Peer-reviewed research papers:

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​​​]

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​​​]