Scientific Publications

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

Cell, 2020-5-14

Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L

A collection of genetic mouse lines and related tools for inducible and reversible intersectional misexpression

Development, 2020-5-4

Ahmadzadeh E, Bayin NS, Qu X, Singh A, Madisen L, Stephen D, Zeng H, Joyner AL, Rosello-Diez A

Contextual Integration in Cortical and Convolutional Neural Networks

Frontiers in Computational Neuroscience, 2020-4-23

Iyer R, Hu B, Mihalas S

RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations

Nature Methods, 2020-3-23

Yao S, Yuan P, Ouellette B, Zhou T, Mortrud M, Balaram P, Chatterjee S, Wang Y, Daigle TL, Tasic B, Kuang X, Gong H, Luo Q, Zeng S, Curtright A, Dhaka A, Kahan A, Gradinaru V, Chrapkiewicz R, Schnitzer M, Zeng H, Cetin A

Recurrent architecture for adaptive regulation of learning in the insect brain

Nature Neuroscience, 2020-3-23

Eschbach C, Fushiki A, Winding M, Schneider-Mizell CM, Shao M, Arruda R, Eichler K, Valdes-Aleman J, Ohyama T, Thum AS, Gerber B, Fetter RD, Truman JW, Litwin-Kumar A, Cardona A, Zlatic M

Whole-Neuron Synaptic Mapping Reveals Spatially Precise Excitatory/Inhibitory Balance Limiting Dendritic and Somatic Spiking

Neuron, 2020-3-12

Iascone DM, Li Y, Sümbül U, Doron M, Chen H, Andreu V, Goudy F, Blockus H, Abbott LF, Segev I, Peng H, Polleux F

Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex

Neuron, 2020-3-5

Billeh YN, Cai B, Gratiy SL, Dai K, Iyer R, Gouwens NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A

Experience shapes activity dynamics and stimulus coding of VIP inhibitory and excitatory cells

eLife, 2020-2-26

Garrett M, Manavi S, Roll K, Ollerenshaw D, Groblewski P, Kiggins J, Jia X, Casal L, Mace K, Williford A, Leon A, Mihalas S, Olsen SR

The SONATA data format for efficient description of large-scale network models

PLoS Computational Biology, 2020-2-24

Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, Courcol JD, Arkhipov A

Capillary- and Stokes-based trapping of serial sections for scalable 3D-EM connectomics

eNeuro, 2020-2-24

Lee TJ, Yip MC, Kumar A, Lewallen CF, Bumbarger DJ, Reid RC, Forest CR

International Brain Initiative: An Innovative Framework for Coordinated Global Brain Research Efforts

Neuron, 2020-1-22

Adams A, Albin S, Amunts K, Asakawa T, Bernard A, Bjaalie JG, Chakli K, Deshler JO, De Koninck Y, Ebell CJ, Egan G, Hale ME, Häusser M, Jeong SJ, Illes J, Lanyon L, Li P, Li Y, Magistretti P, McMahon A, Montojo C, Ohtsuka T, Okabe S, Okano H, Pei G, Pouget A, Reindorp J, Richards LJ, Rommelfanger KS, Sajda P, Scobie KN, Suh PG, Tanaka K, Thiels E, Valdes-Sosa PA, Welchman AE, White S, Wilson G, Yuste R, Zhang X, Zheng J

Superficial Bound of the Depth Limit of Two-Photon Imaging in Mouse Brain

eNeuro, 2020-1-6

Takasaki K, Abbasi-Asl R, Waters J

Single Molecule Localization Microscopy for Quantitative Biology

Journal of Biomolecular Techniques, 2019-12-30

Nicovich, PR

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

Nature Neuroscience, 2019-12-16

de Vries S, Lecoq J, Buice MA, Groblewski PA, Ocker GK, Oliver M, Feng F, Cain N, Ledochowitsch P, Millman D, Roll K, Garrett M, Keenan T, Kuan L, Mihalas S, Olsen S, Thompson C, Wakeman W, Waters J, Williams D, Barber C, Berbesque N, Blanchard B, Bowles N, Caldejon S, Casal L, Cho A, Cross S, Dang C, Dolbeare T, Edwards M, Galbraith J, Gaudreault N, Griffin F, Hargrave P, Howard R, Huang L, Jewell S, Keller N, Knoblich U, Larkin J, Larsen R, Lau C, Lee E, Lee F, Leon A, Li L, Long F, Luviano J, Mace K, Nguyen T, Perkins J, Robertson M, Seid S, Shea-Brown E, Shi J, Sjoquist N, Slaughterbeck C, Sullivan D, Valenza R, White C, Williford A, Witten D, Zhuang J, Zeng H, Farrell C, Ng L, Bernard A, Phillips JW, R Reid C, Koch C

Individual structural features constrain the mouse functional connectome

Proceedings of the National Academy of Sciences, 2019-12-11

Melozzi F, Bergmann E, Harris JA, Kahn I, Jirsa V, Bernard C

Sex-Based Analysis of De Novo Variants in Neurodevelopmental Disorders

American Journal of Human Genetics, 2019-11-25

Turner TN, Wilfert AB, Bakken TE, Bernier RA, Pepper MR, Zhang Z, Torene RI, Retterer K, Eichler EE

Separation of hemodynamic signals from GCaMP fluorescence measured with widefield imaging

Journal of Neurophysiology, 2019-11-20

Valley MT, Moore MG, Zhuang J, Mesa N, Castelli D, Sullivan D, Reimers M, Waters J

Genetic Identification of Vagal Sensory Neurons That Control Feeding

Cell, 2019-11-14

Bai L, Mesgarzadeh S, Ramesh KS, Huey EL, Liu Y, Gray LA, Aitken TJ, Chen Y, Beutler LR, Ahn JS, Madisen L, Zeng H, Krasnow MA, Knight ZA

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks.

eLife, 2019-11-11

Smith SJ, Sümbül U, Graybuck LT, Collman F, Seshamani S, Gala R, Gliko O, Elabbady L, Miller JA, Bakken TE, Rossier J, Yao Z, Lein E, Zeng H, Tasic B, Hawrylycz M

Characterization of hippocampal subfields using ex vivo MRI and histology data: Lessons for in vivo segmentation

Hippocampus, 2019-11-1

de Flores R, Berron D, Ding SL, Ittyerah R, Pluta JB, Xie L, Adler DH, Robinson JL, Schuck T, Trojanowski JQ, Grossman M, Liu W, Pickup S, Das SR, Wolk DA, Yushkevich PA, Wisse LEM

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