher J. Optogenetic Rescue of a Patterning Mutant. Curr Biol. 2020;30(17):3414–3424.e3. PMCID: PMC7730203

Goglia A, Wilson M, Jena S, Silbert J, Basta L, Devenport D, Toettcher J. A Live-Cell Screen for Altered Erk Dynamics Reveals Principles of Proliferative Control. Cell Syst. 2020;10(3):240–253.e6. PMCID: PMC7540725

Golonka D, Fischbach P, Jena S, Kleeberg J, Essen L-O, Toettcher J, Zurbriggen M, Möglich A. Deconstructing and repurposing the light-regulated interplay between phytochromes and interacting factors. Commun Biol. 2019;2:448. PMCID: PMC6888877

Golonka D, Fischbach P, Jena S, Kleeberg J, Essen L-O, Toettcher J, Zurbriggen M, Möglich A. Erratum: Publisher Correction: Deconstructing and repurposing the light-regulated interplay between phytochromes and interacting factors. Commun Biol. 2019;2:475. PMCID: PMC6917782

Patel A, Yeung E, McGuire S, Wu A, Toettcher J, Burdine R, Shvartsman S. Optimizing photoswitchable MEK. Proc Natl Acad Sci U S A. 2019;116(51):25756–25763. PMCID: PMC6926043

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

Goglia A, Toettcher J. A bright future: optogenetics to dissect the spatiotemporal control of cell behavior. Curr Opin Chem Biol. 2019;48:106–113. PMCID: PMC6382565

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

Johnson H, Toettcher J. Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo. Dev Cell. 2019;48(3):361–370.e3. PMCID: PMC6394837

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

Barrio-Real L, Lopez-Haber C, Casado-Medrano V, Goglia A, Toettcher J, Caloca M, Kazanietz M. P-Rex1 is dispensable for Erk activation and mitogenesis in breast cancer. Oncotarget. 2018;9(47):28612–28624. PMCID: PMC6033363

Tanner L, Goglia A, Wei M, Sehgal T, Parsons L, Park J, White E, Toettcher J, Rabinowitz J. Four Key Steps Control Glycolytic Flux in Mammalian Cells. Cell Syst. 2018;7(1):49–62.e8. PMCID: PMC6062487

Winer B, Shirvani-Dastgerdi E, Bram Y, Sellau J, Low B, Johnson H, Huang T, Hrebikova G, Heller B, Sharon Y, Giersch K, Gerges S, Seneca K, Pais M-A, Frankel A, Chiriboga L, Cullen J, Nahass R, Lutgehetmann M, Toettcher J, Wiles M, Schwartz R, Ploss A. Preclinical assessment of antiviral combination therapy in a genetically humanized mouse model for hepatitis delta virus infection. Sci Transl Med. 2018;10(447). PMCID: PMC6337727

Dine E, Gil A, Uribe G, Brangwynne C, Toettcher J. Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Cell Syst. 2018;6(6):655–663.e5. PMCID: PMC6023754

Johnson H, Toettcher J. Illuminating developmental biology with cellular optogenetics. Curr Opin Biotechnol. 2018;52:42–48. PMCID: PMC6082700

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

Dine E, Toettcher J. Optogenetic Reconstitution for Determining the Form and Function of Membraneless Organelles. Biochemistry. 2018;57(17):2432–2436. PMCID: PMC5972035

Wilson M, Ravindran P, Lim W, Toettcher J. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017;67(5):757–769.e5. PMCID: PMC5591080

Goglia A, Wilson M, DiGiorno D, Toettcher J. Optogenetic Control of Ras/Erk Signaling Using the Phy-PIF System. Methods Mol Biol. 2017;1636:3–20. PMID: 28730469

Johnson H, Goyal Y, Pannucci N, Schüpbach T, Shvartsman S, Toettcher J. The Spatiotemporal Limits of Developmental Erk Signaling. Dev Cell. 2017;40(2):185–192. PMCID: PMC5289754

Shin Y, Berry J, Pannucci N, Haataja M, Toettcher J, Brangwynne C. Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. Cell. 2017;168(1-2):159–171.e14. PMCID: PMC5562165

Diner B, Lum K, Toettcher J, Cristea I. Viral DNA Sensors IFI16 and Cyclic GMP-AMP Synthase Possess Distinct Functions in Regulating Viral Gene Expression, Immune Defenses, and Apoptotic Responses during Herpesvirus Infection. mBio. 2016;7(6). PMCID: PMC5111403

Johnson H, Toettcher J. The Duty of an Intracellular Signal: Illuminating Calcium’s Role in Transcriptional Control. Cell Syst. 2016;2(4):223–4. PMID: 27135534

Toettcher J, Apgar J, Castillo A, Tidor B, White J. Recycling circuit simulation techniques for mass-action biochemical kinetics. In Advanced Simulation and Verification of Electronic and Biological Systems. 2011. p. 115–136.

Toettcher J, Castillo A, Tidor B, White J. Oscillator sensitivity analysis in the presence of hidden conservation constraints. In Proceedings of the 48th IEEE Design Automation Conference. 2011.

Toettcher J, Gong D, Lim W, Weiner O. Light control of plasma membrane recruitment using the Phy-PIF system. Methods Enzymol. 2011;497:409–23. PMCID: PMC3121701

Toettcher J, Voigt C, Weiner O, Lim W. The promise of optogenetics in cell biology: interrogating molecular circuits in space and time. Nat Methods. 2011;8(1):35–8. PMCID: PMC3024327

Toettcher J, Gong D, Lim W, Weiner O. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods. 2011;8(10):837–9. PMCID: PMC3184382

Toettcher J, Weiner O, Lim W. Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module. Cell. 2013;155(6):1422–34. PMCID: PMC3925772