Adam Marblestone

In his PhD as a Hertz Fellow in Biophysics at Harvard, with George Church and colleagues, Adam co-authored experimental and theoretical papers on molecular recording devices and road-mapped approaches for whole-brain mapping. He also participated in the development of new epigenomic readout technologies, genome engineering methods, nano-fabrication methods and nano-manipulation systems. More recently, he co-authored papers analyzing our understanding of cortical computation, seeking strategies to integrate deep learning and neuroscience, and proposing new designs for neural interfaces. In his work with Ed Boyden at MIT, he helped to initiate the field of optical connectomics using the combination of expansion microscopy, in-situ sequencing, and machine learning. At MIT, he was an investigator on an IARPA-funded project to map the neural connectome through in-situ sequencing of RNA barcodes. Prior to his work in brain science, Adam studied quantum nonlocality, showing how quantum entanglement can exponentially enhance certain forms of distributed computation, and assisted in the early development of caDNAno, a graphical software tool for design of 3D DNA origami nanostructures, now the standard for the field of structural DNA nanotechnology. He is also a co-founder of BioBright, a company aiming to create a "smart lab" to improve biological experimentation, and a scientific advisor to the Open Philanthropy Project and to OccamzRazor. Dr. Marblestone has also co-taught courses at the MIT Media Lab on Revolutionary Ventures: How to Invent and Deploy Transformative Technologies, and Cognitive Integration.


Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues

bioRxiv | 2024

Tay Won Shin, Hao Wang*, Chi Zhang*, Bobae An, Yangning Lu, Elizabeth Zhang, Xiaotang Lu, Emmanouil D Karagiannis, Jeong Seuk Kang, Amauche Emenari, Panagiotis Symvoulidis, Shoh Asano, Leanne Lin, Emma K Costa; IMAXT Grand Challenge Consortium; Adam H Marblestone, Narayanan Kasthuri, Li-Huei Tsai, Edward S Boyden (2024) Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues, bioRxiv 2024.03.07.583776; doi: (*, equal contribution)

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

Science | 2021

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)

Expansion Microscopy of Lipid Membranes

bioRxiv | 2019

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)

Nanoscale imaging of RNA with expansion microscopy

Nature Methods | 2016

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)

Spatial information in large-scale neural recordings

Frontiers in Computational Neuroscience | 2015

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.

Physical principles for scalable neural recording

Frontiers in Computational Neuroscience | 2013

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)

Statistical analysis of molecular signal recording

PLoS Computational Biology | 2013

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)