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Paper

Oviedo, H. V., Bureau, I., Svoboda, K., Zador, A. M. (October 2010) The functional asymmetry of auditory cortex is reflected in the organization of local cortical circuits. Nature Neuroscience, 13 (11). pp. 1413-1420. ISSN 1097-6256

Wilbrecht, L., Holtmaat, A., Wright, N., Fox, K., Svoboda, K. (April 2010) Structural plasticity underlies experience-dependent functional plasticity of cortical circuits. J Neurosci, 30 (14). pp. 4927-4932. ISSN 1529-2401 (Electronic) 0270-6474 (Linking)

Holtmaat, A., Bonhoeffer, T., Chow, D. K., Chuckowree, J., De Paola, V., Hofer, S. B., Hubener, 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. (July 2009) Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window. Nat Protoc, 4 (8). pp. 1128-44. ISSN 1750-2799 (Electronic)

Bohland, J. W., Wu, C., Barbas, H., Bokil, H., Bota, M., Breiter, H. C., Cline, H. T., Doyle, J. C., Freed, P. J., Greenspan, R. J., Haber, S. N., Hawrylycz, M., Herrera, D. G., Hilgetag, C. C., Huang, Z. J., Jones, A., Jones, E. G., Karten, H. J., Kleinfeld, D., Kotter, R., Lester, H. A., Lin, J. M., Mensh, B. D., Mikula, S., Panksepp, J., Price, J. L., Safdieh, J., Saper, C. B., Schiff, N. D., Schmahmann, J. D., Stillman, B. W., Svoboda, K., Swanson, L. W., Toga, A. W., Van Essen, D. C., Watson, J. D., Mitra, P. P. (March 2009) A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Computational Biology, 5 (3). e1000334. ISSN 1553734X

Zito, K., Scheuss, V., Knott, G., Hill, T., Svoboda, K. (January 2009) Rapid Functional Maturation of Nascent Dendritic Spines. Neuron, 61 (2). pp. 247-258.

Harvey, C. D., Ehrhardt, A. G., Cellurale, C., Zhong, H., Yasuda, R., Davis, R. J., Svoboda, K. (December 2008) A genetically encoded fluorescent sensor of ERK activity. Proc Natl Acad Sci U S A, 105 (49). pp. 19264-9.

Harvey, C. D., Yasuda, R., Zhong, H., Svoboda, K. (July 2008) The spread of ras activity triggered by activation of a single dendritic spine. Science, 321 (5885). pp. 136-40.

Bureau, I., Shepherd, G. M., Svoboda, K. (May 2008) Circuit and plasticity defects in the developing somatosensory cortex of FMR1 knock-out mice. J Neurosci, 28 (20). pp. 5178-88.

Mao, T., O'Connor, D. H., Scheuss, V., Nakai, J., Svoboda, K. (March 2008) Characterization and subcellular targeting of GCaMP-type genetically-encoded calcium indicators. PLoS ONE, 3 (3). e1796.

Huber, D., Petreanu, L., Ghitani, N., Ranade, S., Hromadka, T., Mainen, Z., Svoboda, K. (January 2008) Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature, 451 (7174). pp. 61-4.

Harvey, C. D., Svoboda, K. (December 2007) Locally dynamic synaptic learning rules in pyramidal neuron dendrites. Nature, 450 (7173). pp. 1195-1200. ISSN 0028-0836

Sato, T. R., Gray, N. W., Mainen, Z. F., Svoboda, K. (July 2007) The Functional Microarchitecture of the Mouse Barrel Cortex. PLoS Biology, 5 (7). e189.

Petreanu, L. T., Huber, D., Sobczyk, A., Svoboda, K. (May 2007) Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections. Nat Neurosci, 10 (5). pp. 663-668. ISSN 1097-6256

Sobczyk, A., Svoboda, K. (January 2007) Activity-dependent plasticity of the NMDA-receptor fractional Ca2+ current. Neuron, 53 (1). pp. 17-24. ISSN 0896-6273 (Print)

Bureau, I., Shepherd, G., Svoboda, K. (December 2006) Defects in the developing cortical circuits of fmr1 mutant mice. International Journal of Developmental Neuroscience, 24 (8). p. 480. ISSN 0736-5748

Bureau, I., von Saint Paul, F., Svoboda, K. (December 2006) Interdigitated paralemniscal and lemniscal pathways in the mouse barrel cortex. PLoS Biology, 4 (12). pp. 2361-2371. ISSN 1544-9173

Gray, N. W., Weimer, R. M., Bureau, I., Svoboda, K. (November 2006) Rapid redistribution of synaptic PSD-95 in the neocortex in vivo. PLoS Biol, 4 (11). e370. ISSN 1545-7885 (Electronic)

Knott, G. W., Holtmaat, A. J. G. D., Wilbrecht, L., Welker, E., Svoboda, K. (August 2006) Spine growth precedes synapse formation in the adult neocortex in vivo. Nature Neuroscience, 9 (9). pp. 1117-1124. ISSN 10976256

Scheuss, V., Yasuda, R., Sobczyk, A., Svoboda, K. (August 2006) Nonlinear [Ca2+] signaling in dendrites and spines caused by activity-dependent depression of Ca2+ extrusion. J Neurosci, 26 (31). pp. 8183-94. ISSN 1529-2401 (Electronic)

Holtmaat, A. J. G. D., Wilbrecht, L., Knott, G. W., Welker, E., Svoboda, K. (June 2006) Experience-dependent and cell-type-specific spine growth in the neocortex. Nature, 441 (7096). pp. 979-83. ISSN 1476-4687 (Electronic)

Svoboda, K., Yasuda, R. (June 2006) Principles of two-photon excitation microscopy and its applications to neuroscience. Neuron, 50 (6). pp. 823-39. ISSN 0896-6273 (Print)

De Paola, V., Holtmaat, A. J. G. D., Knott, G. W., Song, S., Wilbrecht, L., Caroni, P., Svoboda, K. (March 2006) Cell type-specific structural plasticity of axonal branches and boutons in the adult neocortex. Neuron, 49 (6). pp. 861-75. ISSN 0896-6273 (Print)

Yasuda, Ryohei, Harvey, Christopher D., Zhong, Haining, Sobczyk, Aleksander, Van Aelst, Linda, Svoboda, Karel (2006) Supersensitive Ras activation in dendrites and spines revealed by two-photon fluorescence lifetime imaging. Nature Neuroscience, 9 (2). pp. 283-291. ISSN 10976256

Karpova, A. Y., Tervo, D. G., Gray, N. W., Svoboda, K. (December 2005) Rapid and reversible chemical inactivation of synaptic transmission in genetically targeted neurons. Neuron, 48 (5). pp. 727-35. ISSN 0896-6273 (Print)

Harwell, C., Burbach, B., Svoboda, K., Nedivi, E. (October 2005) Regulation of cpg15 expression during single whisker experience in the barrel cortex of adult mice. Journal of Neurobiology, 65 (1). pp. 85-96. ISSN 0022-3034

Portera-Cailliau, Carlos, Weimer, Robby M., De Paola, Vincenzo, Caroni, Pico, Svoboda, Karel (August 2005) Diverse modes of axon elaboration in the developing neocortex. PLoS Biol, 3 (8). e272. ISSN 1545-7885 (Electronic)

Sobczyk, A., Scheuss, V., Svoboda, K. (June 2005) NMDA receptor subunit-dependent [Ca2+] signaling in individual hippocampal dendritic spines. J Neurosci, 25 (26). pp. 6037-46. ISSN 1529-2401 (Electronic)

Shepherd, G. M., Svoboda, K. (June 2005) Laminar and columnar organization of ascending excitatory projections to layer 2/3 pyramidal neurons in rat barrel cortex. J Neurosci, 25 (24). pp. 5670-9. ISSN 0270-6474

Egger, V., Svoboda, K., Mainen, Z. F. (April 2005) Dendrodendritic synaptic signals in olfactory bulb granule cells: local spine boost and global low-threshold spike. J Neurosci, 25 (14). pp. 3521-30. ISSN 1529-2401 (Electronic)

Holtmaat, A. J. G. D., Trachtenberg, J. T., Wilbrecht, L., Shepherd, G. M., Zhang, Xi., Knott, G. W., Svoboda, Karel. (January 2005) Transient and persistent dendritic spines in the neocortex in vivo. Neuron, 45 (2). pp. 279-91. ISSN 0896-6273 (Print)

Di Cristo, G., Wu, C., Chattopadhyaya, B., Ango, F., Knott, G., Welker, E., Svoboda, K., Huang, Z. J. (November 2004) Subcellular domain-restricted GABAergic innervation in primary visual cortex in the absence of sensory and thalamic inputs. Nature Neuroscience, 7 (11). pp. 1184-6. ISSN 1546-1726 (Electronic)1097-6256 (Linking)

Pologruto, T. A., Yasuda, R., Svoboda, K. (October 2004) Monitoring neural activity and [Ca2+] with genetically encoded Ca2+ indicators. J Neurosci, 24 (43). pp. 9572-9. ISSN 1529-2401 (Electronic)

Zito, K., Knott, G., Shepherd, G. M., Shenolikar, S., Svoboda, K. (October 2004) Induction of spine growth and synapse formation by regulation of the spine actin cytoskeleton. Neuron, 44 (2). pp. 321-34. ISSN 0896-6273 (Print)

Chklovskii, D. B., Mel, B. W., Svoboda, K. (October 2004) Cortical rewiring and information storage. Nature, 431 (7010). pp. 782-788. ISSN 0028-0836

Brecht, M., Fee, M. S., Garaschuk, O., Helmchen, F., Margrie, T. W., Svoboda, K., Osten, P. (October 2004) Novel approaches to monitor and manipulate single neurons in vivo. Journal of Neuroscience, 24 (42). pp. 9223-9227. ISSN 0270-6474

Svoboda, K. (August 2004) Do spines and dendrites distribute dye evenly? Trends in Neurosciences, 27 (8). pp. 445-446. ISSN 0166-2236

Maravall, M., Stern, E. A., Svoboda, K. (July 2004) Development of intrinsic properties and excitability of layer 2/3 pyramidal neurons during a critical period for sensory maps in rat barrel cortex. J Neurophysiol, 92 (1). pp. 144-56. ISSN 0022-3077 (Print)

Wang, Y. L., Guo, H. F., Pologruto, T. A., Hannan, F., Hakker, I., Svoboda, K., Zhong, Y. (July 2004) Stereotyped odor-evoked activity in the mushroom body of Drosophila revealed by green fluorescent protein-based Ca2+ imaging. Journal of Neuroscience, 24 (29). pp. 6507-6514. ISSN 0270-6474

Bureau, I., Shepherd, G. M., Svoboda, K. (June 2004) Precise development of functional and anatomical columns in the neocortex. Neuron, 42 (5). pp. 789-801. ISSN 0896-6273 (Print)

Maravall, M., Koh, I. Y., Lindquist, W. B., Svoboda, K. (June 2004) Experience-dependent changes in basal dendritic branching of layer 2/3 pyramidal neurons during a critical period for developmental plasticity in rat barrel cortex. Cereb Cortex, 14 (6). pp. 655-64. ISSN 1047-3211 (Print)

Nimchinsky, E. A., Yasuda, R., Oertner, T. G., Svoboda, K. (February 2004) The number of glutamate receptors opened by synaptic stimulation in single hippocampal spines. J Neurosci, 24 (8). pp. 2054-64. ISSN 1529-2401 (Electronic)

Yasuda, R., Nimchinsky, E. A., Scheuss, V., Pologruto, T. A., Oertner, T. G., Sabatini, B. L., Svoboda, K. (February 2004) Imaging calcium concentration dynamics in small neuronal compartments. Sci STKE, 2004 (219). pl5. ISSN 1525-8882 (Electronic)

Svoboda, K., Ugurbil, K. (October 2003) New technologies: probing neurons and their networks - Editorial Overview. Current Opinion in Neurobiology, 13 (5). pp. 568-569. ISSN 0959-4388

Yasuda, R., Sabatini, B. L., Svoboda, K. (September 2003) Plasticity of calcium channels in dendritic spines. Nature Neuroscience, 6 (9). pp. 948-55. ISSN 1097-6256

Egger, V., Svoboda, K., Mainen, Z. F. (August 2003) Mechanisms of lateral inhibition in the olfactory bulb: Efficiency and modulation of spike-evoked calcium influx into granule cells. Journal of Neuroscience, 23 (20). pp. 7551-7558. ISSN 0270-6474

Pologruto, T. A., Sabatini, B. L., Svoboda, K. (May 2003) ScanImage: flexible software for operating laser scanning microscopes. Biomedical Engineering Online, 2. p. 13. ISSN 1475-925X (Electronic)

Shepherd, G. M., Pologruto, T. A., Svoboda, K. (April 2003) Circuit analysis of experience-dependent plasticity in the developing rat barrel cortex. Neuron, 38 (2). pp. 277-89. ISSN 0896-6273 (Print)

Takahashi, T., Svoboda, K., Malinow, R. (March 2003) Experience strengthening transmission by driving AMPA receptors into synapses. Science, 299 (5612). pp. 1585-1588. ISSN 0036-8075

Svoboda, K., Yasuda, R., Sabatini, B. (February 2003) Using [Ca2+] imaging to probe synaptic channels at the level of single molecules. Biophysical Journal, 84 (2). 479A-479A. ISSN 0006-3495

Trachtenberg, J. T., Chen, B. E., Knott, G. W., Feng, G. P., Sanes, J. R., Welker, E., Svoboda, K. (December 2002) Long-term in vivo imaging of experience-dependent synaptic plasticity in adult cortex. Nature, 420 (6917). pp. 788-794. ISSN 0028-0836

Zito, K., Svoboda, K. (September 2002) Activity-dependent synaptogenesis in the adult mammalian cortex. Neuron, 35 (6). pp. 1015-1017. ISSN 0896-6273

Oertner, T. G., Svoboda, K. (September 2002) Subliminal messages in hippocampal pyramidal cells. Journal of Physiology, 543 (2). p. 397. ISSN 0022-3751

Oertner, T. G., Sabatini, B. L., Nimchinsky, E. A., Svoboda, K. (July 2002) Facilitation at single synapses probed with optical quantal analysis. Nature Neuroscience, 5 (7). pp. 657-664. ISSN 1097-6256

Koh, I. Y. Y., Lindquist, W. B., Zito, K., Nimchinsky, E. A., Svoboda, K. (June 2002) An image analysis algorithm for dendritic spines. Neural Computation, 14 (6). pp. 1283-1310. ISSN 0899-7667

Sabatini, B. L., Oertner, T. G., Svoboda, K. (January 2002) The life cycle of Ca2+ ions in dendritic spines. Neuron, 33 (3). pp. 439-452. ISSN 0896-6273

Nimchinsky, E. A., Sabatini, B. L., Svoboda, K. (2002) Structure and function of dendritic spines. Annual Review of Physiology, 64. pp. 313-353. ISSN 0066-4278

O'Donnell, W. T., Zito, K., Burbach, B., Svoboda, K., Warren, S. T. (October 2001) Identification of genes differentially expressed in wildtype and Fmr1 knockout mouse barrel cortex. American Journal of Human Genetics, 69 (4). p. 577. ISSN 0002-9297

Stern, E. A., Maravall, M., Svoboda, K. (August 2001) Rapid development and plasticity of layer 2/3 maps in rat barrel cortex in vivo. Neuron, 31 (2). pp. 305-315. ISSN 0896-6273

Nimchinsky, E. A., Oberlander, A. M., Svoboda, K. (July 2001) Abnormal development of dendritic spines in FMR1 knock-out mice. Journal of Neuroscience, 21 (14). pp. 5139-5146. ISSN 0270-6474

Sabatini, B. L., Maravall, M., Svoboda, K. (June 2001) Ca2+ signaling in dendritic spines. Current Opinion in Neurobiology, 11 (3). pp. 349-356. ISSN 0959-4388

Wang, Y. L., Wright, N. J. D., Guo, H. F., Xie, Z. P., Svoboda, K., Malinow, R., Smith, D. P., Zhong, Y. (January 2001) Genetic manipulation of the odor-evoked distributed neural activity in the Drosophila mushroom body. Neuron, 29 (1). pp. 267-276. ISSN 0896-6273

Sabatini, B. L., Svoboda, K. (November 2000) Analysis of calcium channels in single spines using optical fluctuation analysis. Nature, 408 (6812). pp. 589-593. ISSN 0028-0836

Chen, B. E., Lendvai, B., Nimchinsky, E. A., Burbach, B., Fox, K., Svoboda, K. (November 2000) Imaging high-resolution structure of GFP-expressing neurons in neocortex in vivo. Learning & Memory, 7 (6). pp. 433-441. ISSN 1072-0502

Cox, C. L., Denk, W., Tank, D. W., Svoboda, K. (August 2000) Action potentials reliably invade axonal arbors of rat neocortical neurons. Proceedings of the National Academy of Sciences of the United States of America, 97 (17). pp. 9724-9728. ISSN 0027-8424

Lendvai, B., Chen, B., Svoboda, K. (August 2000) Sensory deprivation induces plasticity of dendritic spines in layer 2/3 of the developing rat barrel cortex in vivo. Journal of Physiology, 526. 63P-63P. ISSN 0022-3751

Maravall, M., Mainen, Z. F., Sabatini, B. L., Svoboda, K. (May 2000) Estimating intracellular calcium concentrations and buffering without wavelength ratioing. Biophysical Journal, 78 (5). pp. 2655-2667. ISSN 0006-3495

Lendvai, B., Stern, E. A., Chen, B., Svoboda, K. (April 2000) Experience-dependent plasticity of dendritic spines in the developing rat barrel cortex in vivo. Nature, 404 (6780). pp. 876-881. ISSN 0028-0836

Helmchen, F., Svoboda, K., Denk, W., Tank, D. W. (November 1999) In vivo dendritic calcium dynamics in deep-layer cortical pyramidal neurons. Nature Neuroscience, 2 (11). pp. 989-96. ISSN 1097-6256

Shi, S. H., Hayashi, Y., Petralia, R. S., Zaman, S. H., Wenthold, R. J., Svoboda, K., Malinow, R. (June 1999) Rapid spine delivery and redistribution of AMPA receptors after synaptic NMDA receptor activation. Science, 284 (5421). pp. 1811-6. ISSN 0036-8075 (Print)

Mainen, Z. F., Maletic-Savatic, M., Shi, S. H., Hayashi, Y., Malinow, R., Svoboda, K. (June 1999) Two-photon imaging in living brain slices. Methods, 18 (2). pp. 231-39. ISSN 1046-2023 (Print)

Mainen, Z. F., Malinow, R., Svoboda, K. (May 1999) Synaptic calcium transients in single spines indicate that NMDA receptors are not saturated. Nature, 399 (6732). pp. 151-5. ISSN 0028-0836 (Print)

Maletic-Savatic, M., Malinow, R., Svoboda, K. (March 1999) Rapid dendritic morphogenesis in CA1 hippocampal dendrites induced by synaptic activity. Science, 283 (5409). pp. 1923-7. ISSN 0036-8075 (Print)

Svoboda, K., Mainen, Z. F. (March 1999) Synaptic [Ca2+]: intracellular stores spill their guts. Neuron, 22 (3). pp. 427-30. ISSN 0896-6273 (Print)

Svoboda, K., Helmchen, F., Denk, W., Tank, D. W. (January 1999) Spread of dendritic excitation in layer 2/3 pyramidal neurons in rat barrel cortex in vivo. Nature Neuroscience, 2 (1). pp. 65-73. ISSN 1097-6256 (Print)

Svoboda, K. (June 1998) Shining light on spiny matters. Nature Neuroscience, 1 (2). pp. 93-4. ISSN 1097-6256

Denk, W., Svoboda, K. (March 1997) Photon upmanship: why multiphoton imaging is more than a gimmick. Neuron, 18 (3). pp. 351-7. ISSN 0896-6273

Svoboda, K., Denk, W., Kleinfeld, D., Tank, D. W. (January 1997) In vivo dendritic calcium dynamics in neocortical pyramidal neurons. Nature, 385 (6612). pp. 161-5. ISSN 0028-0836

Svoboda, K. (August 1996) New insights into the workings of the ultimate swimming machine. Biophysical Journal, 71 (2). pp. 539-40. ISSN 0006-3495

Denk, W., Yuste, R., Svoboda, K., Tank, D. W. (June 1996) Imaging calcium dynamics in dendritic spines. Curr Opin Neurobiol, 6 (3). pp. 372-8. ISSN 0959-4388

Svoboda, K., Tank, D. W., Denk, W. (May 1996) Direct measurement of coupling between dendritic spines and shafts. Science, 272 (5262). pp. 716-9. ISSN 0036-8075

Yin, Hong, Wang, Michelle D., Svoboda, Karel, Landick, Robert, Block, Steven M., Gelles, Jeff (December 1995) Transcription against an applied force. Science, 270 (5242). pp. 1653-7. ISSN 0036-8075

Block, S. M., Svoboda, K. (April 1995) Analysis of high resolution recordings of motor movement. Biophys J, 68 (4 Supp). 230S-239S; discussion 239S. ISSN 0006-3495

Svoboda, K., Block, S. M. (June 1994) Force and velocity measured for single kinesin molecules. Cell, 77 (5). pp. 773-84. ISSN 0092-8674

Svoboda, K., Block, S. M. (1994) Biological applications of optical forces. Annu Rev Biophys Biomol Struct, 23. pp. 247-85. ISSN 1056-8700

Svoboda, Karel, Schmidt, Christoph F., Schnapp, Bruce J., Block, Steven M. (October 1993) Direct observation of kinesin stepping by optical trapping interferometry. Nature, 365 (6448). pp. 721-7. ISSN 0028-0836

Schmidt, Christoph F., Svoboda, Karel, Lei, Ning, Petsche, Irena B., Berman, Lonny E., Safinya, Cyrus R., Grest, Gary S. (February 1993) Existence of a flat phase in red cell membrane skeletons. Science, 259 (5097). pp. 952-5. ISSN 0036-8075

Svoboda, K., Schmidt, C. F., Branton, D., Block, S. M. (September 1992) Conformation and elasticity of the isolated red blood cell membrane skeleton. Biophys J, 63 (3). pp. 784-93. ISSN 0006-3495 (Print)0006-3495 (Linking)

Book Section

Chen, B., Trachtenberg, J.T., Holtmaat, A. J., Svoboda, K. (2005) Long-term, high-resolution imaging in the neocortex in vivo. In: Live cell imaging: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 423-424. ISBN 0879696826

Svoboda, K., Tank, D. W., Stepnoski, R. A. , Denk, W. (2000) Two-photon Imaging of Neuronal Function in the Neocortex In Vivo. In: Imaging neurons: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. ISBN 0-87969-542-0