Select Publications

  • De novo design of phospho-tyrosine peptide binders

    Bauer M.S.*, Zhang J.Z.*, Wu K.*, Lee G.R.*, Coventry B.*, Klupt K., Shi J., Brent R.I., Li X., Moller C., Roullier N., Vafeados D.K., Kalvet I., Skotheim R.K., Zhu S., Motmaen A., Hermann L.C., Sturmfels P., Tischer D., Altae-Tran H.R., Juergens D., Krishna R., Ahern W., Yim J., Bera A.K., Kang A., Joyce E., Lu A., Stewart L., DiMaio F., Baker D. De novo design of phospho-tyrosine peptide binders. (2025) bioRxiv doi: https://doi.org/10.1101/2025.09.29.678898

  • Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution

    Zhang J.Z.†, Nguyen W.H., Greenwood N., Ong S.E., Maly D.J.†, Baker D.† (2024) Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution. Nature Biotechnology https://doi.org/10.1038/s41587-023-02107-w

  • Single-cell sensor analyses reveal signaling programs enabling Ras-G12C drug resistance

    Zhang J.Z.†, Ong S.E., Baker D., Maly D.J.† (2024) Single-cell sensor analyses reveal signaling programs enabling Ras-G12C drug resistance. Nature Chemical Biology https://doi.org/10.1038/s41589-024-01684-4

  • Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Nature Biotechnology

    Zhang J.Z.*†, Yeh H.W.*, Walls A.C., Wicky B.I.M, Sprouse K., VanBlargan L.A., Treger R., Quijano-Rubio A., Pham M.N., Kraft J.C., Haydon I.C., Yang W., DeWitt M., Chow C., Carter L., Wener M.H., Stewart L., Veesler D., Diamond M.S., Baker D.† (2022) Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Nature Biotechnology. 40, 1336–1340.

  • Phase separation of a PKA regulatory subunit controls cAMP compartmentation and oncogenic signaling

    Zhang J.Z., Lu T.W., Stolerman L.M., Tenner B., Yang J., Zhang J.F., Falcke, M., Rangamani P., Taylor S.S., Mehta S., Zhang J. (2020) Phase separation of a PKA regulatory subunit controls cAMP compartmentation and oncogenic signaling. Cell. 182,1531-1544.e15.

Other Publications

  • De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors

    Muratspahić E.*, Feldman D.*, Kim D.E.*, Qu X.L.*, Bratovianu A.M.*, Rivera-Sánchez P.*, Dimtri F., Cao J., Cary B.P., Belousoff M.J., Keov P., Chen Q., Ren Y., Fine J., Sappington I., Schilchthaerle T., Zhang J.Z., Pillai A., Mihaljević L., Bauer M., Torres S.V., Motmaen A., Lee G.R., Tran L., Wang X., Goreshnik I., Vafeados D.K., Svendsen J.E., Hosseinzadeh P., Lindegaard N., Brandt M., Waltenspühl Y., Deibler K., Oostdyk L., Cao W., Anantharman L., Steward L., Halloran L., Spangler J.B., Sexton P.M., Roth B.L., Krumm B.E., Wootten D., Tate C.G., Norn C.#, Baker D.# (2025) De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors. Biorxiv

  • De novo design of Ras isoform selective binders

    Zhang J.Z.†, Li X., Liu C.X., Jiang H.L., Wu K.†, Baker D†. De novo design of Ras isoform selective binders. Biorxiv DOI: 10.1101/2024.08.29.610300v2

  • De novo designed Hsp70 activator dissolves intracellular condensates. Cell Chemical Biology

    Zhang J.Z.†, Greenwood N., Hernandez J., Cuperus J.T., Huang B., Queitsch C., Gestwicki J.E., Baker D.† (2025) De novo designed Hsp70 activator dissolves intracellular condensates. Cell Chemical Biology https://www.sciencedirect.com/science/article/pii/S2451945625000297

  • Designed Endocytosis-Triggering Proteins mediate Targeted Degradation and amplify signaling

    Huang B.*, Abedi M.*, Ahn G.*, Coventry B.*, Sappington I., Tang C., Wang R., Schlichthaerle T., Zhang J.Z., Wang Y., Goreshnik I., Chiu C.W., Chazin-Gray, A., Chan S., Gerben S., Murray A., Wang S., O’Neill J., Yeh R., Misquith A., Wolf A., Tomasovic L.M., Piraner D.I., Gonzalez M.J.D., Bennett N.R., Venkatesh P., Ahlrichs M., Dobbins C., Yang W., Wang X., Sahtoe D., Vafeados D., Mout R., Shivaei S., Cao L., Carter L., Stewart L., Spangler J.D., Roybal K.T., Greisen P.J., Li X., Bernardes G.J.L., Bertozzi C.R., Baker D. (2024) Designed Endocytosis-Triggering Proteins mediate Targeted Degradation and amplify signaling.  Nature https://www.nature.com/articles/s41586-024-07948-2

  • Computational design of non-porous pH-responsive antibody nanoparticles

    Yang E.C., Divine R., Miranda M., Borst A., Sheffler W., Khmelinskaia A., Zhang J.Z., Goldbach N., Choi H.J., Abedi M., Lubner J., Hendel S., Fallas J., Ueda G., Norris A., Wysocki V., King N.P., Baker D. (2024) Computational design of non-porous pH-responsive antibody nanoparticles. Nature Structural and Molecular Biology https://www.nature.com/articles/s41594-024-01288-5

  • De novo design of luciferases using deep learning

    Yeh H.W.*, Norn C.*, Kipnis Y., Tischer D., Pellock S.J., Evans D., Ma P., Lee G.Y., Zhang J.Z., Anishchenko I., Coventry B., Cao L., Halabiya S., DeWitt M., Carter L., Houk K.N., Baker D. (2023) De novo design of luciferases using deep learning. Nature. 614, 774–780.

  • Liquid-liquid phase separation: a principal organizer of the cell's biochemical activity architecture

    Zhang J.Z., Mehta S, Zhang J. (2021) Liquid-liquid phase separation: a principal organizer of the cell's biochemical activity architecture. Trends in Pharmacological Sciences. 42, 845-856.

  • Genetically encoded fluorescent biosensors to measure native signaling activities at endogenous signaling compartments

    Zhang J.Z., Tenner B., Mehta S., Zhang J. (2021) Genetically encoded fluorescent biosensors to measure native signaling activities at endogenous signaling compartments. STAR Protocols. 3, 100693

  • Characterizing Protein Kinase A (PKA) subunits as macromolecular regulators of PKA RIα liquid-liquid phase separation

    Ahn S.H., Qin S., Zhang J.Z., McCammon J.A., Zhang J., Zhou H.X. (2021) Characterizing Protein Kinase A (PKA) subunits as macromolecular regulators of PKA RIα liquid-liquid phase separation. Journal of Chemical Physics. 154, 221101

  • Fluorescent biosensors for monitoring compartmentalized signaling within endogenous microdomains

    Tenner B.*, Zhang J.Z.*, Huang B., Mehta S., Zhang J. (2021) Fluorescent biosensors for monitoring compartmentalized signaling within endogenous microdomains. Science Advances. 7, eabe4091.

  • An ultrasensitive biosensor for high-resolution kinase activity imaging in awake mice.

    Zhang J.F., Liu B., Hong I., Mo A., Roth R.H., Tenner B., Lin W., Zhang J.Z., Johnson R.C., Molina R.S., Drobizhev M., Taylor S.S., Hughes T.E., Tian L., Huganir R.L., Mehta S., Zhang J. (2021) An ultrasensitive biosensor for high-resolution kinase activity imaging in awake mice. Nature Chemical Biology. 17, 39-46.

  • Histamine-induced biphasic activation of RhoA allows for persistent RhoA signaling

    Zhang J.Z., Nguyen A., Miyamoto S., McCulloch A.D., Brown J.H., Zhang J. (2020) Histamine-induced biphasic activation of RhoA allows for persistent RhoA signaling. PLoS Biology. 18, e3000866.