PIATKEVICH LAB

School of Life Sciences

Westlake University

 

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ADDRESS

 

Bld 3, room 514

No.18, Shilongshan Road, Cloud Town

Xihu District, Hangzhou

Zhejiang, China 310024

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Copyright 2019-present, Kiryl Piatkevich kiryl.piatkevich@westlake.edu.cn.

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 Publications

Peer-reviewed research papers:

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.

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.

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).

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.

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).

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.

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.

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.

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.

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;

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.

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

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.

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.

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.

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.

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.

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.

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.

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.  

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.

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).

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.

Peer-reviewed review articles and chapters in books:
Peer-reviewed review articles and chapters in books:

7. Piatkevich K.D.*, Murdock M.H., Subach F.V.* Advances in engineering and application of optogenetic indicators for neuroscience. Applied Sciences. 2019, 9(3), 562. (*co-corresponding).

6. Piatkevich K.D., Subach F.V., Verkhusha V.V. Engineering of bacterial phytochromes for near-infrared imaging, sensing, and light-control in mammals. Chemical Society Reviews. 2013. 42(8):3441-52. ·

5. Wu B.*, Piatkevich K.D.*, Lionnet T., Singer R.H., Verkhusha V.V. Modern fluorescent proteins and imaging technologies to study gene expression, nuclear localization, and dynamics. Curr. Opin. Cell Biol. 2011. 23:310-317. (*equal contribution).

4. Subach F.V.*, Piatkevich K.D.*, Verkhusha V.V. Directed molecular evolution to design advanced red fluorescent proteins. Nature Methods. 2011, 8:1019-26. (*equal contribution).

3. Piatkevich K.D., Verkhusha V.V. Guide to red fluorescent proteins and biosensors for flow cytometry. Methods in Cell Biology. 2011. 102:431-461.

2. Piatkevich K.D., Verkhusha V.V. Advances in engineering of fluorescent proteins and photoactivatable protein with red emission. Curr. Opin. Chem. Biol. 2010. 14: 23-29.

1. Piatkevich K.D., Efremenko E.N., Verkhusha V.V., Varfolomeev S.D. Red fluorescent proteins and their properties. Russ. Chem. Reviews. 2010. 79: 243-258.

Patents:

2. Boyden E., Piatkevich K., Jung E. Genetically encoded red fluorescent voltage sensors enabling millivolt-resolution and high-speed neural voltage imaging. US Patent App. 16/026,551

1. Adamala K., Xu G., Boyden E., Piatkevich K.D. Spatial multiplexing for multisignal cellular imaging. US Patent US20160304861 A1