Journal Papers

117 - Barykina NV, Subach OM, Piatkevich KD, Jung EE, Malyshev AY, Smirnov IV, Bogorodskiy AO, Borshchevskiy VI, Varizhuk AM, Pozmogova GE, Boyden ES, Anokhin KV, Enikolopov GN, Subach FV (2017) Green fluorescent genetically encoded calcium indicator based on calmodulin/M13-peptide from fungi, PLoS One 12(8):e0183757.

116 - Ho-Jun Suk, Ingrid van Welie, Suhasa B. Kodandaramaiah, Brian Allen, Craig R. Forest, Edward S. Boyden (2017) Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo, Neuron 95(5):1037-1047.

115 - Zhao Y*, Bucur O*, Irshad H, Chen F, Weins A, Stancu AL, Oh EY, DiStasio M, Torous V, Glass B, Stillman IE, Schnitt SJ, Beck AH**, Boyden ES** (2017) Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy, Nature Biotechnology 35(8):757-764. (*, co-first authors; **, co-corresponding authors)

114 - Shaun Berry, Shawn Redmond, Paul Robinson, Todd Thorsen, Mordechai Rothschild, and Edward S. Boyden (2017) Fluidic microoptics with adjustable focusing and beam steering for single cell optogenetics, Optics Express 25(14):16825-16839.

113 - Wu J, de Paz A, Zamft BM, Marblestone AH, Boyden ES, Kording KP, Tyo KEJ (2017) DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase, Scientific Reports 7(1):4756.

112 - Gao R.*, Asano S.M.*, Boyden E.S. (2017) Q&A: Expansion microscopy, BMC Biology 15:50. (*, co-first authors)

111 - Caravaca AS*, Tsaava T*, Goldman L*, Silverman H, Riggott G, Chavan S, Bouton C, Tracey KJ, Desimone R**, Boyden E**, Sohal HS**, Olofsson PS** (2017) A novel flexible cuff-like microelectrode for dual purpose, acute and chronic electrical interfacing with the mouse cervical vagus nerve, Journal of Neural Engineering, doi:10.1088/1741-2552/aa7a42. [Epub ahead of print] (*, co-first authors; **, co-last authors)

110 - Giwa S, Lewis JK, Alvarez L, Langer R, Roth AE, Church GM, Markmann JF, Sachs DH, Chandraker A, Wertheim JA, Rothblatt M, Boyden ES, Eidbo E, Lee WPA, Pomahac B, Brandacher G, Weinstock DM, Elliott G, Nelson D, Acker JP, Uygun K, Schmalz B, Weegman BP, Tocchio A, Fahy GM, Storey KB, Rubinsky B, Bischof J, Elliott JAW, Woodruff TK, Morris GJ, Demirci U, Brockbank KGM, Woods EJ, Ben RN, Baust JG, Gao D, Fuller B, Rabin Y, Kravitz DC, Taylor MJ, Toner M (2017) The promise of organ and tissue preservation to transform medicine, Nature Biotechnology 35(6):530-542.

109 - Stoy WA, Kolb I, Holst G, Liew YJ, Pala A, Yang B, Boyden ES, Stanley GB, Forest CR (2017) Robotic navigation to sub-cortical neural tissue for intracellular electrophysiology in vivo, Journal of Neurophysiology 118(2):1141-1150.

108 - Grossman N, Bono D, Dedic N*, Kodandaramaiah SB*, Rudenko A, Suk HJ, Cassara AM, Neufeld E, Kuster N, Tsai LH, Pascual-Leone A, Boyden ES (2017) Noninvasive Deep Brain Stimulation via Temporally Interfering Electric Fields, Cell 169(6):1029-1041. (* equal contribution)

107 - Annabelle C. Singer*, Giovanni Talei Franzesi*, Suhasa B. Kodandaramaiah, Francisco J. Flores, Jeremy D. Cohen, Albert K. Lee, Christoph Borgers, Craig R. Forest, Nancy J. Kopell, Edward S. Boyden (2017) Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain, Journal of Neurophysiology 118(2):1270-1291.

106 - Alvarez MM, Aizenberg J, Analoui M, Andrews AM, Bisker G, Boyden ES, Kamm RD, Karp JM, Mooney DJ, Oklu R, Peer D, Stolzoff M, Strano MS, Trujillo-de Santiago G, Webster TJ, Weiss PS, Khademhosseini A (2017) Emerging Trends in Micro- and Nanoscale Technologies in Medicine: From Basic Discoveries to Translation, ACS Nano 11(6):5195–5214.

105 - Rowlands, C.J., Park, D., Bruns, O.T., Piatkevich, K.D., Fukumura, D., Jain, R.K., Bawendi, M.G., Boyden, E.S. and So, P.T. (2017) Wide-field three-photon excitation in biological samples, Light: Science & Applications 6(5):e16255.

104 - Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP (2017) Nucleotide-time alignment for molecular recorders, PLoS Computational Biology 13(5):e1005483.

103 - Quadrato G, Nguyen T, Macosko EZ, Sherwood JL, Min Yang S, Berger DR, Maria N, Scholvin J, Goldman M, Kinney JP, Boyden ES, Lichtman JW, Williams ZM, McCarroll SA, Arlotta P (2017) Cell diversity and network dynamics in photosensitive human brain organoids, Nature 545(7652):48-53.

102 - Chang, J.-B., Chen, F., Yoon, Y.-G., Jung, E. E., Babcock H., Kang J.-S., Asano S., Suk H.-J., Pak N., Tillberg P.W., Wassie A., Cai D., Boyden E.S. (2017) Iterative expansion microscopy, Nature Methods 14:593-599.

101 - Yu Shrike Zhang, Grissel Trujillo-de Santiago, Mario Moisés Alvarez, Steven J. Schiff, Edward S. Boyden*, Ali Khademhosseini* (2017) Expansion Mini-Microscopy: An Enabling Alternative in Point-of-Care Diagnostics, Current Opinion in Biomedical Engineering 1:45-53. (*, co-corresponding authors)

100 - Kruss S, Salem DP, Vukovic L, Lima B, Vander Ende E, Boyden ES, Strano MS (2017) High-resolution imaging of cellular dopamine efflux using a fluorescent nanosensor array, Proceedings of the National Academy of Sciences 114(8):1789–1794.

99 - Kumar A, Kim JH, Ranjan P, Metcalfe MG, Cao W, Mishina M, Gangappa S, Guo Z, Boyden ES, Zaki S, York I, García-Sastre A, Shaw M, Sambhara S (2017) Influenza virus exploits tunneling nanotubes for cell-to- cell spread, Scientific Reports 7:40360.

98 - Gao, R.*, Gupta, I.*, Boyden, E. S. (2017) Sonofragmentation of ultra-thin 1D nanomaterials, Particle and Particle Systems Characterization 34.1. (*, co-first authors)

97 - Iaccarino HF*, Singer AC*, Martorell AJ, Rudenko A, Gao F, Gillingham TZ, Mathys H, Seo J, Kritskiy O, Abdurrob F, Adaikkan C, Canter RG, Rueda R, Brown EN, Boyden ES, Tsai LH (2016) Gamma frequency entrainment attenuates amyloid load and modifies microglia, Nature 540(7632):230-235. (*, co-first authors)

96 - Zhuo JM, Tseng HA, Desai M, Bucklin ME, Mohammed AI, Robinson NT, Boyden ES, Rangel LM, Jasanoff AP, Gritton HJ, Han X (2016) Young adult born neurons enhance hippocampal dependent performance via influences on bilateral networks, eLIFE 5:e22429.

95 - Adamala KP*, Martin-Alarcon DA*, Guthrie-Honea KR, Boyden ES (2016) Engineering genetic circuit interactions within and between synthetic minimal cells, Nature Chemistry 9(5):431-439.

94 - Taylor NE, Van Dort CJ, Kenny JD, Pei J, Guidera JA, Vlasov KY, Lee JT, Boyden ES, Brown EN, Solt K (2016) Optogenetic activation of dopamine neurons in the ventral tegmental area induces reanimation from general anesthesia, Proceedings of the National Academy of Sciences 113(45):12826-12831.

93 - Acker L, Pino EN, Boyden ES, Desimone R (2016) FEF inactivation with improved optogenetic methods, Proceedings of the National Academy of Sciences 113(46):E7297-E7306.

92 - Crittenden JR, Tillberg PW, Riad MH, Shima Y, Gerfen CR, Curry J, Housman DE, Nelson SB, Boyden ES, Graybiel AM (2016) Striosome-dendron bouquets highlight a unique striatonigral circuit targeting dopamine-containing neurons, Proceedings of the National Academy of Sciences, 113(40):11318–11323.

91 - Stauffer WR, Lak A, Yang A, Borel M, Paulsen O, Boyden ES, Schultz W (2016) Dopamine Neuron-Specific Optogenetic Stimulation in Rhesus Macaques, Cell 166(6):1564-1571

90 - Wu Q, Kolb I, Callahan BM, Su Z, Stoy W, Kodandaramaiah SB, Neve RL, Zeng H, Boyden ES, Forest CR, Chubykin AA (2016) Integration of autopatching with automated pipette and cell detection in vitro, Journal of Neurophysiology 116(4):1564-1578.

89 - Chen, F.*, Wassie, A.T.*, Cote, A.J., Sinha, A., Alon, S., Asano, S., Daugharthy, E.R., Chang, J.-B., Marblestone, A., Church, G.M., Raj, A., Boyden, E.S. (2016) Nanoscale Imaging of RNA with Expansion Microscopy, Nature Methods 13(8):679-84. (*, co-first authors)

88 - Tillberg, P.W.*, Chen, F.*, Piatkevich, K.D., Zhao, Y., Yu, C.-C., English, B.P., Gao, L., Martorell, A., Suk, H.-J., Yoshida, F., DeGennaro, E.M., Roossien, D.H., Gong, G., Seneviratne, U., Tannenbaum, S.R., Desimone, R., Cai, D., Boyden, E.S. (2016) Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies, Nature Biotechnology 34:987–992. (*, co-first authors)

87 - Rodriques, S.G.*, Marblestone, A.H*, Scholvin, J., Dapello, J., Sarkar, D., Mankin, M., Gao, R., Wood, L., and Boyden, E.S. (2016) Multiplexed neural recording along a single optical fiber via optical reflectometry, Journal of Biomedical Optics 21(5):057003. (*, co-first authors)

86 - Adamala, K.P.*, Martin-Alarcon, D. A.*, Boyden E. S. (2016) Programmable RNA-binding protein composed of repeats of a single modular unit, Proceedings of the National Academy of Sciences 113(19):E2579–E2588. (*, co-first authors)

85 - Karaveli S, Gaathon O, Wolcott A, Sakakibara R, Shemesh OA, Peterka DS, Boyden ES, Owen JS, Yuste R, Englund D (2016) Modulation of nitrogen vacancy charge state and fluorescence in nanodiamonds using electrochemical potential, Proceedings of the National Academy of Sciences 113(15):3938–3943.

84 - Zhang YS*, Chang JB*, Alvarez MM, Trujillo-de Santiago G, Aleman J, Batzaya B, Krishnadoss V, Ramanujam AA, Kazemzadeh-Narbat M, Chen F, Tillberg PW, Dokmeci MR, Boyden ES**, Khademhosseini A.** (2016) Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications, Scientific Reports 6:22691. (* co-first authors, ** co-corresponding authors)

83 - Kodandaramaiah, S.B., Holst, G.L., Wickersham, I.R., Singer, A.C., Talei Franzesi, G., McKinnon, M.L., Forest, C.R., Boyden, E.S. (2016) Assembly and operation of the autopatcher for automated intracellular neural recording in vivo, Nature Protocols 11:634–654.

82 - Glantz, S.T., Carpenter, E.J., Melkonian, M., Gardner, K.H., Boyden, E.S., Wong, G. K.-S., Chow, B.Y. (2016) Functional and topological diversity of LOV domain photoreceptors, Proceedings of the National Academy of Sciences, 113(11):E1442–E1451.

81 - Boyden, E. S. (2015) Optogenetics and the future of neuroscience (Overview, Optogenetics 10th Anniversary Issue), Nature Neuroscience 18:1200–1201.

80 - Kinney, J.P., Bernstein, J.G., Meyer, A.J., Barber, J.B., Bolivar, M., Newbold, B., Scholvin, J., Moore-Kochlacs, C., Wentz, C.T., Kopell, N.J., Boyden, E.S. (2015) A direct-to-drive neural data acquisition system, Frontiers in Neural Circuits 9:46.

79 - Rueckemann JW, DiMauro AJ, Rangel LM, Han X, Boyden ES, Eichenbaum H (2015) Transient optogenetic inactivation of the medial entorhinal cortex biases the active population of hippocampal neurons, Hippocampus 26(2):246–260.

78 - Baratta MV, Kodandaramaiah SB, Monahan PE, Yao J, Weber MD, Lin PA, Gisabella B, Petrossian N, Amat J, Kim K, Yang A, Forest CR, Boyden ES, Goosens KA (2015) Stress Enables Reinforcement-Elicited Serotonergic Consolidation of Fear Memory, Biological Psychiatry 79(10):814-22.

77 - Sakaguchi M, Kim K, Yu LM, Hashikawa Y, Sekine Y, Okumura Y, Kawano M, Hayashi M, Kumar D, Boyden ES, McHugh TJ, Hayashi Y (2015) Inhibiting the Activity of CA1 Hippocampal Neurons Prevents the Recall of Contextual Fear Memory in Inducible ArchT Transgenic Mice, PLoS One 10(6):e0130163.

76 - Afraz, A., Boyden, E. S., DiCarlo, J. J. (2015) Optogenetic and pharmacological suppression of spatial clusters of face neurons reveal their causal role in face gender discrimination, Proceedings of the National Academy of Sciences 112(21):6730-5.

75 - Guo W, Hight AE, Chen JX, Klapoetke NC, Hancock KE, Shinn-Cunningham BG, Boyden ES, Lee DJ, Polley DB (2015) Hearing the light: neural and perceptual encoding of optogenetic stimulation in the central auditory pathway, Scientific Reports 5:10319.

74 - Bernstein, J.G., Allen, B. D., Guerra, A.A., Boyden, E.S. (2015) Processes for design, construction and utilisation of arrays of light-emitting diodes and light-emitting diode-coupled optical fibres for multi-site brain light delivery, The Journal of Engineering, advance online publication, DOI: 10.1049/joe.2014.0304.

73 - Pak N, Siegle JH*, Kinney JP*, Denman DJ, Blanche TJ, Boyden ES (2015) Closed-loop, ultraprecise, automated craniotomies, Journal of Neurophysiology 113(10):3943-53. (*, equal contribution)

72 - Allen, B.D.*, Singer, A.C.*, Boyden, E.S. (2015) Principles of designing interpretable optogenetic behavior experiments, Learning and Memory 22:232-238. (*, equal contribution)

71 - Edward Hight A, Kozin ED, Darrow K, Lehmann A, Boyden E, Brown MC, Lee DJ (2015) Superior Temporal Resolution of Chronos versus Channelrhodopsin-2 in an Optogenetic Model of the Auditory Brainstem Implant, Hearing Research 322:235-241.

70 - Madisen, L., Garner, A.R., Shimaoka, D., Chuong, A.S., Klapoetke, N.C., Li, L., van der Bourg, A., Niino, Y., Egolf, L., Monetti, C., Gu, H., Mills, M., Cheng, A., Tasic, B., Nguyen, T.N., Sunkin, S.M., Benucci, A., Nagy, A., Miyawaki, A., Helmchen, F., Empson, R.M., Knöpfel, T., Boyden, E.S., Reid, R.C., Carandini, M., Zeng, H. (2015) Transgenic Mice for Intersectional Targeting of Neural Sensors and Effectors with High Specificity and Performance, Neuron 85(5):889-892.

69 - Li P, Rial D, Canas PM, Yoo JH, Li W, Zhou X, Wang Y, van Westen GJ, Payen MP, Augusto E, Gonçalves N, Tomé AR, Li Z, Wu Z, Hou X, Zhou Y, PIJzerman A, Boyden ES, Cunha RA, Qu J, Chen JF (2015) Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory, Molecular Psychiatry 20:1339–1349.

68 - Scholvin, J., Kinney, J. P., Bernstein, J. G., Moore-Kochlacs, C., Kopell, N., Fonstad, C.G., Boyden, E. S. (2016) Close-Packed Silicon Microelectrodes for Scalable Spatially Oversampled Neural Recording, IEEE Transactions on Biomedical Engineering, 63(1):120-30.

67 - Cybulski TR, Glaser JI, Marblestone AH, Zamft BM, Boyden ES, Church GM, Kording KP (2015) Spatial information in large-scale neural recordings, Frontiers in Computational Neuroscience 8:172.

66 - Chen, F.*, Tillberg, P.W.*, Boyden, E.S. (2015) Expansion Microscopy, Science 347(6221):543-548. (*, equal contribution)

65 - Johansen J.P., Diaz-Mataix L., Hamanaka H., Ozawa T., Ycu E., Koivumaa J., Kumar A., Hou M., Deisseroth K., Boyden E.S., LeDoux J.E. (2014) Hebbian and neuromodulatory mechanisms interact to trigger associative memory formation, Proceedings of the National Academy of Sciences 111(51):E5584–E5592.

64 - Darrow KN, Slama MC, Kozin E, Owoc M, Hancock K, Kempfle J, Edge A, Lacour S, Boyden E, Polley D, Brown MC, Lee DJ (2014) Optogenetic stimulation of the cochlear nucleus using channelrhodopsin-2 evokes activity in the central auditory pathway, Brain Research 1599:44-56.

63 - Danilo Boada M., Martin T.J., Peters C.M., Hayashida K., Harris M.H., Houle T.T., Boyden E.S., Eisenach J.C., Ririe D.G. (2014) Fast Conducting Mechanoreceptors Contribute to Withdrawal Behavior in Normal and Nerve Injured Rats, Pain 155(12):2646-2655.

62 - Harrison R.R., Kolb I., Kodandaramaiah S.B., Chubykin A.A., Yang A., Bear M.F., Boyden E.S.*, Forest C.* (2014) Microchip amplifier for in vitro, in vivo, and automated whole-cell patch-clamp recording, Journal of Neurophysiology 113(4):1275-82. (*, equal contribution)

61 - Marblestone, A.H., Boyden, E.S. (2014) Designing Tools for Assumption-Proof Brain Mapping, Neuron 83(6):1239-1241.

60 - Fukunaga I., Herb J.T., Kollo M., Boyden E.S., Schaefer A.T. (2014) Independent control of gamma and theta activity by distinct interneuron networks in the olfactory bulb, Nature Neuroscience 17(9):1208-16.

59 - Chuong, A. S., Miri, M. L.*, Busskamp, V.*, Matthews, G.A.C.*, Acker, L.C.*, Soresnsen, A.T., Young, A., Klapoetke, N. C., Henninger, M.A., Kodandaramaiah, S.B., Ogawa, M., Ramanlal, S. B., Bandler, R. C., Allen, B. D., Forest, C.R., Chow, B.Y., Han, X., Lin, Y., Tye, K.M., Roska, B., Cardin, J.A., Boyden, E. S. (2014) Noninvasive optical inhibition with a red-shifted microbial rhodopsin, Nature Neuroscience 17:1123-1129. (*, equal contribution)

58 - Hochbaum, D.R.*, Zhao, Y.*, Farhi, S.L., Klapoetke, N.C., Werley, C.A., Kapoor, V., Zou, P., Kralj, J.M., Maclaurin, D., Smedemark-Margulies, N., Saulnier, J., Boulting, G.L., Straub, C., Cho, Y., Melkonian, M., Wong, G.K.-S., Harrison, D. J., Murthy, V.N., Sabatini, B., Boyden, E.S.**, Campbell, R.E.**, Cohen, A.E. (2014) All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins, Nature Methods, 11(8):825-33. (*, equal contribution, **, jointly directed work)

57 - Prevedel, R.**, Yoon, Y.-G.**, Hoffman, M., Pak, N., Wetzstein, G., Kato, S., Schrodel, T., Raskar, R., Zimmer, M., Boyden, E. S.*, Vaziri, A. * (2014) Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy, Nature Methods 11:727-730. (** equal contribution, * co-corresponding authors)

56 - Klapoetke, N. C., Murata, Y., Kim S. S., Pulver, S. R., Birdsey-Benson, A., Cho, Y. K., Morimoto, T. K., Chuong, A. S., Carpenter, E. J., Tian, Z., Wang, J., Xie, Y., Yan, Z., Zhang, Y., Chow, B.Y., Surek, B., Melkonian, M., Jayaraman, V., Constantine-Paton, M., Wong, G. K.*, Boyden, E. S.* (2014) Independent Optical Excitation of Distinct Neural Populations, Nature Methods 11:338–346. (* co-corresponding authors)

55 - Perea, G., Yang, A., Boyden, E. S., Sur, M. (2014) Optogenetic astrocyte activation modulates response selectivity of visual cortex neurons in vivo, Nature Communications 5:3262.

54 - Schmidt, D., Tillberg, P. W.*, Chen, F.*, Boyden, E. S. (2014) A fully genetically-encoded protein architecture for optical control of peptide ligand concentration, Nature Communications, 5:3019. (* equal contribution)

53 - Marblestone, A. H.**+, Zamft, B. M.+, Maguire, Y. G., Shapiro, M. G., Cybulski, T. R., Glaser, J. I., Amodei, D., Stranges, P. B., Kalhor, R., Dalrymple, D. A., Seo, D., Alon, E., Maharbiz, M. M., Carmena, J. M., Rabaey, J. M., Boyden, E. S.*, Church, G. M. *, Kording, K. P. * (2013) Physical Principles for Scalable Neural Recording, Frontiers in Computational Neuroscience, 7:137. (** corresponding author, + equal contribution, * equal contribution)

52 - Glaser J.I.**, Zamft B.M.*, Marblestone A.H.*, Moffitt J.R., Tyo K., Boyden E.S., Church G., Kording K.P. (2013) Statistical analysis of molecular signal recording, PLoS Computational Biology 9(7):e1003145. (** corresponding author, * equal contribution)

51 - Kodandaramaiah, S. B., Boyden, E. S.*, Forest, C. F.* (2013) In vivo robotics: the automation of neuroscience and other intact-system biological fields, Annals of the New York Academy of Sciences, 1305(1):63-71. (* co-corresponding authors)

50 - Tsunematsu T., Tabuchi S., Tanaka K.F., Boyden E.S., Tominaga M., Yamanaka A. (2013) Long-lasting silencing of orexin/hypocretin neurons using archaerhodopsin induces slow-wave sleep in mice, Behavioural Brain Research, 255:64-74.

49 - Famm, K., Litt, B., Tracey, K.J., Boyden, E.S., Slaoui, M. (2013) Drug discovery: a jump-start for electroceuticals, Nature 496(7444):159-61.

48 - Kahn, I., Knoblich, U., Desai, M., Bernstein, J., Graybiel, A.M., Boyden, E.S., Buckner, R.L., Moore C.I. (2013) Optogenetic drive of neocortical pyramidal neurons generates fMRI signals that are correlated with spiking activity, Brain Research, 1511:33-45.

47 - Chow, B. Y.* and Boyden, E. S.* (2013) Optogenetics and Translational Medicine, Science Translational Medicine 5(177):177ps5. (* co-corresponding authors)

46 - Alivisatos, A., Andrews, A., Boyden, E. S., Chun, M., Church, G., Deisseroth, K., Donoghue, J., Fraser, S., Lippincott-Schwartz, J., Looger, L., Masmanidis, S., McEuen, P., Nurmikko, A., Park, H., Peterka, D., Reid, C., Roukes, M., Scherer, A., Schnitzer, M., Sejnowski, T., Shepard, K., Tsao, D., Turrigiano, G., Weiss, P., Xu, C., Yuste, R., Zhuang, X. (2013) Nanotools for Neuroscience and Brain Activity Mapping, ACS Nano, 7(3):1850-66.

45 - Cavanaugh, J., Monosov, I. E., McAlonan, K., Berman, R. A., Smith, M. K., Cao, V., Wang, K. H., Boyden, E. S., Wurtz, R. H. (2012) Optogenetic Inactivation Modifies Monkey Visuomotor Behavior, Neuron 76:901–907.

44 - Gurkan, U. A., Fan, Y., Xu, F., Erkmen, B., Urkac, E. S., Parlakgul, G., Bernstein, J., Xing, W.*, Boyden, E. S.*, Demirci, U.* (2013) Simple precision creation of digitally specified, spatially heterogeneous, engineered tissue architectures, Advanced Materials 25(8):1192-1198. (* co-corresponding authors)

43 - Zorzos, A. N., Scholvin, J., Boyden, E. S.*, Fonstad, C. G. (2012) Three-dimensional multiwaveguide probe array for light delivery to distributed brain circuits, Optics Letters 37(23):4841-4843. (* corresponding author)

42 - Boyden, E. S. (2013) Interview with Edward S. Boyden, Trends in Neurosciences 36(1):1-2.

41 - Zamft, B. M.*, Marblestone, A. H.*, Kording, K., Schmidt, D., Martin-Alarcon, D., Tyo, K., Boyden, E. S., Church, G. (2012) Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing, PLoS ONE 7(8): e43876. (* co-first authors)

40 - Lee, S.-H., Kwan, A. C., Zhang, S., Phoumthipphavong, V., Flannery, J. G., Masmanidis, S. C., Taniguchi, H., Huang, Z. J., Zhang, F., Boyden, E. S., Deisseroth, K., Dan, Y. (2012) Activation of specific interneurons improves V1 feature selectivity and visual perception, Nature 488(7411):379-8.

39 - Gerits, A., Farivar, R., Rosen, B. R., Wald, L. L., Boyden, E. S., Vanduffel, W. (2012) Optogenetically Induced Behavioral and Functional Network Changes in Primates, Current Biology 22(18):1722-6.

38 - Karayiorgou M., Flint J., Gogos J.A., Malenka R.C.; the Genetic and Neural Complexity in Psychiatry 2011 Working Group (Bargmann C.I., Boyden E.S., Bullmore E.T., Chan A.W., Davis M., Deisseroth K., Dolmetch R.E., Eggan K., Fears S.C., Freimer N.B., Geschwind D.H., Gordon J., Nickerson D.A., Vanderhaeghen P., Axel R., Zuker C.S., Fischbach G.) (2012) The best of times, the worst of times for psychiatric disease, Nature Neuroscience 15(6):811-812.

37 - Kodandaramaiah, S., Talei Franzesi, G., Chow, B., Boyden, E. S.*, Forest, C.* (2012) Automated whole-cell patch clamp electrophysiology of neurons in vivo, Nature Methods 9:585–587. (* co-corresponding authors)

36 - Kim K.M., Baratta M.V., Yang A., Lee D., Boyden E.S.*, Fiorillo C.D.* (2012) Optogenetic mimicry of the transient activation of dopamine neurons by natural reward is sufficient for operant reinforcement, PLoS One 7(4):e33612. (* co-corresponding authors)

35 - Madisen, L., Mao, T., Koch, H., Zhuo, J.-m., Berenyi, A., Fujisawa, S., Hsu, Y.-W., Garcia, A. J., Gu, X., Zanella, S., Kidney, J., Gu, H., Mao, Y., Hooks, B. M., Boyden, E. S., Buzsáki, G., Ramirez, J. M., Jones, A. R., Svoboda, K., Han, X., Turner, E. E., Zeng, H. (2012) A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing, Nature Neuroscience 15(5):793-802.

34 - Chow B.Y., Han, X., Boyden, E. S. (2012) Genetically encoded molecular tools for light-driven silencing of targeted neurons, Progress in Brain Research 196:49-61.

33 - Knopfel, T., Boyden, E. S. (2012) Tools for observing and controlling specific molecular or physiological pathways in intact cells and tissues. Preface, Progress in Brain Research 196:vii–viii.

32 - Börgers C., Talei Franzesi G., LeBeau F. E. N. , Boyden E. S., Kopell N.J. (2012) Minimal Size of Cell Assemblies Coordinated by Gamma Oscillations, PLoS Computational Biology 8(2):e1002362.

31 - Bernstein, J. G., Boyden, E. S. (2011) Optogenetic tools for analyzing the neural circuits of behavior, Trends in Cognitive Sciences 15(12):592-600.

30 - Kleinlogel, S., Terpitz, U., Legrum, B., Gokbuget, D., Boyden, E. S., Bamann, C., Wood, P. G., Bamberg, E. (2011) A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins, Nature Methods 8(12):1083-1088.

29 - Bernstein, J. G., Garrity, P. A.*, Boyden, E. S.* (2012) Optogenetics and thermogenetics: technologies for controlling the activity of targeted cells within intact neural circuits, Current Opinion in Neurobiology 22(1):61-71. (* co-corresponding authors)

28 - Boyden ES. (2011) Optogenetics: using light to control the brain, Cerebrum 2011:16.

27 - Kahn, I. * Desai, M., Knoblich, U., Bernstein, J., Henninger, M., Graybiel, A. M., Boyden, E. S.*, Buckner, R. L. *, Moore, C. I. * (2011) Characterization of the Functional MRI Response Temporal Linearity via Optical Control of Neocortical Pyramidal Neurons, Journal of Neuroscience 31(42):15086-15091. (* co-corresponding authors)

26 - Tsunematsu, T., Kilduff, T., Boyden, E. S., Takahashi, S., Tominaga, M., Yamanaka, A. (2011) Acute optogenetic silencing of orexin/hypocretin neurons induces slow wave sleep in mice, Journal of Neuroscience 31(29): 10529-10539.

25 - Joo, J., Chow, B. Y., Prakash, M., Boyden, E. S., Jacobson, J. M. (2011) Face-selective electrostatic control of hydrothermal zinc oxide nanowire synthesis, Nature Materials 10(8):596-601.

24 - Wentz, C. T., Bernstein, J. G., Monahan, P., Guerra, A., Rodriguez, A., Boyden, E. S. (2011) A Wirelessly Powered and Controlled Device for Optical Neural Control of Freely-Behaving Animals, Journal of Neural Engineering 8(4):046021.

23 - Chow, B. Y. and Boyden, E. S. (2011) Synthetic Physiology, Science 332(6037):1508-1509.

22 - McCarthy, M. M., Moore-Kochlacs, C., Xuan Gu, T., Boyden, E. S., Han, X., Kopell, N. J. (2011) Striatal origin of the pathologic beta oscillations in Parkinson’s disease, Proceedings of the National Academy of Sciences 108(28):11620-5.

21 - Chow, B. Y.*, Chuong, A. S. *, Klapoetke, N. C. *, Boyden, E. S. (2011) Synthetic Physiology: Strategies for Adapting Tools from Nature for Genetically-Targeted Control of Fast Biological Processes, Methods in Enzymology 497:425-43. (* co-first authors)

20 - Boyden, E.S. (2011) A history of optogenetics: the development of tools for controlling brain circuits with light, F1000 Biology Reports 3:11.

19 - Doroudchi, M. M., Greenberg, K. P., Liu, J., Silka, K. A., Boyden, E. S., Lockridge, J. A., Arman, A. C., Janani, R., Boye, S. E., Boye, S. L., Gordon, G. M., Matteo, B. C., Sampath, A. P., Hauswirth, W. W., Horsager, A. (2011) Virally delivered Channelrhodopsin-2 Safely and Effectively Restores Visual Function in Multiple Mouse Models of Blindness, Molecular Therapy 19(7):1220-9.

18 - Han, X.*, Chow, B. Y.*, Zhou, H., Klapoetke, N. C., Chuong, A., Rajimehr, R., Yang, A., Baratta, M. V., Winkle, J., Desimone, R., Boyden, E. S. (2011) A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex, Frontiers in Systems Neuroscience 5:18. (* co-first authors)

17 - Desai M., Kahn I., Knoblich U., Bernstein J., Atallah H., Yang A., Kopell, N., Buckner R.L., Graybiel A. M., Moore C. I.*, and Boyden E. S.* (2011) Mapping Brain Networks in Awake Mice Using Combined Optical Neural Control and fMRI, Journal of Neurophysiology 105(3):1393-405. (* co-corresponding authors)

16 - Zorzos, A. N., Boyden, E. S.*, and Fonstad, C. G. (2010) Multiwaveguide implantable probe for light delivery to sets of distributed brain targets, Optics Letters 35(24):4133-5. (* corresponding author)

15 - Knopfel, T., Lin, M. Z., Levskaya, A., Tian, L., Lin, J. Y., Boyden, E. S. (2010) Toward the Second Generation of Optogenetic Tools, Journal of Neuroscience 30(45):14998-15004.

14 - Chan, S. Y., Bernstein, J. G., Boyden, E. S. (2010) Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits, Journal of Visualized Experiments 35:1489.

13 - Chow, B. Y.*, Han, X.*, Dobry, A. S., Qian, X., Chuong, A. S., Li, M., Henninger, M. A., Belfort, G. M., Lin, Y., Monahan, P. E., Boyden, E. S. (2010) High-performance genetically targetable optical neural silencing by light- driven proton pumps, Nature 463:98-102. (* co-first authors)

12 - Han X., Qian X., Stern P., Chuong A. and Boyden E.S. (2009) Informational Lesions: Optical Perturbation of Spike Timing and Neural Synchrony Via Microbial Opsin Gene Fusions, Frontiers in Molecular Neuroscience 2:12.

11 - Han, X.*, Qian, X., Bernstein, J.G., Zhou, H.-H., Talei Franzesi, G., Stern, P., Bronson, R.T., Graybiel, A.M., Desimone, R., and Boyden, E.S.* (2009) Millisecond-Timescale Optical Control of Neural Dynamics in the Nonhuman Primate Brain, Neuron 62(2):191-198. (* co-corresponding authors)

10 - Liao, Y. J., Safa, P., Chen, Y.-R., Sobel, R. A., Boyden, E. S., Tsien, R. W. (2008) Anti-Ca2+ channel antibody attenuates Ca2+ currents and mimics cerebellar ataxia in vivo, Proceedings of the National Academy of Sciences 105(7):2705-2710.

9 - Wang, H., Peca, J., Matsusaki, M., Matsusaki, K., Noguchi, J., Qiu, L., Wang, D., Zhang, F., Boyden, E. S., Deisseroth, K., Kasai, H., Hall, W. C., Feng, G., Augustine, G. J. (2007) High-speed mapping of synaptic connectivity using photostimulation in channelrhodopsin-2 transgenic mice, Proceedings of the National Academy of Sciences 104(19):8143-848.

8 - Han, X. and Boyden, E. S. (2007) Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution, PLoS ONE 2(3): p. e299.

7 - Zhang, F., Wang, L.-P., Boyden, E. S., Deisseroth, K. (2006) Optical control of excitable cells and Channelrhodopsin-2, Nature Methods 3(10):785-92.

6 - Boyden, E. S., Katoh, A., Pyle, J. L., Chatila, T. A., Tsien, R. W., Raymond, J. L. (2006) Selective engagement of plasticity mechanisms for motor memory storage, Neuron 51(6):823-834.

5 - Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., Deisseroth, K. (2005) Millisecond-timescale, genetically-targeted optical control of neural activity, Nature Neuroscience 8(9):1263-1268.

4 - Kimpo, R. R.*, Boyden, E. S.*, Katoh, A., Ke, M. C., Raymond, J. L. (2005) Distinct patterns of stimulus generalization of increases and decreases in VOR gain, Journal of Neurophysiology 94(5):3092-3100. (* co-first authors)

3 - Boyden, E. S.*, Katoh, A.*, Raymond, J. L. (2004) Cerebellum-dependent learning: The role of multiple plasticity mechanisms, Annual Review of Neuroscience 27:581-609. (* co-first authors)

2 - Boyden, E. S., Raymond, J. L. (2003) Active reversal of motor memories reveals rules governing memory encoding, Neuron 39(6):1031-42.

1 - Maguire, Y., Boyden, E. S., Gershenfeld, N. (2000) Toward a table-top quantum computer, IBM Systems Journal 39:3&4, p.823.