An updated list of publications can be found on Google ScholarPubMed or ORCID

(*corresponding authors)

Journal Cover

Payel Mondal, Vishnu Krishnamurthy, Savanna Sharum, Neeka Haack, Huiwen Zhou, Jennifer Cheng, Jing Yang, and Kai Zhang* “Repurposing protein degradation for optogenetic modulation of protein activities”, ACS Synthetic Biology, 2019,  8, 11, 2585-2592. [Link][PDF]

About the Cover:

The GLIMPSe optogenetic system uses a degradation module to constitutively degrade a target protein until a protease-mediated rescue module cleaves the degradation sequence and stabilizes the protein. Stabilization of proteins that downregulate (MKP3) or upregulate (CA MEK) the ERK signaling pathway reduces or enhances neurite outgrowth in PC12 neuronal cells. View the article.

Parinaz Fathi, Ayman Roslend, Kritika Mehta, Parikshit Moitra, Kai Zhang and Dipanjan Pan “UV-Trained and Metal-Enhanced Fluorescence of Biliverdin and Biliverdin Nanoparticles”, Nanoscale, 2020 (Inside Front Cover). [Link][PDF]

Vishnu V. Krishnamurthy, Hyojeong Hwang, Jia Fu, Jing Yang*, Kai Zhang*, “Optogenetic control of the canonical Wnt signaling pathway during Xenopus laevis embryonic development”, Journal of Molecular Biology, 2021 (Outside Front Cover) [Link][PDF].

The low-density lipoprotein receptor protein 6, or LRP6, mediates the canonical Wnt signaling pathway and plays an essential role during development and disease. The authors demonstrated optogenetic activation of the Wnt pathway by light-inducible cytoplasm-to-membrane translocation of the LRP6 cytosolic domain, which induces body axis duplication in developing frog embryos. The cover refers to the article by Krishnamurthy et al. “Optogenetic control of the canonical Wnt signaling pathway during Xenopus laevis embryonic development ” in JMB Volume 433, Issue 18, Pages 1–12. Ella Maru Studio designed the illustration.


Guest Edited Article Collection in the Journal of Molecular Biology

Chemogenetics and Optogenetics – Control intracellular signal transduction in living cells and organisms


59. Kangqiang Qiu, Weiwei Zou, Hongbao Fang, Mingang Hao, Kritika Mehta, Zhiqi Tian, Jun-Lin Guan*, Kai Zhang*, Taosheng Huang*, Jiajie Diao*, “Light-activated mitochondrial fission through optogenetic control of mitochondria-lysosome contacts,” Nature Communications, 13, 4303 (2022). [LINK][PDF]

58. Savanna Sharum Skeeters; Tyler Camp; Huaxun Fan; Kai Zhang*, “The expanding role of split protein complementation in opsin-free optogenetics”, Current Opinion in Pharmacology, 2022, 65:102236 [Link][PDF].

57. Vishnu V. Krishnamurthy, Hyojeong Hwang, Jia Fu, Jing Yang*, Kai Zhang*, “Optogenetic control of the canonical Wnt signaling pathway during Xenopus laevis embryonic development”, Journal of Molecular Biology, 2021, 433,18,167050. (Featured Communication, Outside Front Cover) [Link][PDF].

Highlighted in UI News Bureau, School of MCB
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56. Parinaz Fathi, Ayman Roslend, Kritika Mehta, Parikshit Moitra, Kai Zhang and Dipanjan Pan “UV-Trained and Metal-Enhanced Fluorescence of Biliverdin and Biliverdin Nanoparticles”, Nanoscale, 2021 (Inside Front Cover). [Link][PDF]

55. Teak-Jung Oh, Huaxun Fan, Savanna S. Skeeters, Kai Zhang* “Steering Molecular Activity with light: Recent Advances and Perspectives”, Advanced Biology, 2021, 202000180. [Link][PDF].  (These authors contributed to this work equally).

54. Qixin Chen, Hongbao Fang, Xintian Shao, Zhiqi Tian, Yuming Zhang, Huaxun Fan, Kai Zhang*, Weijiang He*, Zijian Guo*, Jiajie Diao*, “A dual-labeling probe to track functional mitochondria–lysosome interactions in live cells”, Nature Communications, 2020,11, 6290. [Link][PDF].

53. Savanna S. Skeeters, Ana C. Rosu, Divyanshi, Jing Yang, Kai Zhang* “Comparative determination of cytotoxicity of sub-10-nm copper nanoparticles to prokaryotic and eukaryotic cells”, ACS Applied Materials & Interfaces, 2020,12, 45, 50203–50211. [Link][PDF].

52. Qin Wang, Huaxun Fan, Feng Li, Savanna R. Sharum, Vishnu Krishnamurthy, Yuanquan Song*, Kai Zhang* “Spatiotemporal optogenetic control of neurotrophin signaling accelerates axon regeneration and functional recovery in the peripheral and central nervous system”, eLife, 2020, 9: e57395 [Link][PDF] [bioRxiv].

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51. Taida Huang, Yan Zhang, Zitian Wang, Hongda Chen, Nan Wang, Huaxun Fan, Zhangsen Huang, Yixun Su, Xiaomin Huang, Hui Chen, Kai Zhang*, Chenju Yi*, Optogenetically-controlled TrkA activity improves the regenerative capacity of hair-follicle-derived stem cells to differentiate into neurons and glia”, Advanced Biosystems, 2020, 2000134. [LINK][PDF].

50. Kai Zhang*, Vishnu V. Krishnamurthy, “Enabling versatile control of molecular activity with small molecules and light”, Journal of Molecular Biology, 2020, 432, 19, 5209-5211. [Link][PDF]

49. Miaoling Li§, Teak-Jung Oh§, Huaxun Fan§, Jiajie Diao*, Kai Zhang*, “Syntaxin Clustering and Optogenetic Control for Synaptic Membrane Fusion”,  Journal of Molecular Biology, 2020, 432, 4773-4782. (§ These authors contributed to this work equally). [Link][PDF][Corrigendum]

48. Yixun Su, Xiaomin Huang, Zhangsen Huang, Taida Huang, Tao Li, Huaxun Fan, Kai Zhang*, Chenju Yi*, “Early but not Delayed RAF Activation Promotes Astrocytogenesis in Mouse Neural Progenitors Resolved by Optogenetics”, Journal of Molecular Biology, 2020, 432, 16, 4358-4368. [Link][PDF]

47. Melody Esmaeili, Shelby Blythe, Kai Zhang, Jing Yang, Peter Klein “Loss of Competence in early development is mediated by loss of chromatin accessibility”, Developmental Biology, 2020, 452,1, 20-35. [Link][PDF].

46. Vishnu V. Krishnamurthy, Jia Fu,  Teak-Jung Oh, John Khamo, Jing Yang*, Kai Zhang* “A Generalizable Optogenetic Strategy to Regulate Receptor Tyrosine Kinases during Vertebrate Embryonic Development”, Journal of Molecular Biology, 2020, 432, 10, 3149-3158. [Link][PDF].

45. Tyler Camp, Kritika Mehta, Stephen Sligar*, Kai Zhang*, “Molecular Orientation Determination in Nanodiscs at the Single-Molecule Level”, Analytical Chemistry, 2019, 92, 2, 2229-2236  [Link][PDF].

44. Zichen Wang, Huaxun Fan, Xiao Hu, John Khamo, Jiajie Diao*, Kai Zhang*, Taras Pogorelov* “Coaction of Electrostatic and Hydrophobic Interactions: Dynamic Constraints on Disordered TrkA Juxtamembrane Domain”, Journal of Physical Chemistry B, 2019, 123, 50, 10709-10717. [Link][PDF].

43. Payel Mondal, Vishnu Krishnamurthy, Savanna Sharum, Neeka Haack, Huiwen Zhou, Jennifer Cheng, Jing Yang, and Kai Zhang* “Repurposing protein degradation for optogenetic modulation of protein activities”, ACS Synthetic Biology, 2019. 8, 11, 2585-2592. [Link][PDF](Cover).

Research highlighted in UIUC News Bureau and Beckman Bulletin

Highlighted in Science Daily.

Highlighted in Nanowerk.

42. Indrajit Srivastava, John S. Khamo, Subhendu Pandit, Parinaz Fathi, Xuedong Huang, Anleen Cao, Richard T. Haasch, Shuming Nie, Kai Zhang*, Dipanjan Pan* “Influence of Electron Acceptor and Electron Donor on the Photophysical Properties of Carbon Dots: A Comparative Investigation at the Bulk‐State and Single‐Particle Level. Advanced Functional Materials, 2019, 29,1902466 [Link][PDF].

41. Bin Cai, Luning Yu, Savanna R. Sharum, Kai Zhang*, and Jiajie Diao*, “Single-vesicle measurement of protein-induced membrane tethering”, Colloids and Surfaces B: Biointerfaces, 2019, 177, 267-273. [Link][PDF].,

40. Hyojeong Hwang, Zhigang Jin, Vishnu Vardhan Krishnamurthy, Anumita Saha, Peter S. Klein, Benjamin Garcia, Wenyan Mei, Mary Lou King, Kai Zhang, Jing Yang “Novel functions of the ubiquitin-independent proteasome system in regulating Xenopus germline development”, Development, 2019: vol. 146 no. 8, dev172700. DOI: 10.1242/dev.172700. [Link][PDF]

39. Vishnu Krishnamurthy, John Khamo, Payel Mondal, Savanna Sharum, Jing Yang, and Kai Zhang* “Reversible Optogenetic Control of Growth Factor Signaling During Cell Differentiation and Vertebrate Embryonic Development”, Biophotonics Congress: Optics in the Life Sciences Congress, 2019, AW1E.1. [Link][PDF].

38. John S. Khamo, Vishnu V. Krishnamurthy, Qixin Chen, Jiajie Diao*, and Kai Zhang*, “Optogenetic delineation of receptor tyrosine kinase subcircuits in PC12 cell differentiation“, Cell Chemical Biology, 2019, 26, 400-410. [Link][PDF].

Highlighted in UIUC MCB and Neuroscience Program News

37. Qixin Chen, Xintian Shao, Zhiqi Tian, Yang Chen, Payel Mondal, Fei Liu, Fengshan Wang, Peixue Ling*, Weijiang He*, Kai Zhang*, Zijian Guo, and Jiajie Diao*, “Nanoscale Monitoring of Mitochondria and Lysosome Interactions for Drug Screening and Discovery”, Nano Research, 2019, 12, 5, 1009–1015. [Link][PDF].

36. Parinaz Fathi, John S. Khamo, Xuedong Huang, Indrajit Srivastava, Mandy B. Esch, Kai Zhang*, and Dipanjan Pan* “Bulk-state and single-particle imaging are central to understanding carbon dot photo-physics and elucidating the effects of precursor composition and reaction temperature” Carbon, 2019, 145, 572-585. [Link] [PDF].

35. Santosh K. Misra, Indrajit Srivastava,  John S. Khamo, Vishnu V. Krishnamurthy, Dinabandhu Sar, Aaron S. Schwartz-Duval, Julio A. N. T. Soares, Kai Zhang*, and Dipanjan Pan*Carbon Dots with Induced Surface Oxidation Permits Imaging at Single-Particle Level for Intracellular Studies”, Nanoscale, 2018, 10(39) 18510-18519. (DOI: 10.1039/c8nr04065f). [Link][PDF]

The press release can be found UIUC MCB and Neuroscience Program News

34. Vishnu V. Krishnamurthy, and Kai Zhang* “Chemical physics in living cells – using light to visualize and control intracellular signal transduction” Chinese Journal of Chemical Physics, 2018, 31(4), 375-392. [Link][PDF]

  • Happy 60th Birthday, USTC!

33. Kijung SungLuiz F. FerrariWanlin YangChiHye ChungXiaobei ZhaoYingli GuSuzhen LinKai ZhangBianxiao CuiMatthew L. PearnMichael T. MaloneyWilliam C. MobleyJon D. Levine, and Chengbiao Wu “Swedish Nerve Growth Factor Mutation (NGFR100W) Defines a role for TrkA and p75NTR in Nociception”, Journal of Neuroscience, 2018 38(14): 3394-3413. [Link][PDF]

32. John S. Khamo, Vishnu V. Krishnamurthy, Payel Mondal, Savanna R. Sharum, and Kai Zhang*  “Applications of optobiology in intact cells and multi-cellular organisms”, Journal of Molecular Biology, 2017, 429, 2999-3017. [Link][PDF]

Highlight: Journal of Molecular Biology: Spotlight on Early Career Researchers

31. Vishnu V. Krishnamurthy, Aurora. J. Turgeon, John S. Khamo, Payel Mondal, Savanna. R. Sharum, Wenyan Mei, Jing Yang*, and Kai Zhang* “Light-mediated reversible modulation of the mitogen-activated protein kinase pathway during cell differentiation and Xenopus embryonic development”, Journal of Visualized Experiments, 2017, 124, e55823. [Link][PDF]

30. Yasuko Osakada, and Kai Zhang “Single-particle tracking reveals a dynamic role of actin filaments in assisting long-range axonal transport in neurons” Bulletin of the Chemical Society of Japan (BCSJ), 2017, 90, 714-719. [Link][PDF]

29. Payel Mondal, John S. Khamo, Vishnu V. Krishnamurthy, Qi Cai, and Kai Zhang*  “Drive The Car(go)s—New Modalities to Control Cargo Trafficking in Live Cells” Frontier in Molecular Neuroscience, 2017, 10, 4. [Link][PDF].


28. Vishnu V. Krishnamurthy, and Kai Zhang* ” Simultaneous removal of multiple DNA segments by polymerase chain reactions” Methods in Molecular Biology, Synthetic DNA, Ed R. Hughes. (Springer New York)  2017, 1472, 193-203. [Link][PDF]ZhangCoverart

27. Vishnu V. Krishnamurthy, John S. Khamo, Wenyan Mei, Aurora J. Turgeon, Humza M. Ashraf, Payel Mondal, Dil B. Patel, Noah Risner, Ellen E. Cho, Jing Yang*, and Kai Zhang* “Reversible optogenetic control of kinase activity during differentiation and embryonic development” Development, 2016, 143, 4085-4094. [Link][PDF]


26. Vishnu V. Krishnamurthy, John S. Khamo, Ellen Cho, Cara Schornak, and Kai Zhang* “Polymerase chain reaction-based gene removal from plasmids”, Data in Brief, 2015, 4, 75-82.  [Link][PDF]

25. Vishnu V. Krishnamurthy, John S. Khamo, Ellen Cho, Cara Schornak, and Kai Zhang* “Multiplex gene removal by two-step polymerase chain reactions”, Analytical Biochemistry, 2015, 481, 7-9. [Link][PDF]


Postdoctoral work at Stanford (2009-2014)

24. Qunxiang Ong, Shunling Guo, Liting Duan, Kai Zhang, Eleanor A. Collier, and Bianxiao Cui “The Timing of Raf/ERK and AKT Activation in Protecting PC12 Cells against Oxidative Stress”, PLOS ONE, 2016, e0153487. [Link][PDF]

23. Kai Zhang* and Bianxiao Cui* “Optogenetic control of intracellular signaling pathways”, Trends in Biotechnology, 2015, 33, 92-100. [Link][PDF]

22. Liting Duan, Daphne Che, Kai Zhang, Qunxiang Ong, Shunling Guo, and Bianxiao Cui, Optogenetic control of molecular motors and organelle distributions in cells, Chemistry & Biology, 2015, 22, 671-682. [Link][PDF]

21. Praveen D. Chowdary, Daphne Che, Kai Zhang, and Bianxiao Cui “Retrograde NGF axonal transport – coordination of opposite polarity motors near unidirectional motility regime” Biophysical Journal, 2015, 108, 2691-2703. [Link][PDF]

20. Daphne L. Che, Liting Duan, Kai Zhang, and Bianxiao Cui, The dual characteristics of light-induced cryptochrome 2 homo-oligomerization and hetero-dimerization for optogenetic manipulation in mammalian cells, ACS Synthetic Biology, 2015, 4, 1124-1135. [Link][PDF]

19. Qunxiang Ong, Shunling Guo, Kai Zhang, and Bianxiao Cui “U0126 Protects Cells against Oxidative Stress Independent of Its Function as a MEK Inhibitor”, ACS Chemical Neuroscience, 2015, 6,130–137. [Link][PDF]

18. Kai Zhang, Praveen D. Chowdary, and Bianxiao Cui “Visualizing directional Rab7 and TrkA cotrafficking in axons by pTIRF microscopy” Methods in Molecular Biology, 2015, 1298:319-29. [Link][PDF]

17. Kai Zhang and Bianxiao Cui “Lighting up FGFR signaling”, Chemistry & Biology, 2014, 21, 806-808. [Link][PDF]

16. Kai Zhang, Liting Duan, Qunxiang Ong, Ziliang Lin, Pooja Varman, Kijung Sung, and Bianxiao Cui “Light-mediated kinetic control reveals the temporal effect of the Raf/Mek/ERK pathway in PC12 cell neurite outgrowth”, PLOS ONE, 2014, 9, e92917. [Link][PDF]

15. Kai Zhang, Rotem F. B. Kenan, Yasuko Osakada, Wei Xu, Rachel S. Sinit, Liang Chen, Xiaobei Zhao, Jia-Yun Chen, Bianxiao Cui, and Chengbiao Wu “Defective Axonal Transport of Rab7 GTPase Results in Dysregulated Trophic Signaling”, J. Neuroscience 2013, 33, 7451-7462. [Link][PDF]

14. Wenjun Xie, Kai Zhang, and Bianxiao Cui “Functional characterization and axonal transport of quantum dot labeled BDNF”, Integrative Biology, 2012, 4, 953-960. [Link][PDF]

13. Kai Zhang, Yasuko Osakada, Wenjun Xie, and Bianxiao Cui “Automated image analysis for tracking cargo transport in axons”, Microscopy Research and Technique 2011, 74, 605-613. [Link][PDF]

12. Keith A. Vossel, Kai Zhang, Jens Brodbeck, Aaron C. Daub, Punita Sharma, Steven Finkbeiner, Bianxiao Cui, and Lennart Mucke “Tau reduction ameliorates Aβ-induced impairments in axonal transport”, Science 2010, 330 198. [Link][PDF]

11. K. Zhang, Yasuko Osakada, Marijia Vrljic, Liang Chen, Harsha V. Mudrakola, and Bianxiao Cui “Single-molecule imaging of NGF axonal transport in a microfluidic device ”, Lab Chip 2010, 10, 2566-2573. [Link][PDF]

10. Harsha V. Mudrakola, Chengbiao Wu, Kai Zhang, and Bianxiao Cui, “Single Molecule Imaging of Axonal Transport in Live Neurons”, in Laser Science XXV, OSA Technical Digest (CD) (Optical Society of America, 2009), LSThB3. [Link][PDF]

9. Harsha V. Mudrakola*, Kai Zhang*, and Bianxiao Cui “Optically resolving individual microtubules in live axons using dynamic object tracking”, Structure 2009, 17, 1433-1441. [Link][PDF]

Graduate work at UC-Berkeley (2002-2008)

8. Kai Zhang, Wenkai Zhang, Chia-Yi Yang, and Haw Yang “Bipolar Cellular Morphology of Malignant Melanoma in Unstained Human Melanoma Skin Tissue”, J. Biomed. Opt. 2009, 14, 024042. [Link][PDF]

7. Sha Li, Kai Zhang, Jui-Ming Yang, Liwei Lin, and Haw Yang “MEMS Temperature Characterization by CdSe Quantum Dots”, The 14th International Conference on Solid-State Sensors, Actuators and Microsystems, 2007, 1369-1372. [Link][PDF]

6. Kai Zhang, Na Ji, Yuen-Ron Shen, and Haw Yang “Optically Active Sum Frequency Generation Microscopy for Cellular Imaging”, Ultrafast Phenomena XV Eds. P. Corkum, D. Jonas, D. Miller, A. M. Weiner, (Springer-Verlag, Berlin Heidelberg), 2007, 825. [Link][PDF]

5. Sha Li, Kai Zhang, Jui-Ming Yang, Liwei Lin, and Haw Yang “Single Quantum Dots as Local Temperature Markers”, Nano Lett. 2007, 7, 3102-3105. [Link][PDF]

4. Na Ji, Kai Zhang, Haw Yang, and Yuen-Ron Shen “Three-Dimensional Chiral Imaging by Sum Frequency Generation”, J. Am. Chem. Soc. 2006, 128, 3482-3483. [Link][PDF]

3. Kai Zhang, Hauyee Chang, Aihua Fu, A. Paul Alivisatos, and Haw Yang “Continuous Distribution of Emission States from Single CdSe/ZnS quantum dots”, Nano Lett. 2006, 6, 843-847. [Link][PDF]

2. Kai Zhang and Haw Yang “Photon-by-Photon Determination of Emission Burst from Diffusion Single Chromophores”, J. Phys. Chem. B. 2005, 109, 21930-21937. [Link][PDF]

Undergraduate work at USTC (1997-2002)

1. K. Zhang, Zhijing Liu, and Keyi Wang “Formation and Applications of Laser-Excited Surface Plasma Waves”, Chinese J. Nature 2002, 24, 44-47.