Hod Dana Laboratory

Research

Research interests

"Progress in science depends on new techniques, new discoveries, and new ideas, probably in that order" - Sydney Brenner

In the lab, we develop new methods and platforms for enabling large-scale recording and manipulation of neurons in the living brain. We believe that this approach is essential for a better understanding of how the spatially-distributed and highly-interconnected circuits in the mammalian brain integrate sensory input and transform it into motor action, especially in the context of neurodegeneration or various neurologic conditions. This type of computation is also involved in almost any behavior or decision-making process we do in our everyday life; therefore, we want to gain a deeper understanding of its nature. We work with state-of-the-art optical tools, such as ultrafast lasers, nonlinear microscopy and high-harmonic generation, as well as with novel protein sensors and actuators for detecting and manipulating the brain activity.

The research in the lab is interdisciplinary and collaborative in its nature, and combines approaches from different fields - such as engineering, physics, structural biology, and systems neuroscience. Our current projects include:

1) Recording from freely-moving mice. We work with CaMPARI, a sensor that can report the integrated activity of single neurons during a user-defined time window. A CaMPARI-based recording method we developed allows recording of cellular-resolution activity patterns across large cortical area from mice, without using any mechanical restriction during the recording. This recording method enables gaining detailed data from the rodent brain during non-interrupted behaviors, and we work on applying it to study changes in brain activity during the progression of neurodegenerative conditions.  

2) The effect of demyelination on the brain functionality. Myelin is a protective sheath, which insulates axons in the central and peripheral nervous system, and is essential for normal functioning of the brain. In some diseases, such as Multiple Sclerosis, the myelin is damaged, which leads to motor and cognitive deficits. We use a rodent model to study how the brain activity is affected during demyelination and how we can protect the neurons from the associated damage. 

3) Stroke is one of the leading causes for disability in the USA and the western world. Due to improved medical treatment protocols, more patients survive the stroke event, but they may suffer from long-term effects on the quality of their activities of daily living. Currently, the ability to assist these patients to fully recover is limited. We work in the lab with a rat model for ischemic stroke injury, in collaboration with stroke researchers and clinicians, to test new treatments that may be translated in the future to assist stroke patients.

News

Nature Methods

-Dr. Dana's work on genetically encoded calcium indicators (GECIs) was featured in the Nature Methods article "20 years of Nature Methods: how some papers shaped science and careers" (Oct 9, 2024).

-Research Highlights coverage in Nature Methods : "Sensing calcium in red" (2016)   

-Research Highlights coverage in Nature Methods: "A snapshot of active neurons" (2015)

Selected Publications

View publications for Hod Dana, PhD
(Disclaimer: This search is powered by PubMed, a service of the U.S. National Library of Medicine. PubMed is a third-party website with no affiliation with Cleveland Clinic.)

Das A*, Icardi J*, Borovicka J, Holden S, Harrison H F, Hirsch A J, Raber J, and Dana H. (2025) "Exposure to COVID-19 virus-like particles modulates firing patterns of cortical neurons in the living mouse brain", Communications Biology, 8, 993.

Paouri E*, Stanko S*, Gasmi N, Glusauskas G, Mao V, Kwak A, Sarmadi S, Huang E, Hershberger C, Watercutter Q, Burton H, Crockett A, Gjojdeshi A, McMullen MR, Hanamsagar RM, Rotroff DM, Prayson RA, Bilbo SD, Valadkhan S, Dana H, Nagy LE, Davalos D. (2025) Preventing Microglial Reactivity Protects from Acute and Progressive Neuronal Dysfunction, Motor Impairments and Sedation following Alcohol Abuse, Biorxiv preprint.

Das A, Borovicka J, Tobin H, Bhatia S,  Icardi J, Tahmasebi G, Agochiya P,  Singh S, Manworren J, Philopater I, Trapp B, and Dana H. (2025) "Neuronal Silencing and Protection in a Mouse Model of Demyelination", BioRxiv Preprint.

Dana H., "Accelerating protein sensor optimization with machine learning", News&Views, Nature Computational Science 4, 165–166 (2024). DOI: https://doi.org/10.1038/s43588-024-00612-9

Das A, Holden S., Borovicka J., Icardi J., O’Niel A., Chaklai A., Patel D., Patel R., Kaech Petrie S., Raber J., and Dana H. (2023), “Recording large-scale, cellular-resolution neuronal activity from freely-moving mice”, Nature Communications, 14, 6399 .

Chornyy S, Borovicka JA, Patel D, Shin MK, Vazquez-Rosa E, Miller E, Wilson B, Pieper AA, and Dana H. (2023) Longitudinal in vivo monitoring of axonal degeneration after brain injury. Cell Reports Methods, (3), 5, 100481(2023). 

Li B., Kong L. Piatkevich KD, and Dana H. (2023) Editorial: Large-scale recording of neuronal activity at high spatiotemporal resolutions and applications in neuroscience. Frontiers in Neuroscience 17 (Editorial summary of a special issue on Large-scale recording of neuronal activity at high spatiotemporal resolutions and applications in neuroscience).

Das A*, Margevicius D*, Borovicka J, Icardi J, Patel D, Paquet ME, and Dana H. (2023) Enhanced detection sensitivity of neuronal activity patterns using CaMPARI1 vs. CaMPARI2. Frontiers in Neuroscience 16 -2022. PMID: 36704000, PMCID: PMC9871923  

Chornyy S, Das A, Borovicka JA, Patel D, Chan HH, Hermann JK, Jaramillo TC, Machado AG, Baker KB, Dana H. (2021) Cellular-resolution monitoring of ischemic stroke pathologies in the rat cortex. Biomed Optics Express 16;12(8):4901-4919. PMID: 34513232; PMCID: PMC8407830

Jin C, Kong L, Dana H, Xie H, Cao L, Jin G, Dai Q. (2020) Advances in point spread function engineering for functional imaging of neural circuits in vivo. Journal of Physics D: Applied Physics 53 38300

Dana H, Shoham S. (2020). Two-photon microscopy in the mammalian Brain. In: Handbook of Neurophotonics (Pavone F, Shoham S, eds.) CRC Press, Chapter 3, pp. 55-79.

Das A, Bastian C, Trestan L, Suh J, Dey T, Trapp BD, Baltan S, Dana H. (2020) Reversible Loss of Hippocampal Function in a Mouse Model of Demyelination/Remyelination. Frontiers in Cellular Neuroscience Jan 22;13:588. PMID: 32038176; PMCID: PMC6987410

Dana H, Sun Y, Mohar B, Hulse BK, Kerlin AM, Hasseman JP, Tsegaye G, Tsang A, Wong A, Patel R, Macklin JJ, Chen Y, Konnerth A, Jayaraman V, Looger LL, Schreiter ER, Svoboda K, Kim DS. (2019) High-performance calcium sensors for imaging activity in neuronal populations and microcompartments. Nature Methods 16(7):649-657. PMID: 31209382

Moeyaert B, Holt G, Madangopal R, Perez-Alvarez A, Fearey BC, Trojanowski NF, Ledderose J, Zolnik TA, Das A, Patel D, Brown TA, Sachdev RNS, Eickholt BJ, Larkum ME, Turrigiano GG, Dana H, Gee CE, Oertner TG, Hope BT, Schreiter ER. (2018) Improved methods for marking active neuron populations. Nature Communications 25;9(1):4440. PMID: 30361563; PMCID: PMC6202339

Dana H, Novak O, Guardado-Montesino M, Fransen JW, Hu A, Borghuis BG, Guo C, Kim DS, Svoboda K. (2018) Thy1 transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imaging in vivo. PLoS One Oct 11;13(10):e0205444. PMID: 30308007 PMCID: PMC6181368

Shen Y, Dana H, Abdelfattah AS, Patel R, Shea J, Molina RS, Rawal B, Rancic V, Chang YF, Wu L, Chen Y, Qian Y, Wiens MD, Hambleton N, Ballanyi K, Hughes TE, Drobizhev M, Kim DS, Koyama M, Schreiter ER, Campbell RE. (2018) A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578. BMC Biology 16(1):9. PMID: 29338710; PMCID: PMC5771076

Sun Y, Nern A, Franconville R, Dana H, Schreiter ER, Looger LL, Svoboda K, Kim DS, Hermundstad AM, Jayaraman V. (2017) Neural signatures of dynamic stimulus selection in Drosophila. Nature Neuroscience 20(8):1104-1113. PMID: 28604683

Dana H, Mohar B, Sun Y, Narayan S, Gordus A, Hasseman JP, Tsegaye G, Holt GT, Hu A, Walpita D, Patel R, Macklin JJ, Bargmann CI, Ahrens MB, Schreiter ER, Jayaraman V, Looger LL, Svoboda K, Kim DS. (2016) Sensitive red protein calcium indicators for imaging neural activity. Elife Mar 24;5. pii: e12727. PMID: 27011354; PMCID: PMC4846379

Chu J, Oh Y, Sens A, Ataie N, Dana H, Macklin JJ, Laviv T, Welf ES, Dean KM, Zhang F, Kim BB, Tang CT, Hu M, Baird MA, Davidson MW, Kay MA, Fiolka R, Yasuda R, Kim DS, Ng HL, Lin MZ. (2016) A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo. Nature Biotechnology 34(7):760-7. PMID: 27240196; PMCID: PMC4942401

Paluch-Siegler S, Mayblum T, Dana H, Brosh I, Gefen I, Shoham S. (2015) All-optical bidirectional neural interfacing using hybrid multiphoton holographic optogenetic stimulation. Neurophotonics 2(3):031208. PMID: 26217673; PMCID: PMC4512959

Fosque BF*, Sun Y*, Dana H*, Yang CT, Ohyama T, Tadross MR, Patel R, Zlatic M, Kim DS, Ahrens MB, Jayaraman V, Looger LL, Schreiter ER. (2015) Labeling of active neural circuits in vivo with designed calcium integrators. Science 347(6223):755-60. PMID: 25678659

Dana H, Chen TW, Hu A, Shields BC, Guo C, Looger LL, Kim DS, Svoboda K. (2014) Thy1-GCaMP6 transgenic mice for neuronal population imaging in vivo. PLoS One 9(9):e108697. PMID: 25250714; PMCID: PMC4177405

Thestrup T, Litzlbauer J, Bartholomäus I, Mues M, Russo L, Dana H, Kovalchuk Y, Liang Y, Kalamakis G, Laukat Y, Becker S, Witte G, Geiger A, Allen T, Rome LC, Chen TW, Kim DS, Garaschuk O, Griesinger C, Griesbeck O. (2014) Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes. Nature Methods 11(2):175-82. PMID: 24390440

Dana H*, Marom A*, Paluch S, Dvorkin R, Brosh I, Shoham S. (2014) Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks. Nature Communications 5:3997. PMID: 24898000; PMCID: PMC4113029

Dana H, Kruger N, Ellman A, Shoham S. (2013) Line temporal focusing characteristics in transparent and scattering media. Optics Express 21(5):5677-87. PMID: 23482141

Dana H, Shoham S. (2012) Remotely scanned multiphoton temporal focusing by axial grism scanning. Optics Letters 37(14):2913-5. PMID: 22825176

Szameit A*, Shechtman Y*, Osherovich E*, Bullkich E, Sidorenko P, Dana H, Steiner S, Kley EB, Gazit S, Cohen-Hyams T, Shoham S, Zibulevsky M, Yavneh I, Eldar YC, Cohen O, Segev M. (2012) Sparsity-based single-shot subwavelength coherent diffractive imaging. Nature Materials 11(5):455-9. PMID: 22466747

Dana H, Shoham S. (2011) Numerical evaluation of temporal focusing characteristics in transparent and scattering media. Optics Express 19(6):4937-48. PMID: 21445129