Scientific Publications

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.

Alternating sources of perisomatic inhibition during behavior

Neuron, 2021-1-27

Dudok B, Klein PM, Hwaun E, Lee BR, Yao Z, Fong O, Bowler JC, Terada S, Sparks FT, Szabo GG, Farrell JS, Berg J, Daigle TL, Tasic B, Dimidschstein J, Fishell G, Losonczy A, Zeng H, Soltesz I.

Survey of spiking in the mouse visual system reveals functional hierarchy

Nature, 2021-1-20

Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H, Luviano JA, Groblewski PA, Ahmed R, Arkhipov A, Bernard A, Billeh YN, Brown D, Buice MA, Cain N, Caldejon S, Casal L, Cho A, Chvilicek M, Cox TC, Dai K, Denman DJ, de Vries S., Dietzman R, Esposito L, Farrell C, Feng D, Galbraith J, Garrett M, Gelfand EC, Hancock N, Harris JA, Howard R, Hu B, Hytnen R, Iyer R, Jessett E, Johnson K, Kato I, Kiggins J, Lambert S, Lecoq J, Ledochowitsch P, Lee JH, Leon A, Li Y, Liang E, Long F, Mace K, Melchior J, Millman D, Mollenkopf T, Nayan C, Ng L, Ngo D, Nguyen T, Nicovich PR, North K, Ocker GK, Ollerenshaw D, Oliver M, Pachitariu M, Perkins J, Reding M, Reid D, Robertson M, Ronellenfitch K, Seid S, Slaughterbeck C, Stoecklin M, Sullivan D, Sutton B, Swapp J, Thompson C, Turner K, Wakeman W, Whitesell JD, Williams D, Williford A, Young R, Zeng H, Naylor S, Phillips JW, Reid RC, Mihalas S, Olsen SR, Koch C

Spatially resolved transcriptomics in neuroscience

Nature Methods, 2021-1-18

Close JL, Long BR, Zeng H.

Computational Models of Interoception and Body Regulation

Trends in Neurosciences, 2021-1-1

Petzschner FH, Garfinkel SN, Paulus MP, Koch C, Khalsa SS.

Common cell type nomenclature for the mammalian brain

eLife, 2020-12-29

Miller JA, Gouwens NW, Tasic B, Collman F, van Velthoven CT, Bakken TE, Hawrylycz MJ, Zeng H, Lein ES, Bernard A.

Network structure of the mouse brain connectome with voxel resolution

Science Advances, 2020-12-18

Coletta L, Pagani M, Whitesell JD, Harris JA, Bernhardt B, Gozzi A.

Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

Neuron, 2020-12-7

Whitesell JD, Liska A, Coletta L, Hirokawa KE, Bohn P, Williford A, Groblewski PA, Graddis N, Kuan L, Knox JE, Ho A, Wakeman W, Nicovich PR, Nguyen TN, van Velthoven CTJ, Garren E, Fong O, Naeemi M, Henry AM, Dee N, Smith KA, Levi B, Feng D, Ng L, Tasic B, Zeng H, Mihalas S, Gozzi A, Harris JA.

Brain Modeling ToolKit: an Open Source Software Suite for Multiscale Modeling of Brain Circuits

PLoS Computational Biology, 2020-11-30

Dai K, Gratiy SL, Billeh YN, Xu R, Cai B, Cain N, Rimehaug AE, Stasik AJ, Einevoll GT, Mihalas S, Koch C, Arkhipov A

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test

Briefings in Bioinformatics, 2020-11-30

Zhang Y, Aevermann BD, Bakken TE, Miller JA, Hodge RD, Lein ES, Scheuermann RH.

Afferent Projections to Area Prostriata of the Mouse

Frontiers in Neuroanatomy, 2020-11-27

Hu JM, Chen CH, Chen SQ, Ding SL.

Homotopic Commissural Projections of Area Prostriata in Rat and Mouse: Comparison With Presubiculum and Parasubiculum

Frontiers in Neural Circuits, 2020-11-13

Chen CH, Hu JM, Chen SQ, Liu SM, Ding SL.

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells

Cell, 2020-11-12

Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H

Phenotypic variation of transcriptomic cell types in mouse motor cortex

Nature, 2020-11-12

Scala F, Kobak D, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Hartmanis L, Jiang X, Laturnus S, Miranda E, Mulherkar S, Tan ZH, Yao Z, Zeng H, Sandberg R, Berens P, Tolias AS

Linking axon morphology to gene expression: a strategy for neuronal cell-type classification

Current Opinion in Neurobiology, 2020-11-9

Winnubst J, Spruston N, Harris JA

Sources of widefield fluorescence from the brain

eLife, 2020-11-6

Waters J

CamKIIα Positive Interneurons Identified via A microRNA Based Viral Gene Targeting Strategy

Journal of Neuroscience, 2020-11-5

Keaveney MK, Rahsepar B, Tseng HA, Fernandez FR, Mount RA, Ta T, White JA, Berg J, Han X

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

Nucleic Acids Research, 2020-11-4

Gyllborg D, Langseth CM, Qian X, Choi E, Salas SM, Hilscher MM, Lein ES, Nilsson M.

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