Synthetic Neurobiology Group

Ed Boyden, Ph.D., Principal Investigator

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Principal Investigator

  • Ed Boyden

Administration

  • Macey Lavoie

  • Lisa Lieberson

  • Doug Weston

  • Fira Zainal

Students Postdocs and Research Staff

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  • Jenna Aronson

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Visiting Scientists and Affiliates

  • Yosuke (Bandy) Bando

  • Emma Towlson

Alumni - Graduate Students Postdocs and Research Staff

  • Leah Acker

  • Kate Adamala

  • Brian Allen

  • Shahar Alon

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  • Kristina Kitko

  • Nathan Klapoetke

  • Suhasa Kodandaramaiah

  • Mingjie Li

  • Charlotte Luff

  • Adam Marblestone

  • Daniel Martin-Alarcon

  • Azadeh Moini

  • Caroline Moore-Kochlacs

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  • Fumi Yoshida

  • Jay (Chih-Chieh) Yu

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  • Anthony Zorzos

Alumni - Visiting Scientists and Affiliates

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Alumni - Undergraduate Researchers

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Home » People » Alumni - Graduate Students Postdocs and Research Staff » Adam Marblestone

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.

Publications

  • 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)

  • 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)

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

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

  • 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)

  • 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.

  • 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.

  • 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.

  • 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)

  • 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)

  • 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.

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

  • 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)

  • 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)

  • 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)

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