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Aaron Szafer
Researcher at Allen Institute for Brain Science
Publications - 31
Citations - 6973
Aaron Szafer is an academic researcher from Allen Institute for Brain Science. The author has contributed to research in topics: Neocortex & Visual cortex. The author has an hindex of 18, co-authored 29 publications receiving 4260 citations. Previous affiliations of Aaron Szafer include Allen Institute for Artificial Intelligence.
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Journal ArticleDOI
Shared and distinct transcriptomic cell types across neocortical areas
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 E. Bakken,Vilas Menon,Vilas Menon,Jeremy A. 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 A. Groblewski,Ian R. Wickersham,Ali Cetin,Julie A. Harris,Boaz P. Levi,Susan M. Sunkin,Linda Madisen,Tanya L. Daigle,Loren L. Looger,Amy Bernard,John W. Phillips,Ed S. Lein,Michael Hawrylycz,Karel Svoboda,Allan R. Jones,Christof Koch,Hongkui Zeng +48 more
TL;DR: This study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex and identifies 133 transcriptomic types of glutamatergic neurons to their long-range projection specificity.
Journal ArticleDOI
Transcriptional landscape of the prenatal human brain
Jeremy A. Miller,Songlin Ding,Susan M. Sunkin,Kimberly A. Smith,Lydia Ng,Aaron Szafer,Amanda Ebbert,Zackery L. Riley,Joshua J. Royall,Kaylynn Aiona,James M. Arnold,Crissa Bennet,Darren Bertagnolli,Krissy Brouner,Stephanie Butler,Shiella Caldejon,Anita Carey,Christine Cuhaciyan,Rachel A. Dalley,Nick Dee,Tim A. Dolbeare,Benjamin A.C. Facer,David Feng,Tim P. Fliss,Garrett Gee,Jeff Goldy,Lindsey Gourley,Benjamin W. Gregor,Guangyu Gu,Robert Howard,Jayson M. Jochim,Chihchau L. Kuan,Christopher Lau,Changkyu Lee,Felix Lee,Tracy Lemon,Phil Lesnar,Bergen McMurray,Naveed Mastan,Nerick Mosqueda,Theresa Naluai-Cecchini,Nhan Kiet Ngo,Julie Nyhus,Aaron Oldre,Eric Olson,Jody Parente,Patrick D. Parker,Sheana Parry,Allison Stevens,Mihovil Pletikos,Melissa Reding,Kate Roll,David Sandman,Melaine Sarreal,Sheila Shapouri,Nadiya V. Shapovalova,Elaine H. Shen,Nathan Sjoquist,Clifford R. Slaughterbeck,Michael W. Smith,Andy J. Sodt,Derric Williams,Lilla Zöllei,Bruce Fischl,Mark Gerstein,Daniel H. Geschwind,Ian A. Glass,Michael Hawrylycz,Robert F. Hevner,Hao Huang,Allan R. Jones,James A. Knowles,Pat Levitt,John W. Phillips,Nenad Sestan,Paul Wohnoutka,Chinh Dang,Amy Bernard,John G. Hohmann,Ed S. Lein +79 more
TL;DR: An anatomically comprehensive atlas of the mid-gestational human brain is described, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions.
Journal ArticleDOI
Conserved cell types with divergent features in human versus mouse cortex.
Rebecca D. Hodge,Trygve E. Bakken,Jeremy A. Miller,Kimberly A. Smith,Eliza Barkan,Lucas T. Graybuck,Jennie L. Close,Brian Long,Nelson Johansen,Osnat Penn,Zizhen Yao,Jeroen Eggermont,Thomas Höllt,Thomas Höllt,Boaz P. Levi,Soraya I. Shehata,Brian D. Aevermann,Allison Beller,Darren Bertagnolli,Krissy Brouner,Tamara Casper,Charles Cobbs,Rachel A. Dalley,Nick Dee,Songlin Ding,Richard G. Ellenbogen,Olivia Fong,Emma Garren,Jeff Goldy,Ryder P. Gwinn,Daniel Hirschstein,C. Dirk Keene,Mohamed Keshk,Andrew L. Ko,Andrew L. Ko,Kanan Lathia,Ahmed Mahfouz,Ahmed Mahfouz,Zoe Maltzer,Medea McGraw,Thuc Nghi Nguyen,Julie Nyhus,Jeffrey G. Ojemann,Jeffrey G. Ojemann,Aaron Oldre,Sheana Parry,Shannon Reynolds,Christine Rimorin,Nadiya V. Shapovalova,Saroja Somasundaram,Aaron Szafer,Elliot R. Thomsen,Michael Tieu,Gerald Quon,Richard H. Scheuermann,Richard H. Scheuermann,Rafael Yuste,Susan M. Sunkin,Boudewijn P. F. Lelieveldt,Boudewijn P. F. Lelieveldt,David Feng,Lydia Ng,Amy Bernard,Michael Hawrylycz,John W. Phillips,Bosiljka Tasic,Hongkui Zeng,Allan R. Jones,Christof Koch,Ed Lein +69 more
TL;DR: RNA-sequencing analysis of cells in the human cortex enabled identification of diverse cell types, revealing well-conserved architecture and homologous cell types as well as extensive differences when compared with datasets covering the analogous region of the mouse brain.
Journal ArticleDOI
The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.
Quanxin Wang,Songlin Ding,Yang Li,Josh Royall,David Feng,Phil Lesnar,Nile Graddis,Maitham Naeemi,Benjamin A.C. Facer,Anh Ho,Tim A. Dolbeare,Brandon Blanchard,Nick Dee,Wayne Wakeman,Karla E. Hirokawa,Aaron Szafer,Susan M. Sunkin,Seung Wook Oh,Amy Bernard,John W. Phillips,Michael Hawrylycz,Christof Koch,Hongkui Zeng,Julie A. Harris,Lydia Ng +24 more
TL;DR: This work constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice and parcellated the entire brain directly in 3D.
Journal ArticleDOI
Canonical Genetic Signatures of the Adult Human Brain
Michael Hawrylycz,Jeremy A. Miller,Vilas Menon,David Feng,Tim A. Dolbeare,Angela L. Guillozet-Bongaarts,Anil G. Jegga,Bruce J. Aronow,Changkyu Lee,Amy Bernard,Matthew F. Glasser,Donna L. Dierker,Jörg Menche,Jörg Menche,Aaron Szafer,Forrest Collman,Pascal Grange,Kenneth A. Berman,Stefan Mihalas,Zizhen Yao,Lance Stewart,Albert-László Barabási,Jay Schulkin,John W. Phillips,Lydia Ng,Chinh Dang,David R. Haynor,Allan R. Jones,David C. Van Essen,Christof Koch,Ed S. Lein +30 more
TL;DR: Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely patterned genes displayed marked shifts in regulation between species.