Duff, M.K., Li, M.J., Nimmerjahn, A. Astrocyte Regulation of Spinal Circuit Function. (2026) J Neurochem. 170(2):e70366. DOI: 10.1111/jnc.70366

Barykina, N.V., Carey, E.M., Oliinyk, O.S., Mendonça-Gomes, J.M., de Oliveira, S., Nimmerjahn, A., Verkhusha, V.V. Synthetic multicolor antigen-stabilizable nanobody platform for intersectional labelling and functional imaging. (2025) bioRxiv. DOI: 10.1101/2025.10.27.684934

Mi, X., Chen, A.B., Duarte, D., Carey, E., Taylor, C.R., Braaker, P.N., Bright, M., Almeida, R.G., Lim, J.X., Ruetten, V.M.S., Wang, Y., Wang, M., Zhang, W., Zheng, W., Reitman, M.E., Huang, Y., Wang, X., Li, L., Deng, H., Shi, S.H., Poskanzer, K.E., Lyons, D.A., Nimmerjahn, A., Ahrens, M.B., Yu, G. Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals. (2025) Cell. DOI: 10.1016/j.cell.2025.03.012

Barykina, N.V., Carey, E.M., Oliinyk, O.S., Nimmerjahn, A., Verkhusha, V.V. Destabilized near-infrared fluorescent nanobodies enable background-free targeting of GFP-based biosensors for imaging and manipulation. (2024) Nature Communications. 15(1):7788. DOI: 10.1038/s41467-024-51857-x

Su, Y., Xu, J., Zhu, Z., Chin, J., Xu, L., Yu, H., Nudell, V., Dash, B., Moya, E.A., Ye, L., Nimmerjahn, A., Sun, X. Brainstem Dbh neurons control allergen-induced airway hyperreactivity. (2024) Natur. DOI: 10.1038/s41586-024-07608-5

Wu, Y., Temple, B.A., Sevilla, N., Zhang, J., Zhu, H., Zolotavin, P., Jin, Y., Duarte, D., Sanders, E., Azim, E., Nimmerjahn, A., Pfaff, S.L., Luan, L., Xie, C. Ultraflexible electrodes for recording neural activity in the mouse spinal cord during motor behavior. (2024) Cell Reports. 43(5):114199. DOI: 10.1016/j.celrep.2024.114199

Mi, X., Chen, A.B., Duarte, D., Carey, E., Taylor, C.R., Braaker, P.N., Bright, M., Almeida, R.G., Lim, J.X., Rutten, V.M., Zheng, W., Wang, M., Reitman, M.E., Wang, Y., Poskanzer, K.E., Lyons, D.A., Nimmerjahn, A., Ahrens, M.B., Yu, G. Fast, Accurate, and Versatile Data Analysis Platform for the Quantification of Molecular Spatiotemporal Signals. (2024) bioRxiv. DOI: 10.1101/2024.05.02.592259

Schafer, S.T., Mansour, A.A., Schlachetzki, J.C.M., Pena, M., Ghassemzadeh, S., Mitchell, L., Mar, A., Quang, D., Stumpf, S., Ortiz, I.S., Lana, A.J., Baek, C., Zaghal, R., Glass, C.K., Nimmerjahn, A., Gage, F.H. An in vivo neuroimmune organoid model to study human microglia phenotypes. (2023) Cell. 186(10):2111-2126.e20. DOI: 10.1016/j.cell.2023.04.022

Shekhtmeyster, P., Duarte, D., Carey, E.M., Ngo, A., Gao, G., Olmstead, J.A., Nelson, N.A., Nimmerjahn, A. Trans-segmental imaging in the spinal cord of behaving mice. (2023) Nature Biotechnology. DOI: 10.1038/s41587-023-01700-3

Shekhtmeyster, P., Carey, E.M., Duarte, D., Ngo, A., Gao, G., Nelson, N.A., Clark, C.L., Nimmerjahn, A. Multiplex translaminar imaging in the spinal cord of behaving mice. (2023) Nature Communications. 14(1):1427. DOI: 10.1038/s41467-023-36959-2

Ward, S., Riley, C., Carey, E.M., Nguyen, J., Esener, S., Nimmerjahn, A., Sirbuly, D.J. Electro-optical mechanically flexible coaxial microprobes for minimally invasive interfacing with intrinsic neural circuits. (2022) Nature Communications. 13(1):3286. DOI: 10.1038/s41467-022-30275-x

Oliinyk, O.S., Baloban, M., Clark, C.L., Carey, E., Pletnev, S., Nimmerjahn, A., Verkhusha, V.V. Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies. (2022) Nature Methods. DOI: 10.1038/s41592-022-01467-6

Nimmerjahn, A., Hirrlinger, J. Astrocyte regulation of neural circuit function and animal behavior. (2022) Glia. DOI: 10.1002/glia.24223

Hirrlinger, J., Nimmerjahn, A. A perspective on astrocyte regulation of neural circuit function and animal behavior. (2022) Glia. DOI: 10.1002/glia.24168

Abdelfattah, A.S., Ahuja, S., Akkin, T., Allu, S.R., Brake, J., Boas, D.A., Buckley, E.M., Campbell, R.E., Chen, A.I., Cheng, X., Čižmár, T., Costantini, I., De Vittorio, M., Devor, A., Doran, P.R., El Khatib, M., Emiliani, V., Fomin-Thunemann, N., Fainman, Y., Fernandez-Alfonso, T., Ferri, C.G.L., Gilad, A., Han, X., Harris, A., Hillman, E.M.C., Hochgeschwender, U., Holt, M.G., Ji, N., Kılıç, K., Lake, E.M.R., Li, L., Li, T., Mächler, P., Miller, E.W., Mesquita, R.C., Nadella, K.M.N.S., Nägerl, U.V., Nasu, Y., Nimmerjahn, A., Ondráčková, P., Pavone, F.S., Perez Campos, C., Peterka, D.S., Pisano, F., Pisanello, F., Puppo, F., Sabatini, B.L., Sadegh, S., Sakadzic, S., Shoham, S., Shroff, S.N., Silver, R.A., Sims, R.R., Smith, S.L., Srinivasan, V.J., Thunemann, M., Tian, L., Tian, L., Troxler, T., Valera, A., Vaziri, A., Vinogradov, S.A., Vitale, F., Wang, L.V., Uhlířová, H., Xu, C., Yang, C., Yang, M.H., Yellen, G., Yizhar, O., Zhao, Y. Neurophotonic tools for microscopic measurements and manipulation: status report. (2022) Neurophotonics. 9(Suppl 1):013001. DOI: 10.1117/1.NPh.9.S1.013001

Huang, Y., Happonen, K.E., Burrola, P.G., O'Connor, C., Hah, N., Huang, L., Nimmerjahn, A., Lemke, G. Microglia use TAM receptors to detect and engulf amyloid β plaques. (2021) Nature Immunology. DOI: 10.1038/s41590-021-00913-5

Ceto, S., Sekiguchi, K.J., Takashima, Y., Nimmerjahn, A., Tuszynski, M.H. Neural Stem Cell Grafts Form Extensive Synaptic Networks that Integrate with Host Circuits after Spinal Cord Injury. (2020) Cell Stem Cell. DOI: 10.1016/j.stem.2020.07.007

Nimmerjahn, A. Monitoring neuronal health. (2020) Wissenschaft. 367(6477):510-511. DOI: 10.1126/science.aba4472

Patriarchi, T., Cho, J.R., Merten, K., Marley, A., Broussard, G.J., Liang, R., Williams, J., Nimmerjahn, A., von Zastrow, M., Gradinaru, V., Tian, L. Imaging neuromodulators with high spatiotemporal resolution using genetically encoded indicators. (2019) Nature Protocols. 14(12):3471–3505. DOI: 10.1038/s41596-019-0239-2

Nelson, N.A., Wang, X., Cook, D., Carey, E.M., Nimmerjahn, A. Imaging spinal cord activity in behaving animals. (2019) Experimental Neurology. 230:112974. DOI: 10.1016/j.expneurol.2019.112974

Patriarchi, T., Cho, J.R., Merten, K., Howe, M.W., Marley, A., Xiong, W.H., Folk, R.W., Broussard, G.J., Liang, R., Jang, M.J., Zhong, H., Dombeck, D., von Zastrow, M., Nimmerjahn, A., Gradinaru, V., Williams, J.T., Tian, L. Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors. (2018) Wissenschaft. DOI: 10.1126/science.aat4422

Tufail, Y., Cook, D., Fourgeaud, L., Powers, C.J., Merten, K., Clark, C.L., Hoffman, E., Ngo, A., Sekiguchi, K.J., O'Shea, C.C., Lemke, G., Nimmerjahn, A. Phosphatidylserine Exposure Controls Viral Innate Immune Responses by Microglia. (2017) Neuron. 93(3):574-586.e8. DOI: 10.1016/j.neuron.2016.12.021

Sekiguchi, K.J., Shekhtmeyster, P., Merten, K., Arena, A., Cook, D., Hoffman, E., Ngo, A., Nimmerjahn, A. Imaging large-scale cellular activity in spinal cord of freely behaving mice. (2016) Nature Communications. 7:11450. DOI: 10.1038/ncomms11450

Fourgeaud, L., Través, P.G., Tufail, Y., Leal-Bailey, H., Lew, E.D., Burrola, P.G., Callaway, P., Zagórska, A., Rothlin, C.V., Nimmerjahn, A., Lemke, G. TAM receptors regulate multiple features of microglial physiology. (2016) Natur. 532(7598):240-244. DOI: 10.1038/nature17630

Nimmerjahn, A., Bergles, D.E. Large-scale recording of astrocyte activity. (2015) Current Opinion in Neurobiology. 32:95-106. DOI: 10.1016/j.conb.2015.01.015

Knowland, D., Arac, A., Sekiguchi, K.J., Hsu, M., Lutz, S.E., Perrino, J., Steinberg, G.K., Barres, B.A., Nimmerjahn, A., Agalliu, D. Stepwise recruitment of transcellular and paracellular pathways underlies blood-brain barrier breakdown in stroke. (2014) Neuron. 82(3):603-17. DOI: 10.1016/j.neuron.2014.03.003

Devor, A., Bandettini, P.A., Boas, D.A., Bower, J.M., Buxton, R.B., Cohen, L.B., Dale, A.M., Einevoll, G.T., Fox, P.T., Franceschini, M.A., Friston, K.J., Fujimoto, J.G., Geyer, M.A., Greenberg, J.H., Halgren, E., Hämäläinen, M.S., Helmchen, F., Hyman, B.T., Jasanoff, A., Jernigan, T.L., Judd, L.L., Kim, S.G., Kleinfeld, D., Kopell, N.J., Kutas, M., Kwong, K.K., Larkum, M.E., Lo, E.H., Magistretti, P.J., Mandeville, J.B., Masliah, E., Mitra, P.P., Mobley, W.C., Moskowitz, M.A., Nimmerjahn, A., Reynolds, J.H., Rosen, B.R., Salzberg, B.M., Schaffer, C.B., Silva, G.A., So, P.T., Spitzer, N.C., Tootell, R.B., Van Essen, D.C., Vanduffel, W., Vinogradov, S.A., Wald, L.L., Wang, L.V., Weber, B., Yodh, A.G. The challenge of connecting the dots in the B.R.A.I.N. (2013) Neuron. 80(2):270-4. DOI: 10.1016/j.neuron.2013.09.008

Nimmerjahn, A. Two-photon imaging of microglia in the mouse cortex in vivo. (2012) Cold Spring Harbor Protocols. 2012(5). DOI: 10.1101/pdb.prot069294

Nimmerjahn, A. Optical window preparation for two-photon imaging of microglia in mice. (2012) Cold Spring Harbor Protocols. 2012(5). DOI: 10.1101/pdb.prot069286

Nimmerjahn, A. Surgical implantation of a head plate in mice in preparation for in vivo two-photon imaging of microglia. (2012) Cold Spring Harbor Protocols. 2012(5). DOI: 10.1101/pdb.prot069278

Nimmerjahn, A., Helmchen, F. In vivo labeling of cortical astrocytes with sulforhodamine 101 (SR101). (2012) Cold Spring Harbor Protocols. 2012(3):326-34. DOI: 10.1101/pdb.prot068155

Kerr, J.N., Nimmerjahn, A. Functional imaging in freely moving animals. (2012) Current Opinion in Neurobiology. 22(1):45-53. DOI: 10.1016/j.conb.2011.12.002

Tremblay, M., Stevens, B., Sierra, A., Wake, H., Bessis, A., Nimmerjahn, A. The role of microglia in the healthy brain. (2011) Journal of Neuroscience. 31(45):16064-9. DOI: 10.1523/JNEUROSCI.4158-11.2011

Ghosh, K.K., Burns, L.D., Cocker, E.D., Nimmerjahn, A., Ziv, Y., Gamal, A.E., Schnitzer, M.J. Miniaturized integration of a fluorescence microscope. (2011) Nature Methods. 8(10):871-8. DOI: 10.1038/nmeth.1694

Mukamel, E.A., Nimmerjahn, A., Schnitzer, M.J. Automated analysis of cellular signals from large-scale calcium imaging data. (2009) Neuron. 63(6):747-60. DOI: 10.1016/j.neuron.2009.08.009

Nimmerjahn, A., Mukamel, E.A., Schnitzer, M.J. Motor behavior activates Bergmann glial networks. (2009) Neuron. 62(3):400-12. DOI: 10.1016/j.neuron.2009.03.019

Nimmerjahn, A. Astrocytes going live: advances and challenges. (2009) Journal of Physiology. 587(Pt 8):1639-47. DOI: 10.1113/jphysiol.2008.167171

Flusberg, B.A., Nimmerjahn, A., Cocker, E.D., Mukamel, E.A., Barretto, R.P., Ko, T.H., Burns, L.D., Jung, J.C., Schnitzer, M.J. High-speed, miniaturized fluorescence microscopy in freely moving mice. (2008) Nature Methods. 5(11):935-8. DOI: 10.1038/nmeth.1256

Sullivan, M.R., Nimmerjahn, A., Sarkisov, D.V., Helmchen, F., Wang, S.S. In vivo calcium imaging of circuit activity in cerebellar cortex. (2005) Journal of Neurophysiology. 94(2):1636-44. DOI: 10.1152/jn.01013.2004

Nimmerjahn, A., Kirchhoff, F., Helmchen, F. Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo. (2005) Wissenschaft. 308(5726):1314-8. DOI: 10.1126/science.1110647

Dittgen, T., Nimmerjahn, A., Komai, S., Licznerski, P., Waters, J., Margrie, T.W., Helmchen, F., Denk, W., Brecht, M., Osten, P. Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(52):18206-11. DOI: 10.1073/pnas.0407976101

Göbel, W., Kerr, J.N., Nimmerjahn, A., Helmchen, F. Miniaturized two-photon microscope based on a flexible coherent fiber bundle and a gradient-index lens objective. (2004) Opt Lett. 29(21):2521-3.

Nimmerjahn, A., Kirchhoff, F., Kerr, J.N., Helmchen, F. Sulforhodamine 101 as a specific marker of astroglia in the neocortex in vivo. (2004) Nature Methods. 1(1):31-7. DOI: 10.1038/nmeth706

Göbel, W., Nimmerjahn, A., Helmchen, F. Distortion-free delivery of nanojoule femtosecond pulses from a Ti:sapphire laser through a hollow-core photonic crystal fiber. (2004) Optics Letters. 29(11):1285-7.

Kim, J., Dittgen, T., Nimmerjahn, A., Waters, J., Pawlak, V., Helmchen, F., Schlesinger, S., Seeburg, P.H., Osten, P. Sindbis vector SINrep(nsP2S726): a tool for rapid heterologous expression with attenuated cytotoxicity in neurons. (2004) Journal of Neuroscience Methods. 133(1-2):81-90.