Journal Papers and Preprints

187 - Gao R*, Yu CJ*, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES (2021) A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy, Nature Nanotechnology 16:698–707. (*, equal contribution)

186 - Liu S, Punthambaker S, Iyer EPR, Ferrante T, Goodwin D, Fürth D, Pawlowski AC, Jindal K, Tam JM, Mifflin L, Alon S, Sinha A, Wassie AT, Chen F, Cheng A, Willocq V, Meyer K, Ling KH, Camplisson CK, Kohman RE, Aach J, Lee JH, Yankner BA, Boyden ES, Church GM (2021) Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses, Nucleic Acids Research 49(10):e58.

185 - Alon S*, Goodwin DR*, Sinha A*, Wassie AT*, Chen F*, Daugharthy ER**, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A; IMAXT Consortium, Church GM***+, Marblestone AH***, Boyden ES***+ (2021) Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems, Science 371(6528):eaax2656. (* equal contribution, ** key contributions to early stages of project, *** equal contribution, +co-corresponding authors)

184 - Sunshine MD, Cassarà AM, Neufeld E, Grossman N, Mareci TH, Otto KJ, Boyden ES, Fuller DD (2021) Restoration of breathing after opioid overdose and spinal cord injury using temporal interference stimulation, Communications Biology 4(1):107.

183 - Schreglmann SR, Wang D, Peach RL, Li J, Zhang X, Latorre A, Rhodes E, Panella E, Cassara AM, Boyden ES, Barahona M, Santaniello S, Rothwell J, Bhatia KP, Grossman N (2021) Non-invasive suppression of essential tremor via phase-locked disruption of its temporal coherence, Nature Communications 12(1):363.

182 - Payne AC*, Chiang ZD*, Reginato PL*, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES**, Buenrostro JD**, Chen F** (2020) In situ genome sequencing resolves DNA sequence and structure in intact biological samples, Science 371(6532):eaay3446. (* equal contribution, **co-corresponding)

181 - Qian Y, Cosio DMO, Piatkevich KD, Aufmkolk S, Su WC, Celiker OT, Schohl A, Murdock MH, Aggarwal A, Chang YF, Wiseman PW, Ruthazer ES, Boyden ES, Campbell RE (2020) Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging, PLoS Biology 18(11):e3000965.

180 - Changyang Linghu*, Shannon L. Johnson*, Pablo A. Valdes, Or A. Shemesh, Won Min Park, Demian Park, Kiryl D. Piatkevich, Asmamaw T. Wassie, Yixi Liu, Bobae An, Stephanie A. Barnes, Orhan T. Celiker, Chun-Chen Yao, Chih-Chieh (Jay) Yu, Ru Wang, Katarzyna P. Adamala, Mark F. Bear, Amy E. Keating and Edward S. Boyden (2020) Spatial multiplexing of fluorescent reporters for imaging signaling network dynamics, Cell 183(6):1682-1698. (*, equal contribution)

179 - Chih-Chieh (Jay) Yu*, Danielle M. Orozco Cosio*, Edward S. Boyden (2020) ExCel: Super-resolution imaging of C. elegans with expansion microscopy, Methods in Molecular Biology, accepted. (*, equal contribution)

178 - Samuel G. Rodriques*, Linlin M. Chen*, Sophia Liu, Ellen D. Zhong, Joseph R. Scherrer, Edward S. Boyden**, Fei Chen** (2020) RNA timestamps identify the age of single molecules in RNA sequencing, Nature Biotechnology 39:320–325. (*, equal contribution, **, co-corresponding)

177 - Moreaux LC, Yatsenko D, Sacher WD, Choi J, Lee C, Kubat NJ, Cotton RJ, Boyden ES, Lin MZ, Tian L, Tolias AS, Poon JKS, Shepard KL, Roukes ML (2020) Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity - at Depth and in Real Time, Neuron 108(1):66-92.

176 - Young-Gyu Yoon*, Zeguan Wang*, Nikita Pak, Demian Park, Peilun Dai, Jeong Seuk Kang, Ho-Jun Suk, Panagiotis Symvoulidis, Burcu Guner-Ataman, Kai Wang**, and Edward S. Boyden** (2020) Sparse decomposition light-field microscopy for high speed imaging of neuronal activity, Optica 7(10):1457-1468. (* equal contributors, ** equal contributors)

175 - Shen FY, Harrington MM, Walker LA, Cheng HPJ, Boyden ES, Cai D (2020) Light microscopy based approach for mapping connectivity with molecular specificity, Nature Communications 11(1):4632.

174 - Deblina Sarkar*, Jinyoung Kang*, Asmamaw T Wassie*, Margaret E. Schroeder, Zhuyu Peng, Tyler B. Tarr, Ai-Hui Tang, Emily Niederst, Jennie Z. Young, Li-Huei Tsai**, Thomas A. Blanpied**, Edward S. Boyden** (2020) Expansion Revealing: Decrowding Proteins to Unmask Invisible Brain Nanostructures, bioRxiv 2020.08.29.273540. (* co-first authors, ** co-corresponding authors)

173 - Shemesh OA*, Linghu C*, Piatkevich KD*, Goodwin D, Celiker OT, Gritton HJ, Romano MF, Gao R, Yu CJ, Tseng HA, Bensussen S, Narayan S, Yang CT, Freifeld L, Siciliano CA, Gupta I, Wang J, Pak N, Yoon YG, Ullmann JFP, Guner-Ataman B, Noamany H, Sheinkopf ZR, Park WM, Asano S, Keating AE, Trimmer JS, Reimer J, Tolias AS, Bear MF, Tye KM, Han X, Ahrens MB, Boyden ES (2020) Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator, Neuron 107(3):470-486. (*, equal contribution)

172 - Zhang C*, Kang JS*, Asano SM, Gao R, Boyden ES (2020) Expansion Microscopy for Beginners: Visualizing Microtubules in Expanded Cultured HeLa Cells, Current Protocols in Neuroscience 92(1):e96. (*, contributed equally)

171 - Yu CJ, Barry NC, Wassie AT, Sinha A, Bhattacharya A, Asano S, Zhang C, Chen F, Hobert O, Goodman MB, Haspel G, Boyden ES (2020) Expansion microscopy of C. elegans, eLife 9:e46249.

170 - Gong X, Mendoza-Halliday D, Ting JT, Kaiser T, Sun X, Bastos AM, Wimmer RD, Guo B, Chen Q, Zhou Y, Pruner M, Wu CW, Park D, Deisseroth K, Barak B, Boyden ES, Miller EK, Halassa MM, Fu Z, Bi G, Desimone R, Feng G (2020) An Ultra-Sensitive Step-Function Opsin for Minimally Invasive Optogenetic Stimulation in Mice and Macaques, Neuron 107(1):38-51.

169 - Bucur O*, Fu F*, Calderon M, Mylvaganam GH, Ly NL, Day J, Watkin S, Walker BD, Boyden ES**, Zhao Y** (2020) Nanoscale imaging of clinical specimens using conventional and rapid expansion pathology, Nature Protocols 15:1649-1672. (*, equal contribution, **, co-corresponding)

168 - Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV (2020) Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein, International Journal of Molecular Sciences 21(5):1644.

167 - Fan LZ, Kheifets S, Böhm UL, Wu H, Piatkevich KD, Xie ME, Parot V, Ha Y, Evans KE, Boyden ES, Takesian AE, Cohen AE (2020) All-Optical Electrophysiology Reveals the Role of Lateral Inhibition in Sensory Processing in Cortical Layer 1, Cell 180(3):521-535.

166 - Edward S. Boyden (2019) Optogenetics: Tools for Controlling Brain Cells with Light, Molecular Frontiers Journal, 3(2)129-137.

165 - Emmanouil D. Karagiannis*, Jeong Seuk Kang*, Tay Won Shin, Amauche Emenari, Shoh Asano, Leanne Lin, Emma K. Costa, IMAXT Grand Challenge Consortium, Adam H. Marblestone, Narayanan Kasthuri, Edward S. Boyden (2019) Expansion Microscopy of Lipid Membranes, bioRxiv 829903. (*, equal contribution)

164 - Ramirez-Zamora A, Giordano J, Boyden ES, Gradinaru V, Gunduz A, Starr PA, Sheth SA, McIntyre CC, Fox MD, Vitek J, Vedam-Mai V, Akbar U, Almeida L, Bronte-Stewart HM, Mayberg HS, Pouratian N, Gittis AH, Singer AC, Creed MC, Lazaro-Munoz G, Richardson M, Rossi MA, Cendejas-Zaragoza L, D'Haese PF, Chiong W, Gilron R, Chizeck H, Ko A, Baker KB, Wagenaar J, Harel N, Deeb W, Foote KD, Okun MS (2019) Proceedings of the Sixth Deep Brain Stimulation Think Tank Modulation of Brain Networks and Application of Advanced Neuroimaging, Neurophysiology, and Optogenetics, Frontiers in Neuroscience 13:936.

163 - Piatkevich KD*, Bensussen S*, Tseng HA*, Shroff SN, Lopez-Huerta VG, Park D, Jung EE, Shemesh OA, Straub C, Gritton HJ, Romano MF, Costa E, Sabatini BL, Fu Z, Boyden ES**, Han X** (2019) Population imaging of neural activity in awake behaving mice, Nature 574:413–417. (* equal contribution, **, co-corresponding)

162 - Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X (2019) Voices in methods development, Nature Methods 16(10):945-951.

161 - Guo SM, Veneziano R, Gordonov S, Li L, Danielson E, Perez de Arce K, Park D, Kulesa AB, Wamhoff EC, Blainey PC, Boyden ES, Cottrell JR, Bathe M (2019) Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes, Nature Communications 10(1):4377.

160 - Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P (2019) Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues, Nature Biotechnology 37(9):1080-1090.

159 - Suk HJ, Boyden ES, van Welie I (2019) Advances in the automation of whole-cell patch clamp technology, Journal of Neuroscience Methods 326:108357.

158 - Bajo VM, Nodal FR, Korn C, Constantinescu AO, Mann EO, Boyden ES, King AJ (2019) Silencing cortical activity during sound-localization training impairs auditory perceptual learning, Nature Communications 10(1):3075.

157 - Adaikkan C, Middleton SJ, Marco A, Pao PC, Mathys H, Kim DN, Gao F, Young JZ, Suk HJ, Boyden ES, McHugh TJ, Tsai LH (2019) Gamma Entrainment Binds Higher-Order Brain Regions and Offers Neuroprotection, Neuron 102(5):929-943.

156 - Kolb I, Landry CR, Yip MC, Lewallen CF, Stoy WA, Lee J, Felouzis A, Yang B, Boyden ES, Rozell CJ, Forest CR (2019) PatcherBot: a single-cell electrophysiology robot for adherent cells and brain slices, Journal of Neural Engineering 16(4):046003.

155 - Boyden ES, Marblestone AH (2019) Architecting Discovery: A Model for How Engineers Can Help Invent Tools for Neuroscience, Neuron 102(3):523-525.

154 - Holst GL, Stoy W, Yang B, Kolb I, Kodandaramaiah SB, Li L, Knoblich U, Zeng H, Haider B, Boyden ES, Forest CR (2019) Autonomous patch-clamp robot for functional characterization of neurons in vivo: development and application to mouse visual cortex, Journal of Neurophysiology 121(6):2341-2357.

153 - Martorell AJ, Paulson AL, Suk HJ, Abdurrob F, Drummond GT, Guan W, Young JZ, Kim DN, Kritskiy O, Barker SJ, Mangena V, Prince SM, Brown EN, Chung K, Boyden ES, Singer AC, Tsai LH (2019) Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition, Cell 177(2):256-271.

152 - Nardou R, Lewis EM, Rothhaas R, Xu R, Yang A, Boyden E, Dölen G (2019) Oxytocin-dependent reopening of a social reward learning critical period with MDMA, Nature 569(7754):116-120.

151 - Rodriques SG, Marblestone AH, Boyden ES (2019) A theoretical analysis of single molecule protein sequencing via weak binding spectra, PLoS One 14(3):e0212868.

150 - Markus A. Stahlberg, Charu Ramakrishnan, Katrin I. Willig, Edward S. Boyden, Karl Deisseroth, Camin Dean (2019) Investigating the feasibility of channelrhodopsin variants for nanoscale optogenetics, Neurophotonics 6(1):015007.

149 - Qian Y, Piatkevich KD, Mc Larney B, Abdelfattah AS, Mehta S, Murdock MH, Gottschalk S, Molina RS, Zhang W, Chen Y, Wu J, Drobizhev M, Hughes TE, Zhang J, Schreiter ER, Shoham S, Razansky D, Boyden ES, Campbell RE (2018) A genetically encoded near-infrared fluorescent calcium ion indicator, Nature Methods 16(2):171-174.

148 - Ruixuan Gao*, Shoh M. Asano*, Srigokul Upadhyayula*, Igor Pisarev, Daniel E. Milkie, Tsung-Li Liu, Ved Singh, Austin Graves, Grace H. Huynh, Yongxin Zhao, John Bogovic, Jennifer Colonell, Carolyn M. Ott, Christopher Zugates, Susan Tappan, Alfredo Rodriguez, Kishore R. Mosaliganti, Shu-Hsien Sheu, H. Amalia Pasolli, Song Pang, C. Shan Xu, Sean G. Megason, Harald Hess, Jennifer Lippincott-Schwartz, Adam Hantman, Gerald M. Rubin, Tom Kirchhausen, Stephan Saalfeld, Yoshinori Aso, Edward S. Boyden**, Eric Betzig** (2019) Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution, Science 363(6424):eaau8302. (*, equal contribution, **, co-corresponding)

147 - Sara Mederos, Alicia Hernández‐Vivanco, Jorge Ramírez‐Franco, Mario Martín‐Fernández, Marta Navarrete, Aimei Yang, Edward S. Boyden, Gertrudis Perea (2019) Melanopsin for precise optogenetic activation of astrocyte‐neuron networks, Glia 67(5):915-934.

146 - Cho YK, Park D*, Yang A*, Chen F, Chuong AS, Klapoetke NC, Boyden ES (2019) Multidimensional screening yields channelrhodopsin variants having improved photocurrent and order-of-magnitude reductions in calcium and proton currents, Journal of Biological Chemistry 294(11):3806-3821. (*, equal contribution)

145 - Wassie AT*, Zhao Y*, Boyden ES (2019) Expansion microscopy: principles and uses in biological research, Nature Methods 16(1):33-41. (*, equal contributors)

144 - Gambarotto D, Zwettler FU, Le Guennec M, Schmidt-Cernohorska M, Fortun D, Borgers S, Heine J, Schloetel JG, Reuss M, Unser M, Boyden ES, Sauer M, Hamel V, Guichard P (2019) Imaging cellular ultrastructures using expansion microscopy (U-ExM), Nature Methods 16(1):71-74.

143 - D. Oran*, S. G. Rodriques*, R. Gao, S. Asano, M. A. Skylar-Scott, F. Chen, P. W. Tillberg, A. H. Marblestone**, E. S. Boyden** (2018) 3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds, Science 362(6420):1281-1285. (*, equal contributors; **, equal contributors)

142 - Michihiro Igarashi, Motohiro Nozumi, Ling-Gang Wu, Francesca Cella Zanacchi, István Katona, László Barna, Pingyong Xu, Mingshu Zhang, Fudong Xue, Edward Boyden (2018) New observations in neuroscience using superresolution microscopy, Journal of Neuroscience 38 (44) 9459-9467.

141 - Boyden, E. S. (2018) Maps of Mechanisms, “Building a Better Brain” Voices Feature, Cell 175(3):633-634.

140 - Boyden, E. S. (2018) Physical magnification of objects, Materials Horizons 6:11-13.

139 - Nir Grossman, Michael S. Okun, Edward S. Boyden (2018) Translating Temporal Interference Brain Stimulation to Treat Neurological and Psychiatric Conditions, JAMA Neurology 75(11):1307-1308

138 - Jörg Scholvin, Anthony Zorzos, Justin Kinney, Jacob Bernstein, Caroline Moore-Kochlacs, Nancy Kopell, Clifton Fonstad and Edward S. Boyden (2018) Scalable, Modular Three-Dimensional Silicon Microelectrode Assembly via Electroless Plating, Micromachines 9(9):436.

137 - Wolff AR, Bygrave AM, Sanderson DJ, Boyden ES, Bannerman DM, Kullmann DM, Kätzel D (2018) Optogenetic induction of the schizophrenia-related endophenotype of ventral hippocampal hyperactivity causes rodent correlates of positive and cognitive symptoms, Scientific Reports 8(1):12871.

136 - Asano SM*, Gao R*, Wassie AT*, Tillberg PW, Chen F, Boyden ES (2018) Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues, Current Protocols in Cell Biology 80(1):e56. (*, co-first authors)

135 - Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, Zeng H (2018) A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality, Cell 174(2):465-480.

134 - Allen BD, Moore-Kochlacs C, Bernstein JG, Kinney J, Scholvin J, Seoane L, Chronopoulos C, Lamantia C, Kodandaramaiah SB, Tegmark M, Boyden ES (2018) Automated in vivo patch clamp evaluation of extracellular multielectrode array spike recording capability, Journal of Neurophysiology 120(5):2182-2200.

133 - Alon, S.*, Huynh, G. H.*, Boyden, E. S. (2018) Expansion Microscopy: Enabling Single Cell Analysis In Intact Biological Systems, The FEBS Journal 286(8):1482-1494. (*, co-first authors)

132 - Migliori B, Datta MS, Dupre C, Apak MC, Asano S, Gao R, Boyden ES, Hermanson O, Yuste R, Tomer R (2018) Light sheet theta microscopy for rapid high-resolution imaging of large biological samples, BMC Biology 16(1):57.

131 - de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ (2018) High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing, Nucleic Acids Research 46(13):e78.

130 - Piatkevich KD*, Jung EE*, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES (2018) A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters, Nature Chemical Biology 14(4):352-360. (*, co-first authors)

129 - Senova S, Poupon C, Dauguet J, Stewart HJ, Dugué GP, Jan C, Hosomi K, Ralph GS, Barnes L, Drouot X, Pouzat C, Mangin JF, Pain F, Doignon I, Aron-Badin R, Brouillet E, Boyden ES, Mitrophanous KA, Hantraye P, Palfi S (2018) Optogenetic Tractography for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates, Scientific Reports 8(1):3362.

128 - Karagiannis ED, Boyden ES (2018) Expansion microscopy: development and neuroscience applications, Current Opinion in Neurobiology 50:56-63.

127 - Kodandaramaiah SB, Flores FJ, Holst GL, Singer AC, Han X, Brown EN, Boyden ES*, Forest CR* (2018) Multi-neuron intracellular recording in vivo via interacting autopatching robots, Elife 7:e24656. (*, co-corresponding authors)

126 - Kolb I*, Franzesi GT*, Wang M, Kodandaramaiah SB, Forest CR, Boyden ES+, Singer AC+ (2017) Evidence for long-timescale patterns of synaptic inputs in CA1 of awake behaving mice, Journal of Neuroscience 38(7):1821-1834. (*, co-first authors; +, co-corresponding authors)

125 - Piatkevich KD, Suk HJ, Kodandaramaiah SB, Yoshida F, DeGennaro EM, Drobizhev M, Hughes TE, Desimone R, Boyden ES*, Verkhusha VV* (2017) Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging, Biophysical Journal 113(10):2299-2309. (*, co-corresponding authors)

124 - Freifeld L, Odstrcil I, Förster D, Ramirez A, Gagnon JA, Randlett O, Costa EK, Asano S, Celiker OT, Gao R, Martin-Alarcon DA, Reginato P, Dick C, Chen L, Schoppik D, Engert F, Baier H, Boyden ES (2017) Expansion microscopy of zebrafish for neuroscience and developmental biology studies, Proceedings of the National Academy of Sciences 114(50):E10799-E10808.

123 - Richter KN, Revelo NH, Seitz KJ, Helm MS, Sarkar D, Saleeb RS, D'Este E, Eberle J, Wagner E, Vogl C, Lazaro DF, Richter F, Coy-Vergara J, Coceano G, Boyden ES, Duncan RR, Hell SW, Lauterbach MA, Lehnart SE, Moser T, Outeiro T, Rehling P, Schwappach B, Testa I, Zapiec B, Rizzoli SO (2017) Glyoxal as an alternative fixative to formaldehyde in immunostaining and super-resolution microscopy, The EMBO Journal 37(1):139-159.

122 - Or A. Shemesh*, Dimitrii Tanese*, Valeria Zampini*, Changyang Linghu, Kiryl Piatkevich, Emiliano Ronzitti, Eirini Papagiakoumou, Edward S. Boyden+ and Valentina Emiliani+ (2017) Temporally precise single-cell resolution optogenetics, Nature Neuroscience 20:1796–1806. (*, co-first authors; +, co-corresponding authors)

121 - Ronzitti E, Conti R, Zampini V, Tanese D, Foust AJ, Klapoetke N, Boyden ES, Papagiakoumou E, Emiliani V (2017) Sub-millisecond optogenetic control of neuronal firing with two-photon holographic photoactivation of Chronos, Journal of Neuroscience 37(44):10679-10689.

120 - Yoon YG, Dai P, Wohlwend J, Chang JB, Marblestone AH, Boyden ES (2017) Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration, Frontiers in Computational Neuroscience 11:97.

119 - Acker LC, Pino EN, Boyden ES, Desimone R (2017) Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates, Journal of Visualized Experiments 128:e56330.

118 - Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P (2017) Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues, Nano Letters 17(10):6131-6139.

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 14(6):066005. (*, 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 5:177-184.

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.

Conference Papers

13 - An J, Flores FJ, Kodandaramaiah SB, Betta ID, Nikolaeva K, Boyden ES, Forest CR, Brown EN (2018) Automated Assessment of Loss of Consciousness Using Whisker And Paw Movements During Anesthetic Dosing in Head-Fixed Rodents, Conf Proc IEEE Eng Med Biol Soc 730-733.

12 - Shaun Berry, Shawn Redmond, Paul Robinson, Todd Thorsen, Mordechai Rothschild, Edward S. Boyden (2017) Adaptive Fluidic Microoptics for Single Cell Optogenetics, Bio-Optics: Design and Application (BODA): Biochip and optofluidics, OSA Biophotonics Congress: Optics in the Life Sciences, San Diego, CA.

11 - J. Scholvin, C.G. Fonstad, E.S. Boyden (2017) Scaling models for microfabricated in vivo neural recording technologies. 8th International IEEE/EMBS Conference on Neural Engineering (NER), pp. 181-185, May 25, 2017.

10 - Jorg Scholvin, Justin Kinney, Jacob Bernstein, Caroline Moore-Kochlacs, Nancy Kopell, Clifton Fonstad, Edward Boyden (2016) Heterogeneous Neural Amplifier Integration for Scalable Extracellular Microelectrodes, 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 2016:2789-2793.

9 - Uygar Sümbül, Douglas Roossien, Dawen Cai, Fei Chen, Nicholas Barry, John P. Cunningham, Edward Boyden, Liam Paninski (2016) Automated scalable segmentation of neurons from multispectral images, Advances in Neural Information Processing Systems 29 (NIPS 2016).

8 - Ilya Kolb, Gregory L. Holst, Max A. Stockslager, Suhasa B. Kodandaramaiah, William Stoy, Edward S. Boyden, Craig R. Forest (2015) LINEAR MICRO-ACTUATION SYSTEM FOR PATCH-CLAMP RECORDING, Proceedings of the 30th Annual Meeting of the American Society for Precision Engineering.

7 - J. Go, A. Fan, C. Lu, S.B. Kodandaramaiah, G.L. Holst, W. Stoy, I. Kolb, E.S. Boyden, C.R. Forest (2013) Fully-automated, in-vivo, single cell electrophysiology, Proceedings of the 28th Annual Meeting of the American Society for Precision Engineering, Saint Paul, MN, Oct 20-25, 2013.

6 - I. Kolb, G. Holst, B. Goldstein, S.B. Kodandaramaiah, E.S. Boyden, E. Culurciello, C.R. Forest (2013) Automated, in-vivo, whole-cell electrophysiology using an integrated patch-clamp amplifier, Proceedings of the 22nd Annual Computational Neuroscience Meeting (CNS 2013), Paris, France, July 13-18, 2013.

5 - Kodandaramaiah, S., Krijnen, M., Go, J., Malik, S., Sondej, N., Khatait, J. P., Boyden, E. S., Aarts, R. G. K. M., Brouwer, D. M., Forest, C. F. (2011) Characterization of translation of fused silica micropipettes in non-rectilinear trajectories, Proceedings of the 26th Annual Meeting of the American Society for Precision Engineering, Denver, CO.

4 - Doroudchi, M. M., Greenberg, K. P., Zorzos, A. N., Hauswirth, W. W., Fonstad, C. G., Horsager, A., Boyden, E. S. (2011) Towards Optogenetic Sensory Replacement, Conference Proceedings of the IEEE Engineering in Medicine and Biology Society 2011:3139-41.

3 - Boyden, E. S. (2011) Optogenetics. 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC ’11).

2 - Bernstein, J. G., Han, X., Henninger, M. A., Ko, E. Y., Qian, X., Franzesi, G. T., McConnell, J. P., Stern, P., Desimone, R., and Boyden, E. S. (2008) Prosthetic systems for therapeutic optical activation and silencing of genetically-targeted neurons, Proc Soc Photo Opt Instrum Eng 6854:68540H.

1 - Fletcher, R., Omojola, O., Boyden, E. S., Gershenfeld, N. (1999) Reconfigurable Agile Tag Reader Technologies for Combined EAS and RFID capability, Proceedings of the Second IEEE Workshop on Automatic Identification Advanced Technologies, Summit, New Jersey.

Book Chapters

Books

Byline Articles

17 - Boyden, E. S. (2014) Let there be light, Scientific American Mind, November/December 2014.

16 - Boyden, E. S. (2011) The Birth of Optogenetics, The Scientist, July 2011 Issue. (Cover Story.)

15 - Boyden, E. S. (2010) "Molecular Tools for Controlling Brain Circuits with Light," Eppendorf and Science Prize for Neurobiology Competition Essay, Science Magazine.

14 - Boyden, E. S., Allen, B. D., Fritz, D. (2010) "Brain Coprocessors." Column, Technology Review. 9/23/2010.

13 - Boyden, E. S. (2010) Controlling the Brain with Light. SPIE Newsroom. 6/10/2010.

12 - Boyden, E. S. and Chow, B. Y. (2010) "Defining An Algorithm For Inventing From Nature." Column, Technology Review. 1/19/2010.

11 - Boyden, E. S. (2009) “The Singularity and the Fixed Point.” Column, Technology Review. 9/4/2009. (http://www.technologyreview.com/biomedicine/23354/).

10 - Boyden, E. S. (2009) "Civilization as Experiment." Ed Boyden's Blog. Technology Review. 1/19/09. (http://www.technologyreview.com/blog/boyden/22512/).

9 - Boyden, E. S. (2008) "Averting Disasters, Preventing Problems." Ed Boyden's Blog. Technology Review. 9/2/08. (http://www.technologyreview.com/blog/boyden/22122/).

8 - Boyden, E. S. (2008) "Research as a Community-Building Activity." Ed Boyden's Blog. Technology Review. 7/28/08. (http://www.technologyreview.com/blog/boyden/22102/).

7 - Boyden, E. S. (2008) "Inverting the Core." Ed Boyden's Blog. Technology Review. 7/14/08. (http://www.technologyreview.com/blog/boyden/22096/).

6 - Boyden, E. S. (2008) "Training a Generation of Neuroengineers." Ed Boyden's Blog, Technology Review. 4/22/08. (http://www.technologyreview.com/blog/boyden/22055/).

5 - Boyden, E. S. (2007) "How to Think." Ed Boyden's Blog. Technology Review. 11/13/07. (http://www.technologyreview.com/blog/boyden/21925/).

4 - Boyden, E. S. (2007) "Synthetic Neurobiology." Ed Boyden's Blog. Technology Review. 10/9/07. (http://www.technologyreview.com/blog/boyden/21871/).

3 - Boyden, E. S. (2007) "Open Philanthropy." Ed Boyden's Blog. Technology Review. 9/24/07. (http://www.technologyreview.com/blog/boyden/21850/).

2 - Boyden, E. S. (2007) "In Pursuit of Human Augmentation." Ed Boyden's Blog. Technology Review. 9/17/07. (http://www.technologyreview.com/blog/boyden/21839/).

1 - Boyden, E. S. (2007) “Engineering the Brain (‘Notebooks’ column),” Technology Review, March/April 2007 issue, p. 34-35.

Synthetic Neurobiology Memos