Scientific Publications

Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

eLife, 2021-9-2

Bakken TE, van Velthoven CT, Menon V, Hodge RD, Yao Z, Nguyen TN, Graybuck LT, Horwitz GD, Bertagnolli D, Goldy J, Yanny AM, Garren E, Parry S, Casper T, Shehata SI, Barkan ER, Szafer A, Levi BP, Dee N, Smith KA, Sunkin SM, Bernard A, Phillips J, Hawrylycz MJ, Koch C, Murphy GJ, Lein E, Zeng H, Tasic B

Recent ultra-rare inherited variants implicate new autism candidate risk genes

Nature Genetics, 2021-8-0

Wilfert AB, Turner TN, Murali SC, Hsieh P, Sulovari A, Wang T, Coe BP, Guo H, Hoekzema K, Bakken TE, Winterkorn LH, Evani US, Byrska-Bishop M, Earl RK, Bernier RA; SPARK Consortium, Zody MC, Eichler EE.

Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

eLife, 2021-8-13

Lee BR, Budzillo A, Hadley K, Miller JA, Jarsky T, Baker K, Hill D, Kim L, Mann R, Ng L, Oldre A, Rajanbabu R, Trinh J, Vargas S, Braun T, Dalley RA, Gouwens NW, Kalmbach BE, Kim TK, Smith KA, Soler-Llavina G, Sorensen S, Tasic B, Ting JT, Lein E, Zeng H, Murphy GJ, Berg J

A Multisubcellular Compartment Model of AMPA Receptor Trafficking for Neuromodulation of Hebbian Synaptic Plasticity

Frontiers in Synaptic Neuroscience, 2021-8-11

Mihalas S, Ardiles A, He K, Palacios A, Kirkwood A.

Perceptual awareness negativity: a physiological correlate of sensory consciousness

Trends in Cognitive Sciences, 2021-8-1

Dembski C, Koch C, Pitts M.

Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

eLife, 2021-7-16

Siegle JH, Ledochowitsch P, Jia X, Millman DJ, Ocker GK, Caldejon S, Casal L, Cho A, Denman DJ, Durand S, Groblewski PA, Heller G, Kato I, Kivikas S, Lecoq J, Nayan C, Ngo K, Nicovich PR, North K, Ramirez TK, Swapp J, Waughman X, Williford A, Olsen SR, Koch C, Buice MA, de Vries SE.

Cell segmentation-free inference of cell types from in situ transcriptomics data

Nature Communications, 2021-6-10

Park J, Choi W, Tiesmeyer S, Long B, Borm LE, Garren E, Nguyen TN, Tasic B, Codeluppi S, Graf T, Schlesner M, Stegle O, Eils R, Ishaque N.

A machine learning method for the discovery of minimum marker gene combinations for cell-type identification from single-cell RNA sequencing

Genome Research, 2021-6-4

Aevermann BD, Zhang Y, Novotny M, Keshk M, Bakken TE, Miller JA, Hodge RD, Lelieveldt B, Lein ES, Scheuermann RH.

Control of impulsivity by G i-protein signalling in layer-5 pyramidal neurons of the anterior cingulate cortex

Communications Biology, 2021-6-2

van der Veen B, Kapanaiah SKT, Kilonzo K, Steele-Perkins P, Jendryka MM, Schulz S, Tasic B, Yao Z, Zeng H, Akam T, Nicholson JR, Liss B, Nissen W, Pekcec A, Kätzel D.

Making the hard problem of consciousness easier

Science, 2021-5-28

Melloni L, Mudrik L, Pitts M, Koch C.

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Cell, 2021-5-17

Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H.

Chromatic micromaps in primary visual cortex

Nature Communications, 2021-4-19

Chatterjee S, Ohki K, Reid RC

Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Cell Reports, 2021-3-30

Mich JK, Graybuck LT, Hess EE, Mahoney JT, Kojima Y, Ding Y, Somasundaram S, Miller JA, Kalmbach BE, Radaelli C, Gore BB, Weed N, Omstead V, Bishaw Y, Shapovalova NV, Martinez RA, Fong O, Yao S, Mortrud M, Chong P, Loftus L, Bertagnolli D, Goldy J, Casper T, Dee N, Opitz-Araya X, Cetin A, Smith KA, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Keene CD, Silbergeld DL, Sunkin SM, Gradinaru V, Horwitz GD, Zeng H, Tasic B, Lein ES, Ting JT, Levi BP

Enhancer viruses for combinatorial cell-subclass-specific labeling

Neuron, 2021-3-23

Graybuck LT, Daigle TL, Sedeño-Cortés AE, Walker M, Kalmbach B, Lenz GH, Morin E, Nguyen TN, Garren E, Bendrick JL, Kim TK, Zhou T, Mortrud M, Yao S, Siverts LA, Larsen R, Gore BB, Szelenyi ER, Trader C, Balaram P, van Velthoven CTJ, Chiang M, Mich JK, Dee N, Goldy J, Cetin AH, Smith K, Way SW, Esposito L, Yao Z, Gradinaru V, Sunkin SM, Lein E, Levi BP, Ting JT, Zeng H, Tasic B.

Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

eLife, 2021-3-8

Huang L, Ledochowitsch P, Knoblich U, Lecoq J, Murphy GJ, Reid RC, de Vries SEJ, Koch C, Zeng H, Buice MA, Waters J, Li L

Consistent cross-modal identification of cortical neurons with coupled autoencoders

Nature Computational Science, 2021-2-22

Gala R, Budzillo A, Baftizadeh F, Miller J, Gouwens N, Arkhipov A, Murphy G, Tasic B, Zeng H, Hawrylycz M, Sumbul U

Patch-seq: Past, Present, and Future.

Journal of Neuroscience, 2021-2-3

Lipovsek M, Bardy C, Cadwell CR, Hadley K, Kobak D, Tripathy SJ.

Highlights from the Era of Open Source Web-Based Tools

Journal of Neuroscience, 2021-2-3

Anderson KR, Harris JA, Ng L, Prins P, Memar S, Ljungquist B, Fürth D, Williams RW, Ascoli GA, Dumitriu D

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

Science, 2021-1-29

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.

The effect of inclusion criteria on the functional properties reported in mouse visual cortex

eNeuro, 2021-1-28

Mesa N, Waters J, de Vries SEJ.

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