Chen, T.W., Wardill, T.J., Sun, Y.J., Pulver, S., Renninger, S.L., Baohan, A., Schreiter, E.R., Kerr, R.A., Orger, M.B., Jayaraman, V., et al. (2013). Ultra-sensitive fluorescent proteins for imaging neuronal activity. Nature in press.

Hooks, B.M., Mao, T., Gutnisky, D.A., Yamawaki, N., Svoboda, K., and Shepherd, G.M. (2013). Organization of cortical and thalamic input to pyramidal neurons in mouse motor cortex. J Neurosci 33, 748-760. PDF

Petreanu, L., Gutnisky, D.A., Huber, D., Xu, N.L., O'Connor, D.H., Tian, L., Looger, L., and Svoboda, K. (2012). Activity in motor-sensory projections reveals distributed coding in somatosensation. Nature 489, 299-303. PDF

Huber, D., Gutnisky, D.A., Peron, S., O'Connor, D.H., Wiegert, J.S., Tian, L., Oertner, T.G., Looger, L.L., Svoboda, K. (2012) Multiple dynamic representations in the motor cortex during sensorimotor learning. Nature 484, 473-481. PDF

Nem, A., Pfeiffer, B. D., Svoboda, K., and Rubin, G.M. (2011) Multiple new site-specific recombinases for use in manipulating animal genomas. Proceedings of the National Academy of Sciences of the United States of America108, 14198-203.

Komiyama T, Sato TR, O'Connor DH, Zhang YX, Huber D, Hooks BM, Gabitto M, Svoboda K. (2010). Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice. Nature 464, 1182-6. PDF

Tian, L., Hires, S.A., Mao, T., Huber, D., Chiappe, M.E., Chalasani, S.H., Petreanu, L., Akerboom, J., McKinney, S.A., Schreiter, E.R., et al. (2009). Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods 6, 875-881. PDF

Sato TR, Svoboda K. (2010) The functional properties of barrel cortex neurons projecting to the primary motor cortex. J Neurosci 30, 4256-60 (2009). PDF

O'Connor, D.H., Huber, D., and Svoboda, K. (2009). Reverse engineering the mouse brain. Nature 461, 923-929. PDF

Holtmaat, A., Svoboda, K. Experience-dependent structural synaptic plasticity in the mammalian bran. Nat Rev Neurosci 10(9), 647-658 (2009). PDF

Holtmaat, A., Bonhoeffer, T., Chow, D.K., Chuckowree, J., De Paola, V., Hofer, S.B., Hübener, M., Keck, T., Knott, G., Lee, W.C., Mostany, R., Mrsic-Flogel, T.D., Nedivi, E., Portera-Cailliau, C., Svoboda, K., Trachtenberg, J.T., Wilbrecht, L. Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window. Nat Protocol 4(8), 1128-1144 (2009). Epub 2009 Jul 16. PDF

Zito, K., Scheuss, V., Knott, G., Hill, T., and Svoboda, K. Rapid functional maturation of nascent dendritic spines. Neuron 61, 247-258 (2009). PDF

Harvey, C. D., Ehrhardt, A. G., Cellurale, C., Zhong, H., Yasuda, R., Davis, R. J., and Svoboda, K. A genetically encoded fluorescent sensor of ERK activity. Proc Natl Acad Sci U S A 105, 19264-19269. (2008). PDF

Bureau, I., Shepherd, G. M. & Svoboda, K. Circuit and plasticity defects in the developing somatosensory cortex of FMR1 knock-out mice. J Neurosci 28, 5178-88 (2008). PDF

Huber D, Petreanu L, Ghitani N, Ranade S, Hromádka T, Mainen Z, Svoboda K (2008). Sparse optical microstimulation in barrel cortex drives learned behavior in freely moving mice. Nature 451:61-4. PDF

Sato, T. R., Gray, N. W., Mainen, Z. F. & Svoboda, K. The Functional Microarchitecture of the Mouse Barrel Cortex. PLoS Biol 5, e189 (2007). PDF

Huber D, Petreanu L, Ghitani N, Ranade S, Hromádka T, Mainen Z, Svoboda K. Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature 451, 61 -64 (2007). PDF

Sobczyk A, Svoboda K. Activity-dependent plasticity of the NMDA-receptor fractional Ca2+ current. Neuron 53(1), 17 -24 (2007). PDF

Bureau, I., von Saint Paul, F. & Svoboda, K. Interdigitated Paralemniscal and Lemniscal Pathways in the Mouse Barrel Cortex. PLoS Biol 4, e382 (2006). PDF

Knott GW, Holtmaat A, Wilbrecht L, Welker E, Svoboda K.   Spine growth precedes synapse formation in the adult neocortex in vivo. Nat Neurosci 9, 1117 -1124 (2006). PDF

Holtmaat A, Wilbrecht L, Knott GW, Welker E, Svoboda K.   Experience-dependent and cell-type-specific spine growth in the neocortex. Nature 441, 979 -983 (2006). PDF

Yasuda R, Harvey CD, Zhong H, Sobczyk A, van Aelst L, Svoboda K.   Supersensitive Ras activation in dendrites and spines revealed by two-photon fluorescence lifetime imaging. Nat Neurosci 9, 283 -291 (2006). PDF

Shepherd, G. M. G., Stepanyants, A., Bureau, I., Chklovskii, D. B. & Svoboda, K. Geometric and functional organization of cortical circuits. Nature Neuroscience 8, 782-790 (2005).

Karpova AY, Tervo DGR, Gray NW, Svoboda K.   Rapid and Reversible Chemical Inactivation of Synaptic Transmission in Genetically Targeted Neurons. Neuron 48, 727 -737 (2005).

Sobczyk A, Scheuss V, Svoboda K.   NMDA receptor subunit-dependent [Ca2+] signaling in individual hippocampal dendritic spines. J. Neurosci 25, 6037 -6046 (2005).

Shepherd GMG, Stepanyants A, Bureau I, Chklovskii DB, Svoboda K.   Geometric and functional organization of cortical circuits. Nat Neurosci 8, 782 -790 (2005).

Holtmaat AJ, Trachtenberg JT, Wilbrecht L, Shepherd GM, Zhang X, Knott GW, Svoboda K.  Transient and persistent dendritic spines in the neocortex in vivo. Neuron 45, 279 -291 (2005).

Svoboda, K.   Do Spines and Dendrites Distribute Dye Evenly?. Trends in Neurosci. 27, 445 -446(2004).

Wang Y, Guo H, Pologruto TA, Hannan F, Hakker I, Svoboda K & Zhong Y.   Stereotyped Odor-evoked Activity in the Mushroom Body of Drosophila Revealed by GFP-Based Ca2+ Imaging. J. Neuroscience 24, 6507 -6514 (2004).

Zito K, Knott G, Shepherd GM, Shenolikar S, & Svoboda K.   Induction of spine growth and synapse formation by regulation of the spine actin cytoskeleton. Neuron 44, 321 -334 (2004).

Pologruto, T.A., Yasuda, R., & Svoboda, K.   Monitoring Neural Activity and [Ca2+] with Genetically Encoded Calcium Indicators. J. Neuroscience 24, 9572 -9579 (2004).

Yasuda R, Nimchinsky EA, Scheuss V, Pologruto TA, Oertner TG, Sabatini BL, Svoboda K.   Imaging calcium concentration dynamics in small neuronal compartments. Science STKE 219, P5 (2004).

Bureau I, Shepherd GMG, Svoboda K.   Precise development of functional and anatomical columns in the neocortex. Neuron 42, 789 -801 (2004).

Holtmaat AJ, Wilbrecht L, Karpova A, Portera-Cailliau C, Burbach B, Trachtenberg JT, Svoboda K.   Long-term, high-resolution imaging of neurons in the neocortex in vivo. In: Yuste R, Konnerth A, editors. Imaging Neurons. Cold Spring Harbor: Cold Spring Harbor Laboratory -, (2004).

Egger V, Svoboda K & Mainen ZF.   Mechanisms of lateral inhibition in the olfactory bulb: efficiency and modulation of spike-evoked calcium influx into granule cells. J Neurosci 23, 7551 -7558 (2003).

Yasuda, R., Sabatini, B.L., and Svoboda, K.   Plasticity of calcium channels in dendritic spines. Nature Neuroscience 6, 948 -955 (2003).

Takahashi T, Svoboda K, & Malinow R.   Experience strengthening transmission by driving AMPA receptors into synapses. Science 299, 1585 -1588 (2003).

Oertner TG, Sabatini BL, Nimchinsky EA, & Svoboda K.   Facilitation at single synapses probed with optical quantal analysis. Nature Neuroscience 5, 657 -664 (2002).

Zito K & Svoboda K.   Activity-dependent synaptogenesis in the adult Mammalian cortex. Neuron 35, 1015 -1017 (2002).

Stern EA, Maravall M, Svoboda K.   Rapid development and plasticity of layer 2/3 maps in rat barrel cortex in vivo. Neuron 31, 305 -315 (2001).

Sabatini BL, Maravall M, Svoboda K.   Ca(2+) signaling in dendritic spines. Curr. Opin. Neurobiology 11, 349 -356 (2001).

Cox CL, Denk W, Tank DW, Svoboda K.   Action potentials reliably invade axonal arbors of rat neocortical neurons. Proc Natl Acad Sci USA 97, 9724 -9728 (2000).

Maravall, M., Mainen, Z.F., Sabatini, B.L., & Svoboda, K.   Estimating intracellular calcium concentrations and buffering without wavelength ratioing. Biophysical Journal 78, 2655 -2667 (2000).

Helmchen F, Svoboda K, Denk W, Tank DW.   In vivo dendritic calcium dynamics in deep-layer cortical pyramidal neurons. Nature Neuroscience 2, 989 -996 (1999).

Shi SH, Hayashi Y, Petralia RS, Zaman SH, Wenthold RJ, Svoboda K, Malinow R.   Rapid spine delivery and redistribution of AMPA receptors after synaptic NMDA receptor activation. Science 284, 1811 -1816 (1999).

Svoboda K, Mainen ZF.   Synaptic [Ca2+]: intracellular stores spill their guts. Neuron 22, 427 -430 (1999).


Maletic-Savatic M, Malinow R, Svoboda K.   Rapid dendritic morphogenesis in CA1 hippocampal dendrites induced by synaptic activity. Science 283, 1923 -1927 (1999).


Denk W, Svoboda K.   Photon upmanship: why multiphoton imaging is more than a gimmick. Neuron 18, 351 -357 (1997).

Denk W, Yuste R, Svoboda K, Tank DW.   Imaging calcium dynamics in dendritic spines. Curr. Opin. Neurobiology 6, 372 -378(1996).


Svoboda K.   New insights into the workings of the ultimate swimming machine. Biophysical Journal 71, 539 -540 (1996).

Svoboda K, Mitra PP, Block SM.   Fluctuation analysis of kinesin movement. Biophysical Journal 68, 69S (1995).

Latour LL, Svoboda K, Mitra PP, Sotak CH.   Time-dependent diffusion of water in a biological model system. Proc. Natl. Acad. Sci. USA 91, 1229 -1233 (1994).


Svoboda K, Block SM.   Biological applications of optical forces. Annu Rev Biophys Biomol Struct 23, 247 -285 (1994).

Schmidt CF, Svoboda K, Lei N, Petsche IB, Berman LE, Safinya CR, Grest GS.  Existence of a flat phase in red cell membrane skeletons. Science 259, 952 -955 (1993).


Svoboda K, Schmidt CF, Branton D, Block SM.   Conformation and elasticity of the isolated red blood cell membrane skeleton. Biophysical Journal 63, 784 -793 (1992).