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publication / 2019
High-resolution data-driven model of the mouse connectome
Network Neuroscience (Cambridge, Mass.)
Brain Science
MindScope

Joseph E. Knox, Kameron Decker Harris, Nile Graddis, Jennifer D. Whitesell, Hongkui Zeng, Julie A. Harris, Eric Shea-Brown, Stefan Mihalas

publication / 2019
Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas
PloS One
Brain Science
MindScope

Natalie Weed, Trygve Bakken, Nile Graddis, Nathan Gouwens, Daniel Millman, Michael Hawrylycz, Jack Waters

publication / 2019
Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity
Nature Genetics
Brain Science
MindScope

Bradley P. Coe, Holly A. F. Stessman, Arvis Sulovari, Madeleine R. Geisheker, Trygve E. Bakken, Allison M. Lake, Joseph D. Dougherty, Ed S. Lein, Fereydoun Hormozdiari, Raphael A. Bernier, Evan E. Eichler

publication / 2019
Two eARCHT3.0 Lines for Optogenetic Silencing of Dopaminergic and Serotonergic Neurons
Frontiers in Neural Circuits
Brain Science
MindScope

Alexandra Krol, Violeta G. Lopez-Huerta, Taylor E. C. Corey, Karl Deisseroth, Jonathan T. Ting, Guoping Feng

publication / 2018
Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Science (New York, N.Y.)
Brain Science
MindScope

Mingfeng Li, Gabriel Santpere, Yuka Imamura Kawasawa, Oleg V. Evgrafov, Forrest O. Gulden, Sirisha Pochareddy, Susan M. Sunkin, Zhen Li, Yurae Shin, Ying Zhu, André M. M. Sousa, Donna M. Werling, Robert R. Kitchen, Hyo Jung Kang, Mihovil Pletikos, Jinmyung Choi, Sydney Muchnik, Xuming Xu, Daifeng Wang, Belen Lorente-Galdos, Shuang Liu, Paola Giusti-Rodríguez, Hyejung Won, Christiaan A. de Leeuw, Antonio F. Pardiñas, BrainSpan Consortium, PsychENCODE Consortium, PsychENCODE Developmental Subgroup, Ming Hu, Fulai Jin, Yun Li, Michael J. Owen, Michael C. O'Donovan, James T. R. Walters, Danielle Posthuma, Mark A. Reimers, Pat Levitt, Daniel R. Weinberger, Thomas M. Hyde, Joel E. Kleinman, Daniel H. Geschwind, Michael J. Hawrylycz, Matthew W. State, Stephan J. Sanders, Patrick F. Sullivan, Mark B. Gerstein, Ed S. Lein, James A. Knowles, Nenad Sestan

preprint / 2018
The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
Cell Science

Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski

publication / 2018
h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex
Neuron
Brain Science
MindScope

Brian E. Kalmbach, Anatoly Buchin, Brian Long, Jennie Close, Anirban Nandi, Jeremy A. Miller, Trygve E. Bakken, Rebecca D. Hodge, Peter Chong, Rebecca de Frates, Kael Dai, Zoe Maltzer, Philip R. Nicovich, C. Dirk Keene, Daniel L. Silbergeld, Ryder P. Gwinn, Charles Cobbs, Andrew L. Ko, Jeffrey G. Ojemann, Christof Koch, Costas A. Anastassiou, Ed S. Lein, Jonathan T. Ting

publication / 2018
A simplified morphological classification scheme for pyramidal cells in six layers of primary somatosensory cortex of juvenile rats
IBRO reports
Brain Science
MindScope

Yun Wang, Min Ye, Xiuli Kuang, Yaoyao Li, Shisi Hu

publication / 2018
Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections
Medical Image Analysis
Brain Science
MindScope

Juan Eugenio Iglesias, Marc Modat, Loïc Peter, Allison Stevens, Roberto Annunziata, Tom Vercauteren, Ed Lein, Bruce Fischl, Sebastien Ourselin, Alzheimer’s Disease Neuroimaging Initiative

publication / 2018
Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions
Journal of Colloid and Interface Science
Brain Science
MindScope

Timothy J. Lee, Colby F. Lewallen, Daniel J. Bumbarger, Peter J. Yunker, R. Clay Reid, Craig R. Forest

publication / 2018
Publisher Correction: Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes
Scientific Reports
Brain Science
MindScope

Ali Shahbazi, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian Joesch, Marc Takeno, Hongkui Zeng, Nuno Maçarico da Costa, Jaime Grutzendler, Narayanan Kasthuri, Walter J. Scheirer

publication / 2018
Paul G. Allen (1953–2018)
Science
Cell Science

Rick Horwitz, Allan Jones, Tom Daniel

publication / 2018
Distinct descending motor cortex pathways and their roles in movement
Nature
Brain Science
MindScope

Michael N. Economo, Sarada Viswanathan, Bosiljka Tasic, Erhan Bas, Johan Winnubst, Vilas Menon, Lucas T. Graybuck, Thuc Nghi Nguyen, Kimberly A. Smith, Zizhen Yao, Lihua Wang, Charles R. Gerfen, Jayaram Chandrashekar, Hongkui Zeng, Loren L. Looger, Karel Svoboda

publication / 2018
Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy
Nature Methods
Cell Science

Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman, Gregory R. Johnson

publication / 2018
Shared and distinct transcriptomic cell types across neocortical areas
Nature
Brain Science
MindScope

Bosiljka Tasic, Zizhen Yao, Lucas T. Graybuck, Kimberly A. Smith, Thuc Nghi Nguyen, Darren Bertagnolli, Jeff Goldy, Emma Garren, Michael N. Economo, Sarada Viswanathan, Osnat Penn, Trygve Bakken, Vilas Menon, Jeremy Miller, Olivia Fong, Karla E. Hirokawa, Kanan Lathia, Christine Rimorin, Michael Tieu, Rachael Larsen, Tamara Casper, Eliza Barkan, Matthew Kroll, Sheana Parry, Nadiya V. Shapovalova, Daniel Hirschstein, Julie Pendergraft, Heather A. Sullivan, Tae Kyung Kim, Aaron Szafer, Nick Dee, Peter Groblewski, Ian Wickersham, Ali Cetin, Julie A. Harris, Boaz P. Levi, Susan M. Sunkin, Linda Madisen, Tanya L. Daigle, Loren Looger, Amy Bernard, John Phillips, Ed Lein, Michael Hawrylycz, Karel Svoboda, Allan R. Jones, Christof Koch, Hongkui Zeng

publication / 2018
Visual physiology of the layer 4 cortical circuit in silico
PLoS computational biology
Brain Science
MindScope

Anton Arkhipov, Nathan W. Gouwens, Yazan N. Billeh, Sergey Gratiy, Ramakrishnan Iyer, Ziqiang Wei, Zihao Xu, Reza Abbasi-Asl, Jim Berg, Michael Buice, Nicholas Cain, Nuno da Costa, Saskia de Vries, Daniel Denman, Severine Durand, David Feng, Tim Jarsky, Jérôme Lecoq, Brian Lee, Lu Li, Stefan Mihalas, Gabriel K. Ocker, Shawn R. Olsen, R. Clay Reid, Gilberto Soler-Llavina, Staci A. Sorensen, Quanxin Wang, Jack Waters, Massimo Scanziani, Christof Koch

publication / 2018
A rapid readout for many single plasmonic nanoparticles using dark-field microscopy and digital color analysis
Biosensors & Bioelectronics
Brain Science
MindScope

Manish Sriram, Bijan P. Markhali, Philip R. Nicovich, Danielle T. Bennett, Peter J. Reece, D. Brynn Hibbert, Richard D. Tilley, Katharina Gaus, S. R. C. Vivekchand, J. Justin Gooding

publication / 2018
Distinctive Structural and Molecular Features of Myelinated Inhibitory Axons in Human Neocortex
eNeuro
Brain Science
MindScope

Kristina D. Micheva, Edward F. Chang, Alissa L. Nana, William W. Seeley, Jonathan T. Ting, Charles Cobbs, Ed Lein, Stephen J. Smith, Richard J. Weinberg, Daniel V. Madison

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