top of page
Peer-reviewed research papers:

51. Murdock, M. H., Yang, C-Y, Sun, N., Pao, P.-C., Blanco-Duque, C., Kahn, M. C., Kim, T.H., Lavoie, N. S., Victor, M. B., Islam, Md R., Galiana, F., Leary, N., Wang, S., Bubnys, A., Ma, E., Akay, L. A., Sneve, M., Qian, Y., Lai, C., McCarthy, M. M., Kopell, N., Kellis, M., Piatkevich, K. D., Boyden, E. S., and Tsai, L.-H. Multisensory Gamma Stimulation Promotes Glymphatic Clearance of Amyloid. Nature, 2024, 627(8002):149–56.

50. Zhang, H., Lesnov, G. D., Subach, O. M., Zhang, W., Kuzmicheva, T. P., Vlaskina, A. V., Samygina, V. R., Chen, L., Ye, X., Nikolaeva, A. Yu., Gabdulkhakov, A., Papadaki, S., Qin, W., Borshchevskiy, V., Perfilov, M. M., Gavrikov, A. S., Drobizhev, M., Mishin, A. S., Piatkevich, K. D.*, Subach, F. V.* Bright and Stable Monomeric Green Fluorescent Protein Derived from StayGold. Nature Methods, 2024, 21(4): 657–65, 2024

49. Bando, Y., Pillai, R., Kajita, A., Hakeem, F. A., Quemener, Y., Tseng, H.-A., Piatkevich, K. D., Linghu, C., Han, X., & Boyden, E. S. Real-time Neuron Segmentation for Voltage Imaging. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2023. 813–818. [Publisher Link] [Local Copy]

48. Eom, M., Han, S., Park, P., Kim, G., Cho, E.-S., Sim, J., Lee, K.-H., Kim, S., Tian, H., Böhm, U. L., Lowet, E., Tseng, H., Choi, J., Lucia, S. E., Ryu, S. H., Rózsa, M., Chang, S., Kim, P., Han, X., Piatkevich, K.D., Choi, M., Kim, C.-H., Cohen, A.E., Chang, J.-B., Yoon, Y.-G. Statistically unbiased prediction enables accurate denoising of voltage imaging data. Nature Methods. 2023. 20(10), 1581–1592. [Publisher Link] [Local Copy] [On the Cover]

47. Zhang, H., Papadaki, S., Sun, X., Wang, X., Drobizhev, M., Yao, L., Rehbock, M., Köster, R. W., Wu, L., Namikawa, K., Piatkevich, K. D.* Quantitative assessment of near-infrared fluorescent proteins. Nature Methods. 2023. 20(10), 1605–1616. [Publisher Link] [Local Copy] [Behind the Paper] [Plasmids on WeKwikGene]

46. Subach, O. M., Vlaskina, A. V, Agapova, Y. K., Nikolaeva, A. Y., Varizhuk, A. M., Podgorny, O. V, Piatkevich, K. D., Patrushev, M. V, Boyko, K. M., Subach, F. V, Shemyakin, M. M., and Ovchinnikov, Y. A. (2023) YTnC2, an improved genetically encoded green calcium indicator based on toadfish troponin C. FEBS Open Bio. 2023 [Publisher Link] [Local Copy]

45. Lowet, E., Sheehan, D. J., Chialva, U., De Oliveira Pena, R., Mount, R. A., Xiao, S., Zhou, S. L., Tseng, H., Gritton, H., Shroff, S., Kondabolu, K., Cheung, C., Wang, Y., Piatkevich, K. D., Boyden, E. S., Mertz, J., Hasselmo, M. E., Rotstein, H. G., and Han, X. Theta and gamma rhythmic coding through two spike output modes in the hippocampus during spatial navigation. Cell Reports. 2023. 42, 112906.  [Publisher Link] [Local Copy]

44. Subach, O. M., Varfolomeeva, L., Vlaskina, A. V., Agapova, Y. K., Nikolaeva, A. Y., Piatkevich, K. D., Patrushev, M. V., Boyko, K. M., and Subach, F. V. FNCaMP, ratiometric green calcium indicator based on mNeonGreen protein. Biochem. Biophys. Res. Commun. 2023. [Publisher Link] [Local Copy]

43. Subach, O.M., Vlaskina, A. V, Agapova, Y.K., Nikolaeva, A.Y., Anokhin, K. V, Piatkevich, K.D., Patrushev, M. V, Boyko, K.M., and Subach, F. V Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers Int. J. Mol. Sci. 2023 24, 3279. [Publisher Link] [Local Copy]


42. Li, L., Sun, C., Sun, Y., Dong, Z., Wu, R., Sun, X., Zhang, H., Jiang, W., Zhou, Y., Cen, X., Cai, S., Xia, H., Zhu, Y., Guo, T.*, Piatkevich, K. D.* Spatially resolved proteomics via tissue expansion. Nat. Commun. 2022 131 13, 1–13. [Publisher Link] [Local Copy]

41. Subach, O.M., Vlaskina, A. V., Agapova, Y.K., Korzhenevskiy, D.A., Nikolaeva, A.Y., Varizhuk, A.M., Subach, M.F., Patrushev, M. V., Piatkevich, K.D., Boyko, K.M., et al. cNTnC and fYTnC2, Genetically Encoded Green Calcium Indicators Based on Troponin C from Fast Animals Int. J. Mol. Sci. 2022, Vol. 23, Page 14614 2022 23, 14614. [Publisher Link] [Local Copy]

40. Liang, G.-T., Lai, C., Yue, Z., Zhang, H., Li, D., Chen, Z., Lu, X., Tao, L., Subach, F. V., Piatkevich, K.D.* Enhanced small green fluorescent proteins as a multisensing platform for biosensor development Front. Bioeng. Biotechnol. 2022, 0, 1942.  [Publisher Link] [Local Copy]

39. Subach, O.M., Vlaskina, A.V, Agapova, Y.K., Piatkevich, K.D., Patrushev, M.V., Samygina, V.R., Subach, F.V. LSSmScarlet2 and LSSmScarlet3, Chemically Stable Genetically Encoded Red Fluorescent Proteins with a Large Stokes' Shift Int. J. Mol. Sci. 2022 23, 11051. [Publisher Link] [Local Copy]

38. Papadaki, S., Wang, X., Wang, Y., Zhang, H., Jia, S., Liu, S., Yang, M., Zhang, D., Jia, J.-M., Köster, R. W., Namikawa, K., Piatkevich, K. D.* Dual-Expression System for Blue Fluorescent Protein Optimization. Sci. Reports 2022 121 2022, 12 (1), 1–16. [Publisher Link] [Local Copy] [Top 100 in Cell and Molecular Biology - 2022]

37. Cabán C.C.T., Yang M., Lai C., Yang L., Subach F. V., Smith B.O., Piatkevich K.D.*, and Boyden, E.S.* Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies. ACS Sensors 2022 7 (5), 1336–1346. [Publisher Link] [Local Copy] [Resources associated with this publication] [Plasmids on Addgene] [On the cover]


36. Zheng Y., Wang Y., Zhang F., Zhang S., Piatkevich K.D., Zhou N., Pokorski J.K. Coagulation Bath-Assisted 3D Printing of PEDOT: PSS with High Resolution and Strong Substrate Adhesion for Bioelectronic Devices. Advanced Materials Technologies 2022, 2101514. [Publisher Link]

35. Zhang, H., Papadaki, S., Sun, X., Yao, L., Drobizhev, M., Wang, X., Köster, R. W., Wu, L., Namikawa, K., Piatkevich, K. D.* Quantitative assessment of near-infrared fluorescent proteins. Registered Protocol 2021. [Publisher Link] [Resources associated with this publication]


34. Babakhanova, S., Jung, E. E., Namikawa, K., Zhang, H., Wang, Y., Subach, O. M., Korzhenevskiy, D. A., Rakitina, T. V., Xiao, X., Wang, W., Shi, J., Drobizhev, M., Park, D., Eisenhard, L., Tang, H., Köster, R. W., Subach, F. V., Boyden, E. S.*, and Piatkevich, K. D.* Rapid Directed Molecular Evolution of Fluorescent Proteins in Mammalian Cells. Protein Sci. 2021, 15, 16. [Publisher Link] [Resources associated with this publication]

33. Subach, O. M., Vlaskina, A. V., Agapova, Y. K., Dorovatovskii, P. V., Nikolaeva, A. Y., Ivashkina, O. I., Popov, V. O., Piatkevich, K. D., Khrenova, M. G., Smirnova, T. A., Boyko, K. M., and Subach, F. V. LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift. Int. J. Mol. Sci. 2021, 22,  2887. [Publisher Link] [Resources associated with this publication]

32. Xiao, S., Lowet, E., Gritton, H. J., Fabris, P., Wang, Y., Sherman, J., Mount, R. A., Tseng, H., Man, H.-Y., Straub, C., Piatkevich, K. D., Boyden, E. S., Mertz, J., and Han, X. Large-scale voltage imaging in behaving mice using targeted illumination. iScience 2021, 24, 103263. [Publisher Link] [Resources associated with this publication]

31. Wang, Y., Zhu, D., Liu, B. & Piatkevich, K. D.* Craniotomy Procedure for Visualizing Neuronal Activities in Hippocampus of Behaving Mice. Journal of Visualized Experiments 2021. e62266 [Publisher Link] [Resources associated with this publication]

30. Gao R., Yu C.-C., Gao, L., Piatkevich K.D., Neve R.L., Munro J.B., Upadhyayula S., and Boyden, E.S. A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy. Nature Nanotechnology 2021. 3, 12. [Publisher Link]

29. Qian Y., Cosio D. M. O., Piatkevich K. D., Aufmkolk S., Su W.-C., Celiker O. T., Schohl A., Murdock M. H., Aggarwal A., Chang Y.-F., Wiseman P. W., Ruthazer E. S., Boyden E. S., Campbell R. E. Improved Genetically Encoded Near-Infrared Fluorescent Calcium Ion Indicators for in Vivo Imaging. PLOS Biology 2020, 18 (11), e3000965. [Publisher Link]

28. Linghu C., Johnson S.L., Valdes P.A., Shemesh O.A., Park W.M., Park D., Piatkevich K.D., Wassie A.T., Liu Y., An B., Barnes S.A., Celiker O.T, Yao C.-C., Yu C.C., Wang R., Adamala K.P., Bear M.F., Keating A.E., Boyden E.S. Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics, Cell 2020, 183(6), 1682-1698.e24. [Publisher Link]


27. Shemesh O.A.#, Linghu C.#, Piatkevich K.D.#, Goodwin D., Celiker O.T., Gritton H.J., Romano M.F., Gao R., Yu C.-C., Tseng H.-A., Bensussen S., Narayan S., C.-T. Yang C.-T., Freifeld L., Siciliano C.A., Gupta I., Wang J., Pak N., Yoon Y.-G., Ullmann J.F.P., Guner-Ataman B., Noamany H., Sheinkopf Z.R., Park W.M., Asano S., Keating A.E., Trimmer J.S., Reimer J., Tolias A., Bear M.F., Tye K.M., Han X., Ahrens M.B., Boyden E.S. Precision calcium imaging of dense neural populations via a cell body-targeted calcium indicator. Neuron, 2020 107 (3), 470-486. e11 (#equal contribution). [Publisher Link]


26. Fan L.Z., Kheifets S., Böhm U.L., Wu H., Piatkevich K.D., Xie M.E., Parot V., Ha Y., Evans K.E., Boyden E.S., Takesian A.E., Cohen A.E. All-optical electrophysiology reveals the role of lateral inhibition in sensory processing in cortical layer 1. Cell 2020, 180 (3), 521-535. [Publisher Link]

25. Subach O.M., Sotskov V.P., Plusnin V.V., Gruzdeva A.M., Barykina N.V., Ivashkina O.I., Anokhin K.V., Nikolaeva A.Y., Korzhenevskiy D.A., Vlaskina A.V., Lazarenko V.A., Boyko K.M., Rakitina T.V., Varizhuk A.M., Pozmogova G.E., Podgorny O.V., Piatkevich K.D., Boyden E.S., Subach F.V. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Int. J. Mol. Sci., 2020 21 (5), 1644. [Publisher Link]


24. Piatkevich K.D.#, Bensussen S.#, Tseng H.#, Shroff S.N., Lopez-Huerta V.G., Park D., Jung E.E., Shemesh O.A., Straub C., Gritton H.J., Romano M.F., Costa E., Sabatini B.L., Fu Z., Boyden E.S., Han X. Population imaging of neural activity in awake behaving mice. Nature, 2019 574 (7778), 413-417 (#equal contribution). [Publisher Link]


23. Subach O.M, Barykina N.V., Anokhin K.V., Piatkevich K.D., Subach F.V. Near-Infrared Genetically Encoded Positive Calcium Indicator Based on GAF-FP Bacterial Phytochrome. Int. J. Mol. Sci. 2019, 20(14), 3488. [Publisher Link​]

22. Subach O.M., Kunitsyna T.A., Mineyeva O.A., Lazutkin A.A., Bezryadnov D.V., Barykina N.V., Piatkevich K.D., Ermakova Y.G., Bilan D.S., Belousov V.V., Anokhin K.V., Enikolopov G.N., Subach F.V. Slowly reducible genetically encoded green fluorescent indicator for in vivo and ex vivo visualization of hydrogen peroxide. Int. J. Mol. Sci. 2019, 20(13), 3138. [Publisher Link​​]

21. Qian Y.#, Piatkevich K.D.#, McLarney B.#, Abdelfattah A.S., Mehta S., Gottschalk S., Molina R.S., Zhang W., Drobizhev M., Hughes T.E., Zhang J., Schreiter E.R., Shoham S., Razansky D., Boyden E.S., Campbell R.E. A Genetically-Encoded Near-Infrared Fluorescent Calcium Ion Indicator. Nature Methods, 2019. 16 (2), 171 (#equal contribution). [Publisher Link​​]

20. Barykina N.V., Doronin D.A., Subach O.M., Sotskov V.P., Plusnin V.V., Ivleva O.A., Gruzdeva A.M., Kunitsyna T.A., Ivashkina O.I., Lazutkin A.A., Malyshev A.Y., Smirnov I.V., Varizhuk A.M., Pozmogova G.E., Piatkevich K.D., Anokhin K.V., Enikolopov G.N., Subach F.V. NTnC-like genetically encoded calcium indicator with a positive and enhanced response and fast kinetics. Scientific Reports, 8 (1), 15233. [Publisher Link​​​]

19. Piatkevich K.D.#, Jung E.E.#, Straub C., Linghu C., Park D., Suk H.J., Hochbaum D.R., Goodwin D., Pnevmatikakis E., Pak N., Kawashima T., Yang C.-T., Rhoades J.L., Shemesh O., Asano S., Yoon Y.-G., Freifeld L., Saulnier J., Riegler C., Engert F., Hughes T., Drobizhev M., Szabo B., Ahrens M.B., Flavell S.W., Sabatini B.L., Boyden E.S. Robotic multidimensional directed evolution of proteins: development and application to fluorescent voltage reporters. Nature Chemical Biology, 2018. 14 (4), 352. (#equal contribution). [Publisher Link​​​]

18. Doronin D., Barykina N., Subach O., Isaakova E., Varizhuk A., Pozmogova G., Piatkevich K., Anokhin K., Enikolopov G., Subach F. Genetically encoded calcium indicator with NTnC-like design and enhanced fluorescence contrast. BMC Biotechnology, 2018. 18 (1), 10. 

[Publisher Link​​​]

17. Shemesh O.A., Tanese D., Zampini V., Linghu C., Piatkevich K., Ronzitti E., Papagiakoumou E., Boyden E.S., Emiliani V. Temporally precise single-cell resolution optogenetics. Nature Neuroscience. 2017. 20(12), 1796-1806. [Publisher Link​​​]

16. Piatkevich K.D., Suk H.J., Suhasa B.K., Yoshida F., DeGennaro E.M., Drobizhev M., Hughes T.E., Desimone R., Boyden E.S., Verkhusha V.V. Near-infrared fluorescence proteins engineered from bacterial phytochromes in neuroimaging. Biophys. J. 2017. 113(10), 2299-2309. [Publisher Link​​​]

15. Barykina N.V., Subach O.M., Piatkevich K.D., Jung E.E., Malyshev A.Y., Smirnov I.V., Bogorodskiy A.O., Borshchevskiy V.I., Varizhuk A.M., Pozmogova G.E., Boyden E.S., Anokhin K.V., Enikolopov G.N., Subach F.V. Green fluorescent genetically encoded calcium indicator based on calmodulin/M13-peptide from fungi. PLoS One. 2017; 12(8):e0183757. [Publisher Link​​​]

14. Rowlands C.J., Park D., Bruns O.T., Piatkevich K.D., Fukumura D., Jain R.K., Bawendi M.G., Boyden E.S., So P.T.C. Wide-field three-photon excitation in biological samples. Light: Science & Applications. 2017, 6, e16255. [Publisher Link​​​]

13. Barykina N.V., Subach O.M., Doronin D.A., Sotskov V.P., Roshchina M.A., Kunitsyna T.A., Malyshev A.Y., Smirnov I.V., Azieva A.M., Sokolov I.S., Piatkevich K.D., Burtsev M.S., Varizhuk A.M., Pozmogova G.E., Anokhin K.V., Subach F.V., Enikolopov G.N. A new design for a green calcium indicator with a smaller size and a reduced number of calcium-binding sites. Scientific Reports. 2016, 6:34447. [Publisher Link​​​]

12. Konold P.E., Yoon E., Lee J., Allen S.L., Chapagain P.P., Gerstman B.S., Regmi C.K., Piatkevich K.D., Verkhusha V.V., Joo T., Jimenez R. Fluorescence from multiple chromophore hydrogen-bonding states in the far-red protein TagRFP675. J. Phys. Chem. Lett. 2016. 7, 3046-3051. [Publisher Link​​​]

11. Tillberg P.W., Chen F., Piatkevich K.D., Zhao Y., Yu C.C., English B.P., Gao L., Martorell A., Suk H.J., Yoshida F., DeGennaro E.M., Roossien D.H., Gong G., Seneviratne U., Tannenbaum S.R., Desimone R., Cai D., Boyden E.S. Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nature Biotechnology. 2016. 34 (9), 987-992. [Publisher Link​​​]

10. Randino C., Gelabert R., Moreno M., Lluch J.M., Piatkevich K.D. Molecular modeling of the pH influence in the geometry and the absorbance spectrum of near-infrared TagRFP675 fluorescent protein. Phys Chem Chem Phys. 2015. 17:29363. [Publisher Link​​​]

9. Piatkevich K.D., English B.P., Malashkevich V.N., Xiao H., Almo S.C., Singer R.H., Verkhusha V.V. Photoswitchable red fluorescent protein with a large Stokes shift. Chem Biol. 2014. 21:1402. [Publisher Link​​​]

8. Piatkevich K.D., Subach F.V., Verkhusha V.V. Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome. Nature Communications. 2013. 4: 2153. [Publisher Link​​​]

7. Piatkevich K.D., Malashkevich V.N., Morozova K.S., Nemkovich N.A., Almo S.C., Verkhusha V.V. An extended Stokes shift in fluorescent proteins: chromophore-protein interactions in the near-infrared TagRFP675 variant. Scientific Reports. 2013. 3:1847. [Publisher Link​​​]

6. Filonov G.S., Piatkevich K.D., Ting L.M., Zhang J., Kim K., Verkhusha V.V. Bright and stable near-infrared fluorescent protein for in vivo imaging. Nature Biotechnology. 2011 29: 757-61. [Publisher Link​​​]

5. Morozova K.S., Piatkevich K.D., Gould T.J., Zhang J., Bewersdorf J. and Verkhusha V.V. Far-red fluorescent protein excitable with red lasers for flow cytometry and superresolution STED nanoscopy. Biophys. J. 2010. 99: 13-15. [Publisher Link​​​]

4. Piatkevich K.D., Malashkevich V.N., Almo S.C., Verkhusha V.V. Engineering ESPT pathways based on structural analysis of LSSmKate red fluorescent proteins with large Stokes shift. J Am Chem Soc. 2010. 132: 10762-10770. [Publisher Link​​​]

3. Subach O.M., Malashkevich V.N., Zencheck W.D., Morozova K.S., Piatkevich K.D., Almo S.C., and Verkhusha V.V. Structural characterization of acylimine-containing blue and red chromophores in mTagBFP and TagRFP fluorescent proteins. Chem. Biol. (Cell press). 2010. 17: 333-341. [Publisher Link​​​]

2. Piatkevich K.D.#, Hulit J.#, Subach O.M., Wu B., Abdulla A., Segall J.E., Verkhusha V.V. Monomeric red fluorescent proteins with a large Stokes shift. Proc Natl Acad Sci USA. 2010. 107: 5369-5374 (#equal contribution). [Publisher Link​​​[News in Brief​​​

1. Subach F.V., Subach O.M., Gundorov I.S., Morozova K.S., Piatkevich K.D., Cuervo A.M., Verkhusha V.V. Monomeric fluorescent timers that change color from blue to red report on cellular trafficking. Nature Chemical Biology. 2009. 5, 118-126. [Publisher Link​​​[Local Copy] [On the Cover] [News & Views]

bottom of page