Publications

Nature | 2026

Scalable and multiplexed recorders of gene regulation dynamics across weeks

Lirong Zheng*, Dongqing Shi*, Yixiao Yan*, Bingxin Zhou, Jormay Lim, Yongjie Hou, Bobae An, Jason K. Adhinarta, Michael Lin, BumJin Ko, William C. Joesten, Mehul Gautam, Elie D. M. Huez, Eung Chang Kim, Emily G. Klyder, Boxuan Chang, Sethuramasundaram Pitchiaya, Michael T. Roberts, Denise J. Cai, Edward S. Boyden, Donglai Wei, Pietro Liò and Changyang Linghu (* co-first authors)

Summary: we developed CytoTape, a genetically encoded, flexible, intracellular protein tape recorder for spatiotemporally scalable and multiplexed recording of cellular activities continuously across weeks in vitro and in vivo.

Cell Systems | 2025

Integrating synthetic biology to understand and engineer the heart, lung, blood, and sleep systems

Elliot L. Chaikof, Jichao Chen, Martha U. Gillette, Laurie A. Boyer, Tara L. Deans, Pulin Li, Isaac B. Hilton, Kyle Daniels, Yogesh Goyal, Ying Mei, Changyang Linghu, Theresa B. Loveless, David M. Truong, Michael R. Blatchley, Mingxia Gu, Caleb J. Bashor, Jason H. Yang, Ritu Raman, Akhilesh B. Reddy, Krishanu Saha, Jennifer Davis, Kalpna Gupta, Xiaojing J. Gao and Kate E. Galloway

Summary: synthetic biology is transitioning from microbial engineering to the precise control of human cells and tissues, utilizing AI and gene circuits to advance personalized therapies while addressing ongoing technical challenges.

Nature Communications | 2024

Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy

Jie Zhang, Jonathan Newman, Zeguan Wang, Yong Qian, Pedro Feliciano-Ramos, Wei Guo, Takato Honda, Zhe Sage Chen, Changyang Linghu, Ralph Etienne-Cummings, Eric Fossum, Edward S. Boyden and Matthew Wilson

Summary: signal-to-noise ratio in high-speed imaging can be largely enhanced by new cameras with pixel-level control of light exposure timing.

Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM) | 2023

Real-time Neuron Segmentation for Voltage Imaging

Yosuke Bando, Ramdas Pillai, Atsushi Kajita, Farhan Abdul Hakeem, Yves Quemener, Hua-An Tseng, Kiryl D. Piatkevich, Changyang Linghu, Xue Han and Edward S. Boyden

Summary: high-speed image processing enables real-time readout of neural activities during kilohertz voltage imaging.

Nature Biotechnology | 2023

Recording of cellular physiological histories along optically readable self-assembling protein chains

Changyang Linghu, Bobae An, Monika Shpokayte, Orhan T. Celiker, Nava Shmoel, Ruihan Zhang, Chi Zhang, Demian Park, Won Min Park, Steve Ramirez and Edward S. Boyden

Summary: we found that biological information over time, such as gene expression history, can be recorded onto the ordered structure of intracellular protein self-assembly for scalable readout in large cell populations both in vitro and in vivo.

Methods in Molecular Biology | 2022

Single-cell resolution optogenetics via expression of soma-targeted rhodopsins

Changyang Linghu, I-Wen Chen, Dimitrii Tanese, Valeria Zampini and Or A. Shemesh

Summary: methods for temporally precise single-cell resolution optogenetics in tissue and in the living brain.

Cell | 2020 (Cover Story)

Spatial multiplexing of fluorescent reporters for imaging signaling network dynamics

Changyang Linghu*, Shannon L. Johnson*, Pablo A. Valdes, Or A. Shemesh, Won Min Park, Demian Park, Kiryl D. Piatkevich, Asmamaw T. Wassie, Yixi Liu, Bobae An, Stephanie A. Barnes, Orhan T. Celiker, Chun-Chen Yao, Chih-Chieh (Jay) Yu, Ru Wang, Katarzyna P. Adamala, Mark F. Bear, Amy E. Keating and Edward S. Boyden (* co-first authors)

Summary: clustering fluorescent reporters at random points in cells enables many biological signals to be recorded at once.

Neuron | 2020

Precision calcium imaging of dense neural populations via a cell-body-targeted calcium indicator

Or A. Shemesh*, Changyang Linghu*, Kiryl D. Piatkevich*, Daniel Goodwin, Orhan Tunc Celiker, Howard J. Gritton, Michael F. Romano, Ruixuan Gao, Chih-Chieh (Jay) Yu, Hua-An Tseng, Seth Bensussen, Sujatha Narayan, Chao-Tsung Yang, Limor Freifeld, Cody A. Siciliano, Ishan Gupta, Joyce Wang, Nikita Pak, Young-Gyu Yoon, Jeremy F.P. Ullmann, Burcu Guner-Ataman, Habiba Noamany, Zoe R. Sheinkopf, Won Min Park, Shoh Asano, Amy E. Keating, James S. Trimmer, Jacob Reimer, Andreas S. Tolias, Mark F. Bear, Kay M. Tye, Xue Han, Misha B. Ahrens and Edward S. Boyden (* co-first authors)

Summary: restricting fluorescent calcium reporter expression to neuronal somata enables in vivo imaging of neuronal population activity at true single-cell resolution.

Nature Chemical Biology | 2018

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

Kiryl D. Piatkevich*, Erica E. Jung*, Christoph Straub, Changyang Linghu, Demian Park, Ho-Jun Suk, Daniel R. Hochbaum, Daniel Goodwin, Eftychios Pnevmatikakis, Nikita Pak, Takashi Kawashima, Chao-Tsung Yang, Jeffrey L. Rhoades, Or Shemesh, Shoh Asano, Young-Gyu Yoon, Limor Freifeld, Jessica L. Saulnier, Clemens Riegler, Florian Engert, Thom Hughes, Mikhail Drobizhev, Balint Szabo, Misha B. Ahrens, Steven W. Flavell, Bernardo L. Sabatini and Edward S. Boyden (* co-first authors)

Summary: a robotic multidimensional screening system for mammalian cells enables rapid development of bright fluorescent proteins and faithful fluorescent voltage indicators.

Nature Neuroscience | 2017

Temporally precise single-cell resolution optogenetics

Or A. Shemesh*, Dimitrii Tanese*, Valeria Zampini*, Changyang Linghu, Kiryl Piatkevich, Emiliano Ronzitti, Eirini Papagiakoumou, Edward S. Boyden+ and Valentina Emiliani+ (* co-first authors; + co-corresponding authors)

Summary: soma-targeted opsins, together with computer-generated holography systems, enable temporally precise, single-cell resolution optogenetics.

Chinese Physics B | 2013

Graphene applications in electronic and optoelectronic devices and circuits

Huaqiang Wu, Changyang Linghu, Hongming Lu and He Qian

Summary: a review of how the unique properties of graphene could be utilized for better electronic and optoelectronic devices.

Proceedings of International Conference on Simulation of Semiconductor Processes and Devices (SISPAD) | 2012

Compact model of graphene field effect transistors and its application in circuit simulation of RF mixer consisting of GFETs and CMOS

Weinan Zhu, Changyang Linghu, Jinyu Zhang, Lei Zhang, and Zhiping Yu

Summary: modeling graphene-based transistors helps to design integrated circuits that contain both graphene-based transistors and conventional semiconductor transistors.