Publications
We believe in open publishing and fast distribution of results. All lab papers will be posted to bioRxiv. PDFs of pre-prints and published papers can be found below.
Research Papers
Clifton K*, Anant M*, Aihara G, Atta L, Aimiuwu OK, Kebschull JM, Miller MI, Tward D, Fan J. STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping. Nat Commun. 2023 Dec 8;14(1):8123. doi: 10.1038/s41467-023-43915-7. PDF
Chen Y, Chen X, Baserdem B, Zhan H, Li Y, Davis MB, Kebschull JM, Zador AM, Koulakov AA, Albeanu DF. High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex. Cell. 2022 Oct 27;185(22):4117-4134.e28. PDF
Li S-B, Damonte VM, Chen C, Wang GX, Kebschull JM, Yamaguchi H, Bian W-J, Purmann C, Pattni R, Urban AE, Mourrain P, Kauer JA, Scherrer G, Lecea L. Hyperexcitable arousal circuits drive sleep instability during aging. Science 375, 838. 2022. PDF
Klingler E, Tomasello U*, Prados J*, Kebschull JM, Contestabile A, Galiñanes GL, Fièvre S, Huber D, Dayer A, Bellone C, Zador AM, Jabaudon D. Temporal controls over interareal cortical projection neuron fate diversity. Nature, 2021; 599, 453-457. PDF
McLaughlin CN, Brbić M, Xie Q, Li T, Horns F, Kolluru SS, Kebschull JM, Vacek D, Xie A, Li J, Jones RC, Leskovec J, Quake SR, Luo L, Li H. Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila. eLife 2021;10:e63856 DOI: 10.7554/eLife.63856. PDF
Kebschull JM, Richman EB, Ringach N, Friedmann D, Albarran E, Kolluru SS, Jones RC, Allen WE, Wang Y, Cho SW, Zhou H, Ding JB, Chang HY, Deisseroth K, Quake SR, Luo L. Cerebellar nuclei evolved by repeatedly duplicating a conserved cell-type set. Science 370, eabd5059 (2020). DOI: 10.1126/science.abd5059 PDF
Lui JH, Nguyen ND, Grutzner SM, Darmanis S, Peixoto D, Wagner MJ, Allen WE, Kebschull JM, Richman EB, Ren J, Newsome WT, Quake SR, Luo L. Differential encoding in prefrontal projection neuron classes across cognitive tasks. Cell, in press. bioRxiv. 2020; 10.1101/2020.03.14.991018. PDF
Huang L*, Kebschull JM*, Furth D, Musall S, Kaufman MT, Churchland AK, Zador AM. BRICseq bridges brain-wide interregional connectivity to neural activity and gene expression in single animals. Cell. 2020; 182(1), 117-188.e7. PDF
Friedmann D, Pun A, Adams EL, Lui JH, Kebschull JM, Grutzner SM, Castagnola C, Tessier-Lavigne M, Luo L. Mapping mesoscale axonal projections in the mouse brain using A 3D convolutional network. PNAS. 2020. PDF
Li H, Li T, Horns F, Li J, Xie Q, Xu C, Wu B, Kebschull JM, McLaughlin CN, Kolluru SS, Jones RC, Vacek D, Xie A, Luginbuhl DJ, Quake SR, Luo L. Single-cell transcriptomes reveal diverse regulatory strategies for olfactory receptor expression and axon targeting. Current Biology. 2020; 30(7), 1189-1198. PDF
Dore K, Pao Y, Soria Lopez J, Aronson S, Zhan H, Ghosh S, Merrill S, Zador AM, Malinow R, Kebschull JM. SYNPLA, A synapse-specific method for identifying learning-induced synaptic plasticity loci. PNAS. 2020; 117(6), 3214-3219. PDF
Chen X, Sun Y, Zhan H, Kebschull JM, Fischer S, Matho K, Huang ZJ, Gillis J, Zador AM. High-throughput mapping of long-range neuronal projection using in situ sequencing. Cell. 2019; 179(3), 772-786. PDF
Han Y*, Kebschull JM*, Campbell RAA*, Cowan D, Imhof F, Zador AM, Mrsic-Flogel TM. The logic of single-cell projections from visual cortex. Nature. 2018; 556(7699), 51-56. PDF
Peikon ID*, Kebschull JM*, Vagin VV*, Ravens DI, Sun Y, Brouzes E, Correa Jr. IR, Bressan D, Zador AM. Using high-throughput barcode sequencing to efficiently map connectomes. Nucleic Acids Research. 2017; gkx292. PDF
Kebschull JM, Garcia da Silva P, Reid AP, Peikon ID, Albeanu DF, Zador AM. High-throughput mapping of single-neuron projections by sequencing of barcoded RNA. Neuron. 2016; 91(5), 975-987. PDF
Kebschull JM, Garcia da Silva P, Zador AM. A new Defective Helper RNA to produce recombinant Sindbis virus that infects neurons but does not propagate. Frontiers in Neuroanatomy. 2016; 10:56. PDF
Kebschull JM, Zador AM. Sources of PCR-induced distortions in high-throughput sequencing data sets. Nucleic Acids Research. 2015; 43(21):e143. PDF
Reviews
Kebschull JM, Casoni F, Consalez GG, Goldowitz D, Hawkes R, Ruigrok TJH, Schilling K, Wingate R, Wu J, Yeung J, Uusisaari MY. Cerebellum Lecture: the Cerebellar Nuclei-Core of the Cerebellum. Cerebellum. 2023 Feb 13. PDF
Faltine-Gonzalez DZ, Kebschull JM. A mosaic of new and old cell types. Science. 2022; 377(6610). PDF
Charles AS, Falk B, Turner N, Pereira TD, Tward D, Pedigo BD, Chung J, Burns R, Ghosh SS, Kebschull JM, Silversmith W, Vogelstein JT. Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics. Annual Review of Neuroscience. 2020; 43. PDF
Kebschull JM. DNA sequencing in high-throughput neuroanatomy. Journal of Chemical Neuroanatomy. 2019; 101653. PDF
Kebschull JM, Zador AM. Cellular barcoding: lineage tracing, screening and beyond. Nature Methods. 2018; 15(11), 871-879. PDF
Marblestone AH, Daugharthy ER, Kalhor R, Peikon ID, Kebschull JM, Shipman SL, Mishchenko Y, Lee J, Kording KP, Boyden ES, Zador AM, Church GM. Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics. arXiv. 2014; 1404.5103. PDF
Marblestone AH, Daugharthy E R, Kalhor R, Peikon ID, Kebschull JM, Shipman SL, Mishchenko Y, Lee J, Dalrymple DA, Zamft BM, Kording KP, Boyden ES, Zador AM, Church GM. Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics. bioRxiv. 2013; 001214. PDF