bioRxiv Channel: BICCN/BICAN
https://biorxiv.org
This feed contains articles for bioRxiv Channel "BICCN/BICAN"
bioRxivbioRxiv
https://biorxiv.org
<![CDATA[
Transcriptomic diversity of cell types across the adult human brain
]]>
https://biorxiv.org/cgi/content/short/2022.10.12.511898v1?rss=1"
Siletti, K.Hodge, R. D.Mossi Albiach, A.Hu, L.Lee, K. W.Lönnerberg, P.Bakken, T. E.Ding, S.-L.Clark, M.Casper, T.Dee, N.Gloe, J.Keene, C. D.Nyhus, J.Tung, H.Yanny, A. M.Arenas, E.Lein, E. S.Linnarsson, S.2022-10-14doi:10.1101/2022.10.12.511898Cold Spring Harbor Laboratory Press2022-10-14
<![CDATA[
Comparative transcriptomics reveals human-specific cortical features
]]>
https://biorxiv.org/cgi/content/short/2022.09.19.508480v1?rss=1"
Jorstad, N. L.Song, J. H. T.Exposito-Alonso, D.Suresh, H.Castro, N.Krienen, F. M.Yanny, A. M.Close, J.Gelfand, E.Travaglini, K. J.Basu, S.Beaudin, M.Bertagnolli, D.Crow, M.Ding, S.-L.Eggermont, J.Glandon, A.Goldy, J.Kroes, T.Long, B.McMillen, D.Pham, T.Rimorin, C.Siletti, K.Somasundaram, S.Tieu, M.Torkelson, A.Ward, K.Feng, G.Hopkins, W. D.Hollt, T.Keene, C. D.Linnarsson, S.McCarroll, S. A.Lelieveldt, B. P.Sherwood, C. C.Smith, K.Walsh, C. A.Dobin, A.Gillis, J.Lein, E. S.Hodge, R. D.Bakken, T. E.2022-09-19doi:10.1101/2022.09.19.508480Cold Spring Harbor Laboratory Press2022-09-19
<![CDATA[
A marmoset brain cell census reveals persistent influence of developmental origin on neurons
]]>
https://biorxiv.org/cgi/content/short/2022.10.18.512442v1?rss=1"
Krienen, F. M.Levandowski, K. M.Zaniewski, H.del Rosario, R. C.Schroeder, M. E.Goldman, M.Lutservitz, A.Zhang, Q.Li, K. X.Beja-Glasser, V. F.Sharma, J.Shin, T. W.Mauermann, A.Wysoker, A.Nemesh, J.Kashin, S.Vergara, J.Chelini, G.Dimidschstein, J.Berretta, S.Boyden, E.McCarroll, S. A.Feng, G.2022-10-19doi:10.1101/2022.10.18.512442Cold Spring Harbor Laboratory Press2022-10-19
<![CDATA[
A comparative atlas of single-cell chromatin accessibility in the human brain
]]>
https://biorxiv.org/cgi/content/short/2022.11.09.515833v1?rss=1"
Li, Y. E.Preissl, S.Miller, M.Johnson, N. D.Wang, Z.Jiao, H.Zhu, C.Wang, Z.Xie, Y.Poirin, O.Kern, C.Pinto-Duarte, A.Tian, W.Siletti, K.Emerson, N.Osteen, J.Lucero, J.Lin, L.Yang, Q.Espinoza, S.Zhu, Q.Zemke, N.Yanny, A. M.Nyhus, J.Dee, N.Casper, T.Shapovalova, N.Hirschstein, D.Hodge, R. D.Linnarsson, S.Bakken, T. E.Levi, B.Keene, C. D.Shang, J.Lein, E. S.Wang, A.Behrens, M. M.Ecker, J. R.Ren, B.2022-11-10doi:10.1101/2022.11.09.515833Cold Spring Harbor Laboratory Press2022-11-10
<![CDATA[
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
]]>
https://biorxiv.org/cgi/content/short/2022.11.06.515349v1?rss=1"
Jorstad, N. L.Close, J.Johansen, N.Yanny, A. M.Barkan, E. R.Travaglini, K. J.Bertagnolli, D.Campos, J.Casper, T.Crichton, K.Dee, N.Ding, S.-L.Gelfand, E.Goldy, J.Hirschstein, D.Kroll, M.Kunst, M.Lathia, K.Long, B.Martin, N.McMillen, D.Pham, T.Rimorin, C.Ruiz, A.Shapovalova, N.Shehata, S.Siletti, K.Somasundaram, S.Sulc, J.Tieu, M.Torkelson, A.Tung, H.Ward, K.Callaway, E. M.Hof, P. R.Keene, C. D.Levi, B. P.Linnarsson, S.Mitra, P. P.Smith, K.Hodge, R. D.Bakken, T. E.Lein, E. S.2022-11-06doi:10.1101/2022.11.06.515349Cold Spring Harbor Laboratory Press2022-11-06
<![CDATA[
Inter-individual variation in human cortical cell type abundance and expression
]]>
https://biorxiv.org/cgi/content/short/2022.10.07.511366v1?rss=1"
Johansen, N.Somasundaram, S.Travaglini, K. J.Yanny, A. M.Shumyatcher, M.Casper, T.Cobbs, C.Dee, N.Ellenbogen, R.Ferreira, M.Goldy, J.Guzman, J.Gwinn, R.Hirschstein, D.Jorstad, N. L.Keene, C. D.Ko, A.Levi, B. P.Ojemann, J. G.Pham, T.Shapovalova, N.Silbergeld, D.Sulc, J.Torkelson, A.Tung, H.Smith, K.Lein, E. S.Bakken, T. E.Hodge, R. D.Miller, J. A.2022-10-07doi:10.1101/2022.10.07.511366Cold Spring Harbor Laboratory Press2022-10-07
<![CDATA[
Single-cell analysis of prenatal and postnatal human cortical development
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513555v1?rss=1"
Velmeshev, D.Perez, Y.Yan, Z.Valencia, J. E.Castaneda-Castellanos, D. R.Schirmer, L.Mayer, S.Wick, B.Wang, S.Nowakowski, T. J.Paredes, M.Huang, E. J. J.Kriegstein, A.2022-10-25doi:10.1101/2022.10.24.513555Cold Spring Harbor Laboratory Press2022-10-25
<![CDATA[
Comprehensive cell atlas of the first-trimester developing human brain
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.513487v1?rss=1"
Braun, E.Danan-Gotthold, M.Borm, L. E.Vinsland, E.Lee, K. W.Lönnerberg, P.Hu, L.Li, X.He, X.Andrusivova, Z.Lundeberg, J.Arenas, E.Barker, R. A.Sundström, E.Linnarsson, S.2022-10-25doi:10.1101/2022.10.24.513487Cold Spring Harbor Laboratory Press2022-10-25
<![CDATA[
Spatiotemporal molecular dynamics of the developing human thalamus
]]>
https://biorxiv.org/cgi/content/short/2023.08.21.554174v1?rss=1"
Kim, C.Shin, D.Wang, A.Nowakowski, T.2023-08-22doi:10.1101/2023.08.21.554174Cold Spring Harbor Laboratory Press2023-08-22
<![CDATA[
Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon
]]>
https://biorxiv.org/cgi/content/short/2022.10.18.512724v1?rss=1"
Micali, N.Ma, S.Li, M.Kim, S.-K.Mato-Blanco, X.Sindhu, S.Arellano, J. I.Gao, T.Duque, A.Santpere, G.Sestan, N.Rakic, P.2022-10-18doi:10.1101/2022.10.18.512724Cold Spring Harbor Laboratory Press2022-10-18
<![CDATA[
Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
]]>
https://biorxiv.org/cgi/content/short/2022.10.24.511199v1?rss=1"
Chartrand, T.Dalley, R.Close, J.Goriounova, N. A.Lee, B. R.Mann, R.Miller, J. A.Molnar, G.Mukora, A.Alfiler, L.Baker, K.Bakken, T. E.Berg, J.Bertagnolli, D.Braun, T.Brouner, K.Casper, T.Csajbok, E. A.Dee, N.Egdorf, T.Enstrom, R.Galakhova, A. A.Gary, A.Gelfand, E.Goldy, J.Hadley, K.Heistek, T. S.Hill, D.Jorstad, N.Kim, L.Kocsis, A. K.Kruse, L.Leon, G.Long, B.Mallory, M.McGraw, M.McMillen, D.Melief, E. J.Mihut, N.Ng, L.Nyhus, J.Omstead, V.Peterfi, Z.Pom, A.Potekhina, L.Rajanbabu, R.Rozsa, M.Ruiz, A.Sa2022-10-25doi:10.1101/2022.10.24.511199Cold Spring Harbor Laboratory Press2022-10-25
<![CDATA[
Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex
]]>
https://biorxiv.org/cgi/content/short/2022.11.08.515739v1?rss=1"
Lee, B.Dalley, R.Miller, J. A.Chartrand, T.Close, J.Mann, R.Mukora, A.Ng, L.Alfiler, L.Baker, K.Bertagnolli, D.Brouner, K.Casper, T.Csajbok, E.Dee, N.Donadio, N.Driessens, S. L. W.Egdorf, T.Enstrom, R.Galakhova, A. A.Gary, A.Gelfand, E.Goldy, J.Hadley, K.Heistek, T. S.Hill, D.Johansen, N.Jorstad, N.Kim, L.Kocsis, A. K.Kruse, L.Kunst, M.Leon, G.Long, B.Mallory, M.Maxwell, M.McGraw, M.McMillen, D.Melief, E. J.Molnar, G.Mortrud, M. T.Newman, D.Nyhus, J.Opitz-Araya, X.Pham, T.Pom, A.Potekhina, L.Rajanbabu2022-11-09doi:10.1101/2022.11.08.515739Cold Spring Harbor Laboratory Press2022-11-09
<![CDATA[
Integrated platform for multi-scale molecular imaging andphenotyping of the human brain
]]>
https://biorxiv.org/cgi/content/short/2022.03.13.484171v1?rss=1"
Park, J.Wang, J.Guan, W.Kamentsky, L.Evans, N. B.Gjesteby, L.Pollack, D.Choi, S. W.Snyder, M.Chavez, D.Tian, Y.Su-Arcaro, C.Yun, D. H.Zhao, C.Brattain, L.Frosh, M. P.Chung, K.2022-03-15doi:10.1101/2022.03.13.484171Cold Spring Harbor Laboratory Press2022-03-15
<![CDATA[
A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortex
]]>
https://biorxiv.org/cgi/content/short/2021.10.20.464979v1?rss=1"
Costantini, I.Morgan, L.Yang, J.Balbastre, Y.Varadarajan, D.Pesce, L.Scardigli, M.Mazzamuto, G.Gavryusev, V.Castelli, F. M.Roffilli, M.Silvestri, L.Laffey, J.Raia, S.Varghese, M.Wicinski, B.Chang, S.Chen I-Chun, A.Wang, H.Cordero, D.Vera, M.Nolan, J.Nestor, K.Mora, J.Iglesias, J. E.Pallares, E. G.Evancic, K.Augustinack, J.Fogarty, M.Dalca, A. V.Frosch, M.Magnain, C.Frost, R.van der Kouwe, A.Chen, S.-C.Boas, D. A.Pavone, F. S.Fischl, B.Hof, P. R.2021-10-21doi:10.1101/2021.10.20.464979Cold Spring Harbor Laboratory Press2021-10-21
<![CDATA[
A single-cell multi-omic atlas spanning the adult rhesus macaque brain
]]>
https://biorxiv.org/cgi/content/short/2022.09.30.510346v1?rss=1"
Chiou, K. L.Huang, X.Bohlen, M. O.Tremblay, S.O'Day, D. R.Spurrell, C. H.Gogate, A. A.Zintel, T. M.Cayo Biobank Research Unit,Andrews, M. G.Martinez, M. I.Starita, L. M.Montague, M. J.Platt, M. L.Shendure, J.Snyder-Mackler, N.2022-10-03doi:10.1101/2022.09.30.510346Cold Spring Harbor Laboratory Press2022-10-03
<![CDATA[
Multi-omic profiling of the developing human cerebral cortex at the single cell level
]]>
https://biorxiv.org/cgi/content/short/2022.10.14.512250v1?rss=1"
Zhu, K.Bendl, J.Rahman, S.Vicari, J. M.Coleman, C.Clarence, T.Latouche, O.Tsankova, N. M.Li, A.Brennand, K. J.Lee, D.Yuan, G.Fullard, J. F.Roussos, P.2022-10-17doi:10.1101/2022.10.14.512250Cold Spring Harbor Laboratory Press2022-10-17
<![CDATA[
Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the prenatal human hypothalamus
]]>
https://biorxiv.org/cgi/content/short/2021.07.20.453090v1?rss=1"
Herb, B.Glover, H. J.Bhaduri, A.Casella, A. M.Bale, T. L.Kriegstein, A.Doege, C.Ament, S. A.2021-07-20doi:10.1101/2021.07.20.453090Cold Spring Harbor Laboratory Press2021-07-20
<![CDATA[
Temporal disparity of action potentials triggered in axon initial segments and distal axons in the neocortex
]]>
https://biorxiv.org/cgi/content/short/2022.08.09.503303v1?rss=1"
Rozsa, M.Toth, M.Olah, G.Baka, J.Lakovics, R.Barzo, P.Tamas, G.2022-08-10doi:10.1101/2022.08.09.503303Cold Spring Harbor Laboratory Press2022-08-10
<![CDATA[
Human voltage-gated Na+ and K+ channel properties underlie sustained fast AP signaling
]]>
https://biorxiv.org/cgi/content/short/2022.11.29.518317v1?rss=1"
Wilbers, R.Metodieva, V. D.Duverdin, S.Heyer, D. B.Galakhova, A. A.Mertens, E. J.Versluis, T. D.Baayen, J. C.Idema, S.Noske, D. P.Verburg, N.Willemse, R. B.de Witt Hamer, P. C.Kole, M. H. P.de Kock, C. P. J.Mansvelder, H. D.Goriounova, N. A.2022-12-02doi:10.1101/2022.11.29.518317Cold Spring Harbor Laboratory Press2022-12-02
<![CDATA[
Whole Human-Brain Mapping of Single Cortical Neurons for Profiling Morphological Diversity and Stereotypy
]]>
https://biorxiv.org/cgi/content/short/2022.10.29.514375v1?rss=1"
Han, X.Guo, S.Ji, N.Li, T.Liu, J.Ye, X.Wang, Y.Yun, Z.Xiong, F.Rong, J.Liu, D.Ma, H.Wang, Y.Huang, Y.Zhang, P.Wu, W.Ding, L.Hawrylycz, M.Lein, E.Ascoli, G. A.Xie, W.Liu, L.Zhang, L.Peng, H.2022-10-30doi:10.1101/2022.10.29.514375Cold Spring Harbor Laboratory Press2022-10-30
<![CDATA[
Structural and functional specializations of human fast spiking neurons support fast cortical signaling
]]>
https://biorxiv.org/cgi/content/short/2022.11.29.518193v1?rss=1"
Wilbers, R.Galakhova, A. A.Heistek, T. S.Metodieva, V. D.Hagemann, J.Heyer, D. B.Mertens, E. J.Deng, S.Idema, S.de Witt Hamer, P. C.Noske, D. P.van Schie, P.Kommers, I.Luan, G.Li, T.Shu, Y.de Kock, C. P. J.Mansvelder, H. D.Goriounova, N. A.2022-11-29doi:10.1101/2022.11.29.518193Cold Spring Harbor Laboratory Press2022-11-29
<![CDATA[
Early-childhood inflammation blunts the transcriptional maturation of cerebellar neurons
]]>
https://biorxiv.org/cgi/content/short/2022.07.26.501598v1?rss=1"
Ament, S. A.Cortes-Gutierrez, M.Herb, B. R.Mocci, E.Colantuoni, C.McCarthy, M. M.2022-07-26doi:10.1101/2022.07.26.501598Cold Spring Harbor Laboratory Press2022-07-26
<![CDATA[
Conserved coexpression at single cell resolution across primate brains
]]>
https://biorxiv.org/cgi/content/short/2022.09.20.508736v1?rss=1"
Suresh, H.Crow, M.Jorstad, N.Hodge, R.Lein, E.Dobin, A.Bakken, T.Gillis, J.2022-09-22doi:10.1101/2022.09.20.508736Cold Spring Harbor Laboratory Press2022-09-22
<![CDATA[
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
]]>
https://biorxiv.org/cgi/content/short/2023.03.06.531121v1?rss=1"
Yao, Z.van Velthoven, C. T. J.Kunst, M.Zhang, M.McMillen, D.Lee, C.Jung, W.Goldy, J.Abdelhak, A.Baker, P.Barkan, E.Bertagnolli, D.Campos, J.Carey, D.Casper, T.Chakka, A. B.Chakrabarty, R.Chavan, S.Chen, M.Clark, M.Close, J.Crichton, K.Daniel, S.Dolbeare, T.Ellingwood, L.Gee, J.Glandon, A.Gloe, J.Gould, J.Gray, J.Guilford, N.Guzman, J.Hirschstein, D.Ho, W.Jin, K.Kroll, M.Lathia, K.Leon, A.Long, B.Maltzer, Z.Martin, N.McCue, R.Meyerdierks, E.Nguyen, T. N.Pham, T.Rimorin, C.Ruiz, A.Shapovalova, N.Slaug2023-03-06doi:10.1101/2023.03.06.531121Cold Spring Harbor Laboratory Press2023-03-06
<![CDATA[
A molecularly defined and spatially resolved cell atlas of the whole mouse brain
]]>
https://biorxiv.org/cgi/content/short/2023.03.06.531348v1?rss=1"
1,100 genes in [~]8 million cells across the entire adult mouse brain using multiplexed error-robust fluorescence in situ hybridization (MERFISH)12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating MERFISH and single-cell RNA-sequencing (scRNA-seq) data. Using this approach, we generated a comprehensive cell atlas of >5,000 transcriptionally distinct cell clusters, belonging to [~]300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of the MERFISH images to the common coordinate framework (CCF) of the mouse brain further allowed systematic quantifications of the cell composition and organization in individual brain regions defined in the CCF. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes in the gene-expression profiles of cells. Finally, this high-resolution spatial map of cells, with a transcriptome-wide expression profile associated with each cell, allowed us to infer cell-type-specific interactions between several hundred pairs of molecularly defined cell types and predict potential molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a valuable resource for future functional investigations of neural circuits and their dysfunction in diseases.
]]>Zhang, M.Pan, X.Jung, W.Halpern, A.Eichhorn, S. W.Lei, Z.Cohen, L.Smith, K. A.Tasic, B.Yao, Z.Zeng, H.Zhuang, X.2023-03-07doi:10.1101/2023.03.06.531348Cold Spring Harbor Laboratory Press2023-03-07
<![CDATA[
The cell type composition of the adult mouse brain revealed by single cell and spatial genomics
]]>
https://biorxiv.org/cgi/content/short/2023.03.06.531307v1?rss=1"
Langlieb, J.Sachdev, N.Balderrama, K.Nadaf, N.Raj, M.Murray, E.Webber, J.Vanderburg, C.Gazestani, V.Tward, D.Mezias, C.Li, X.Norton, T.Mitra, P. P.Chen, F.Macosko, E.2023-03-08doi:10.1101/2023.03.06.531307Cold Spring Harbor Laboratory Press2023-03-08
<![CDATA[
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain
]]>
https://biorxiv.org/cgi/content/short/2023.04.16.536509v1?rss=1"
Liu, H.Zeng, Q.Zhou, J.Bartlett, A.Wang, B.-A.Berube, P.Tian, W.Kenworthy, M.Altshul, J.Nery, J. R.Chen, H.Castanon, R. G.Zu, S.Li, Y. E.Lucero, J.Osteen, J. K.Pinto-Duarte, A.Lee, J.Rink, J.Cho, S.Emerson, N.Nunn, M.O'Connor, C.Yao, Z.Tasic, B.Smith, K. A.Zeng, H.Luo, C.Dixon, J. R.Ren, B.Behrens, M. M.Ecker, J. R.2023-04-18doi:10.1101/2023.04.16.536509Cold Spring Harbor Laboratory Press2023-04-18
<![CDATA[
Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections
]]>
https://biorxiv.org/cgi/content/short/2023.05.01.538832v1?rss=1"
Zhou, J.Zhang, Z.Wu, M.Liu, H.Pang, Y.Bartlett, A.Rivkin, A. C.Lagos, W. N.Williams, E.Lee, C.-T.Miyazaki, P. A.Aldridge, A. I.Zeng, Q.Salinda, J. L. A.Claffey, N.Liem, M.Fitzpatrick, C.Boggeman, L.Yao, Z.Smith, K. A.Tasic, B.Altshul, J.Kenworthy, M. A.Valadon, C.Nery, J. R.Castanon, R. G.Patne, N. S.Vu, M.Rashid, M.Jacobs, M. W.Ito-Cole, T.Osteen, J.Emerson, N.Lee, J.Cho, S.Rink, J.Huang, H.-H.Pinto-Duartec, A.Dominguez, B.Smith, J. B.O'Connor, C.Zeng, H.Lee, K.-F.Mukamel, E. A.Jin, X.Behrens, M. M.Eck2023-05-01doi:10.1101/2023.05.01.538832Cold Spring Harbor Laboratory Press2023-05-01
<![CDATA[
Spatial Atlas of the Mouse Central Nervous System at Molecular Resolution
]]>
https://biorxiv.org/cgi/content/short/2022.06.20.496914v1?rss=1"
Shi, H.He, Y.Zhou, Y.Huang, J.Wang, B.Tang, Z.Tan, P.Wu, M.Lin, Z.Ren, J.Thapa, Y.Tang, X.Liu, A.Liu, J.Wang, X.2022-06-22doi:10.1101/2022.06.20.496914Cold Spring Harbor Laboratory Press2022-06-22
<![CDATA[
Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development
]]>
https://biorxiv.org/cgi/content/short/2023.04.02.535281v1?rss=1"
Joglekar, A.Hu, W.Zhang, B.Narykov, O.Diekhans, M.Balacco, J.Ndhlovu, L.Milner, T. A.Fedrigo, O.Jarvis, E. D.Sheynkman, G. M.Korkin, D.Ross, M. E.Tilgner, H. U.2023-04-04doi:10.1101/2023.04.02.535281Cold Spring Harbor Laboratory Press2023-04-04
<![CDATA[
A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming
]]>
https://biorxiv.org/cgi/content/short/2023.03.28.534622v1?rss=1"
Stouffer, K. M.Trouve, A.Younes, L.Kunst, M.Ng, L.Zeng, H.Anant, M.Fan, J.Kim, Y.Miller, M. I.2023-03-29doi:10.1101/2023.03.28.534622Cold Spring Harbor Laboratory Press2023-03-29
<![CDATA[
MorphNet Predicts Cell Morphology from Single-Cell Gene Expression
]]>
https://biorxiv.org/cgi/content/short/2022.10.21.513201v1?rss=1"
Lee, H.Welch, J. D.2022-10-21doi:10.1101/2022.10.21.513201Cold Spring Harbor Laboratory Press2022-10-21
<![CDATA[
Evolution of neuronal cell classes and types in the vertebrate retina
]]>
https://biorxiv.org/cgi/content/short/2023.04.07.536039v1?rss=1"
80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.
]]>Hahn, J.Monavarfeshani, A.Qiao, M.Kao, A.Kölsch, Y.Kumar, A.Kunze, V. P.Rasys, A. M.Richardson, R.Baier, H.Lucas, R. J.Li, W.Meister, M.Trachtenberg, J. T.Yan, W.Peng, Y.-R.Sanes, J.Shekhar, K.2023-04-08doi:10.1101/2023.04.07.536039Cold Spring Harbor Laboratory Press2023-04-08
<![CDATA[
Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex
]]>
https://biorxiv.org/cgi/content/short/2023.04.08.536119v1?rss=1"
Zemke, N. R.Armand, E. J.Wang, W.Lee, S.Zhou, J.Li, Y. E.Liu, H.Tian, W.Nery, J. R.Castanon, R. G.Bartlett, A.Osteen, J. K.Li, D.Zhuo, X.Xu, V.Miller, M.Krienen, F. M.Zhang, Q.Taskin, N.Ting, J.Feng, G.McCarroll, S. A.Callaway, E. M.Wang, T.Behrens, M.Lein, E. S.Ecker, J. R.Ren, B.2023-04-08doi:10.1101/2023.04.08.536119Cold Spring Harbor Laboratory Press2023-04-08
<![CDATA[
Preservation of co-expression defines the primary tissue fidelity of human neural organoids
]]>
https://biorxiv.org/cgi/content/short/2023.03.31.535112v1?rss=1"
Werner, J.Gillis, J.2023-03-31doi:10.1101/2023.03.31.535112Cold Spring Harbor Laboratory Press2023-03-31
<![CDATA[
in silico transcriptome dissection of neocortical excitatory neurogenesis via joint matrix decomposition and transfer learning
]]>
https://biorxiv.org/cgi/content/short/2024.02.26.581612v1?rss=1"
Sonthalia, S.Li, G.Blanco, X. M.Casella, A.Liu, J.Stein-O'Brien, G.Caffo, B.Adkins, S.Orvis, J.Hertzano, R.Mahurkar, A.Gillis, J. A.Werner, J.Ma, S.Micali, N.Sestan, N.Rakic, P.Baro, G. S.Ament, S. A.Colantuoni, C.2024-02-28doi:10.1101/2024.02.26.581612Cold Spring Harbor Laboratory Press2024-02-28
<![CDATA[
Developmental Mouse Brain Common Coordinate Framework
]]>
https://biorxiv.org/cgi/content/short/2023.09.14.557789v1?rss=1"
Kronman, F. A.Liwang, J. K.Betty, R.Vanselow, D. J.Wu, Y.-t.Tustison, N. J.Bhandiwad, A.Manjila, S. B.Minteer, J. A.Shin, D.Lee, C. H.Patil, R.Duda, J. T.Puelles, L.Gee, J. C.Zhang, J.Ng, L.Kim, Y.2023-09-15doi:10.1101/2023.09.14.557789Cold Spring Harbor Laboratory Press2023-09-15
<![CDATA[
Molecular and cellular dynamics of the developing human neocortex at single-cell resolution
]]>
https://biorxiv.org/cgi/content/short/2024.01.16.575956v1?rss=1"
Wang, L.Wang, C.Moriano, J. A.Chen, S.Zhang, S.Mukhtar, T.Wang, S.Cebrian-Silla, A.Bi, Q.Augustin, J. J.de Oliveira, L. G.Song, M.Ge, X.Zuo, G.Paredes, M. F.Huang, E. J.Alvarez-Buylla, A.Duan, X.Li, J.Kriegstein, A. R.2024-01-16doi:10.1101/2024.01.16.575956Cold Spring Harbor Laboratory Press2024-01-16
<![CDATA[
A Hypothalamic Circuit Underlying the Dynamic Control of Social Homeostasis
]]>
https://biorxiv.org/cgi/content/short/2023.05.19.540391v1?rss=1"
Liu, D.Rahman, M.Johnson, A.Tsutsui-Kimura, I.Pena, N.Talay, M.Logeman, B. L.Finkbeiner, S.Choi, S.Capo-Battaglia, A.Abdus-Saboor, I.Ginty, D. D.Uchida, N.Watabe-Uchida, M.Dulac, C.2023-05-19doi:10.1101/2023.05.19.540391Cold Spring Harbor Laboratory Press2023-05-19
<![CDATA[
Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development
]]>
https://biorxiv.org/cgi/content/short/2024.10.02.616246v1?rss=1"
Gao, Y.van Velthoven, C. T. J.Lee, C.Thomas, E. D.Bertagnolli, D.Carey, D.Casper, T.Chakka, A. B.Chakrabarty, R.Clark, M.Desierto, M. J.Ferrer, R.Gloe, J.Goldy, J.Guilford, N.Guzman, J.Halterman, C. R.Hirschstein, D.Ho, W.James, K.McCue, R.Meyerdierks, E.Nguy, B.Pena, N.Pham, T.Shapovalova, N. V.Sulc, J.Torkelson, A.Tran, A.Tung, H.Wang, J.Ronellenfitch, K.Levi, B.Hawrylycz, M. J.Pagan, C.Dee, N.Smith, K. A.Tasic, B.Yao, Z.Zeng, H.2024-10-06doi:10.1101/2024.10.02.616246Cold Spring Harbor Laboratory Press2024-10-06
<![CDATA[
The transcriptomic and spatial organization of telencephalic GABAergic neuronal types
]]>
https://biorxiv.org/cgi/content/short/2024.06.18.599583v1?rss=1"
van Velthoven, C. T. J.Gao, Y.Kunst, M.Lee, C.McMillen, D.Chakka, A. B.Casper, T.Clark, M.Chakrabarty, R.Daniel, S.Dolbeare, T.Ferrer, R.Gloe, J.Goldy, J.Guzman, J.Halterman, C.Ho, W.Huang, M.James, K.McCue, R.Nguy, B.Pham, T.Ronellenfitch, K.Thomas, E. D.Torkelson, A.Pagan, C.Kruse, L.Dee, N.Ng, L.Waters, J.Smith, K. A.Tasic, B.Yao, Z.Zeng, H.2024-06-18doi:10.1101/2024.06.18.599583Cold Spring Harbor Laboratory Press2024-06-18
<![CDATA[
Conservation, alteration, and redistribution of mammalian striatal interneurons
]]>
https://biorxiv.org/cgi/content/short/2024.07.29.605664v1?rss=1"
Corrigan, E. K.DeBerardine, M.Poddar, A.Turrero Garcia, M.Schmitz, M. T.Harwell, C.Paredes, M.Krienen, F. M.Pollen, A. A.2024-07-30doi:10.1101/2024.07.29.605664Cold Spring Harbor Laboratory Press2024-07-30
<![CDATA[
Dynamics of chromatin accessibility during human first-trimester neurodevelopment
]]>
https://biorxiv.org/cgi/content/short/2023.08.18.553878v1?rss=1"
Mannens, C. C. A.Hu, L.Lonnerberg, P.Schipper, M.Reagor, C.Li, X.He, X.Barker, R. A.Sundstrom, E.Posthuma, D.Linnarsson, S.2023-08-20doi:10.1101/2023.08.18.553878Cold Spring Harbor Laboratory Press2023-08-20
<![CDATA[
A three-dimensional histological cell atlas of the developing human brain
]]>
https://biorxiv.org/cgi/content/short/2024.12.17.628811v1?rss=1"
Jayakumar, J.Sivaprakasam, M.Verma, R.Bota, M.Joseph, J.Mulay, S.Kumutha, J.Srinivasan, C.S, S.S, L.Kumar, H. E.Bhaduri, A.Nowakowski, T. J.Roy, P. K.Savoia, S.Banerjee, S.Tward, D.Mitra, P. P.2024-12-18doi:10.1101/2024.12.17.628811Cold Spring Harbor Laboratory Press2024-12-18
<![CDATA[
Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping
]]>
https://biorxiv.org/cgi/content/short/2024.07.28.605493v1?rss=1"
Zhang, D.Rubio Rodriguez-Kirby, L. A.Lin, Y.Song, M.Wang, L.Wang, L.Kanatani, S.Jimenez-Beristain, T.Dang, Y.Zhong, M.Kukanja, P.Wang, S.Chen, X. L.Gao, F.Wang, D.Hang, X.Lou, X.Liu, Y.Chen, J.Sestan, N.Uhlen, P.Kriegstein, A.Zhao, H.Castelo-Branco, G.Fan, R.2024-07-28doi:10.1101/2024.07.28.605493Cold Spring Harbor Laboratory Press2024-07-28
<![CDATA[
Multimodal analysis of neuronal maturation in the developing primate prefrontal cortex
]]>
https://biorxiv.org/cgi/content/short/2023.06.02.543460v1?rss=1"
Gao, Y.Dong, Q.Arachchilage, K. H.Risgaard, R.Sheng, J.Syed, M.Schmidt, D. K.Jin, T.Liu, S.Doherty, D.Glass, I.Levine, J. E.Wang, D.Chang, Q.Zhao, X.Sousa, A. M.2023-06-02doi:10.1101/2023.06.02.543460Cold Spring Harbor Laboratory Press2023-06-02
<![CDATA[
Cross-species consensus atlas of the primate basal ganglia
]]>
https://biorxiv.org/cgi/content/short/2025.12.15.694496v1?rss=1"
Johansen, N. J.Fu, Y.Schmitz, M.Dubuc, A.Kempynck, N.Wirthlin, M.Garcia, A. D.Hewitt, M.Turner, M. A.Seeman, S. C.Long, B.Liu, X.-P.Dan, S.DeBerardine, M.Kapen, I.Yanny, A. M.Avola, A.Barlow, S. T.Bertagnolli, D.Bhandiwad, A.Budzillo, A.Caballero, V. E. N.Caceres, L.Casper, T.Chakka, A. B.Chakrabarty, R.Clark, M.Daniel, S.Eggermont, J.Ferrer, R.French, L.Gloe, J.Goldy, J.Guilford, N.Guzman, J.Hirschstein, D.Ho, W.James, K.Jones, D. L.Jungert, M.Kannan, M.Kedzierska, K. Z.Kroes, T.Leytze, M.Manning, A.McCu2025-12-16doi:10.64898/2025.12.15.694496Cold Spring Harbor Laboratory Press2025-12-16
<![CDATA[
A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia
]]>
https://biorxiv.org/cgi/content/short/2025.11.22.688128v1?rss=1"
Hewitt, M. N.Turner, M. A.Johansen, N.McMillen, D. A.Dan, S.DeBerardine, M.Ruiz, A.Huang, M.Quon, J.Fu, Y.Kapen, I.Barta, S.Martin, N.Cuevas, N. V.Olsen, P.Nagra, J.Campos, J.VanNess, M. M.Ransford, S.Juneau, Z.Hastings, S.Ching, L.Kunst, M.Basu, S.Hollt, T.Li, C.Lelieveldt, B.Yazdani, F.Zhang, Q.Levandowski, K.Feng, G.Rosen, B.Glasser, M. F.Hayashi, T.Garcia, A. D.Kana, O.Maltzer, Z. M.Campagnola, L.Jarsky, T.Kruse, L.Freiwald, W.Keene, C. D.Van Essen, D. C.Ariza, J.Waters, J.Krienen, F. M.Bakken, T. E2025-11-24doi:10.1101/2025.11.22.688128Cold Spring Harbor Laboratory Press2025-11-24
<![CDATA[
A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia
]]>
https://biorxiv.org/cgi/content/short/2026.02.12.705594v1?rss=1"
Ding, W.Klein, A.Baez-Becerra, C. T.Rink, J. A.Bartlett, A.Zeng, Q.Wang, R.Castanon, R. G.Nery, J. R.Osgood, E.Owens, W.Petrella, A.Chen, C.Acerbo, A. S.Barcoma, A. S.Liu, J.Russo, K. G.Knutson, K. W.Young, C. K.Willier, J. K.Barragan, C.Arzavala, J.Cho, S.Altshul, J.Chan, D.Soma, E.Luo, J.Jain, M.Velazquez, S.Schenker-Ahmed, N.Sundaram, G. V.Manning, A. C.Sanchez, Y.Bikkina, A.Fu, S.OConnor, C.Liem, M.Marrin, M. V.Rose, C.Alt, S. N.Berry, J.Kern, C.Boone, E.Tian, W.Wu, Y.Hariharan, M.Fu, Y.Xie, Y.L2026-02-14doi:10.64898/2026.02.12.705594Cold Spring Harbor Laboratory Press2026-02-14
<![CDATA[
Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia
]]>
https://biorxiv.org/cgi/content/short/2026.02.03.703645v1?rss=1"
Chang, L.Li, K.Xie, Y.Zhong, G.Rink, J. A.Baez-Becerra, C. T.Lie, A.Indralingam, H. S.Dong, K.Loe, T.Wang, Z.Zu, S.Kern, J. C.Zhao, Z.Boone, E.Flores, J.Monell, A.Olness, J.Barragan, C.Osgood, E.Owens, W.Schenker-Ahmed, N.Zhang, W.Liu, D.Barcoma, A. S.Willier, J. K.Knutson, K. W.Russo, K. G.Liu, J.Cho, S.Arzavala, J.Young, C. K.Sundaram, G. V.Manning, A. C.Sanchez, Y.Bikkina, A.Berry, J.Gao, X.OConnor, C.Liem, M.Marrin, M. V.Rose, C.Alt, S. N.Zhu, C.Zemke, N. R.Ding, W.Klein, A.Fu, Y.Johansen, N.B2026-02-04doi:10.64898/2026.02.03.703645Cold Spring Harbor Laboratory Press2026-02-04
<![CDATA[
Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization
]]>
https://biorxiv.org/cgi/content/short/2025.12.02.691876v1?rss=1"
Berackey, B. T.Tan, Z.Wu, G.Das, S. C.Li, R.Esser, B.Ye, Q.Nafisi, M.Park, S. S.Sequeira Mendieta, P. A.Berry, J.Mamdani, F.Zhu, Q.Holmes, T. C.Li, D.Wang, T.Behrens, M. M.Ren, B.Ecker, J. R.Bintu, B.Xu, X.2025-12-05doi:10.64898/2025.12.02.691876Cold Spring Harbor Laboratory Press2025-12-05
<![CDATA[
Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain
]]>
https://biorxiv.org/cgi/content/short/2026.02.02.703166v1?rss=1"
750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization.
HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes with active or repressive histone modification in >750,000 nuclei across adult human brain.
C_LIO_LIChromatin state annotation of >500,000 candidate cis-regulatory elements distinguishes active enhancers from accessible and Polycomb-repressed regions.
C_LIO_LICell-type-resolved regulatory networks and sequence-based deep learning model prioritize functional neuropsychiatric risk variants.
C_LIO_LISpatial epigenomic imputation reveals laminar layer-specific Polycomb repression programs.
C_LIO_LIIntegration with 3D genome architecture reveals neuron-specific super long-range chromatin loops silencing early developmental genes.
C_LIO_LIEvolutionary analysis uncovers conserved active regulatory grammar but divergent repressive landscape.
C_LI
]]>Xie, Y.Chang, L.Zhong, G.Rink, J. A.Baez-Becerra, T.Armand, E.Ding, W.Li, K.Boone, E.Lie, A.Indralingam, H. S.Dong, K.Loe, T.Huang, B.Wang, Z.Barcoma, A. S.Willier, J. K.Knutson, K. W.Liu, J.Cho, S.Cao, S.Russo, K. G.Young, C. K.Arzavala, J.Sanchez, Y.Bikkina, A.Schenker-Ahmed, N.Kern, C.Zhao, Z.Klein, A.Flores, J.Tai, C.-Y.Olness, J.Monell, A.Moghadami, S.Barragan, C.Chen, C.Owens, W.OConnor, C.Liem, M.Marrin, M. V.Rose, C.Alt, S. N.Emerson, N.Osteen, J.Lucero, J.Li, D.Hodge, R. D.Wang, T.Keene,2026-02-03doi:10.64898/2026.02.02.703166Cold Spring Harbor Laboratory Press2026-02-03
<![CDATA[
Spatial patterning of transcriptional and regulatory programs in the primate subcortex
]]>
https://biorxiv.org/cgi/content/short/2025.11.22.689869v1?rss=1"
Dan, S.Turner, M. A.DeBerardine, M.Caceres, L.Nieto, V. E.Schembri, J.Levandowski, K.Cardenas, C.Wang, N.Li, C.Basu, S.Zheng, H.Liu, X.Hollt, T.Feliciano, J.Zhang, Q.Nakamoto, R.McMillen, D. A.Martin, N.Cuevas, N. V.Olsen, P.Nagra, J.Campos, J.VanNess, M. M.Waters, J.Ransford, S.Juneau, Z.Hastings, S.Barta, S.Ruiz, A.Ariza, J.Raphael, B. J.Zeng, H.Lein, E. S.Lelieveldt, B.Feng, G.Long, B.Krienen, F. M.2025-11-24doi:10.1101/2025.11.22.689869Cold Spring Harbor Laboratory Press2025-11-24
<![CDATA[
Morphoelectric Diversity and Specialization of Neuronal Cell Types in the Primate Striatum
]]>
https://biorxiv.org/cgi/content/short/2026.02.26.708019v1?rss=1"
Liu, X.-P.Dalley, R.Johansen, N.Budzillo, A.Thijssen, J.Miller, J. A.Walling-Bell, S.Sawchuk, S.Alfiler, L.Andrade, J.Ayala, A.Barta, S.Berry, K.Bertagnolli, D.Bhandiwad, A.Bixby, M.Blake, K.Brouner, K.Cardenas, T.Casper, T.Chakka, A. B.Chartrand, T.Daniel, S.Donadio, N.Dotson, N. I.Egdorf, T.Enstrom, R.Fu, Y.Gary, A.Goldy, J.Gorham, M.Hadley, K.Huang, A.Hunker, A. C.Jordan, A.Juneau, Z. C.Jungert, M.Kannan, M.Kapen, I.Khem, S.Koch, M.Kocsis, K.Kutsal, R.Leon, G.Mallory, M.Malone, J.McCutcheon, A.McGr2026-02-26doi:10.64898/2026.02.26.708019Cold Spring Harbor Laboratory Press2026-02-26
<![CDATA[
Circuit specific specialization of human basal ganglia astrocytes
]]>
https://biorxiv.org/cgi/content/short/2025.12.19.695583v1?rss=1"
Fu, Y.Johansen, N. J.Kempynck, N.Ding, W.Turner, M. A.Garcia, A. D.Schmitz, M. T.Close, J.Kapen, I.Hewitt, M.Seeman, S. C.Long, B.Ding, S.-L.Ho, W.Mahoney, J.Mich, J. K.Levi, B. P.Klein, A.Behrens, M. M.Ecker, J.Aerts, S.Hodge, R. D.Lein, E. S.Bakken, T. E.2025-12-22doi:10.64898/2025.12.19.695583Cold Spring Harbor Laboratory Press2025-12-22
<![CDATA[
A Cross-Species Enhancer-AAV Toolkit for Cell Type-Specific Targeting Across the Basal Ganglia
]]>
https://biorxiv.org/cgi/content/short/2026.02.23.706695v1?rss=1"
Wirthlin, M. E.Hunker, A. C.Somasundaram, S.Lerma, M. N.Laird, W. D.Omstead, V.Taskin, N.Kempynck, N.Schmitz, M. T.Gao, Y.Thomas, E.Hooper, M.Ben-Simon, Y.Martinez, R. A.Opitz-Araya, X.Mich, J. K.Oster, A.Dwivedi, D.Groce, E.Roth, J.Thyagarajan, B.Way, S.Amaya, A.Ayala, A.Barta, S.Bertagnolli, D.Bixby, M.Cardenas, T.Casper, T.Clark, M.Donadio, N.Dotson, N. I.Egdorf, T.Peterson, E. L.Gloe, J.Goldy, J.Grasso, C.Han, W.Hastings, S. D.Hewitt, M.Hirschstein, D.Ho, W.Huang, A.Johnson, T.Jones, D.Jordan, A.Jun2026-02-24doi:10.64898/2026.02.23.706695Cold Spring Harbor Laboratory Press2026-02-24
<![CDATA[
Enhancer-based AAV approach for selective AADC delivery reduces motor symptoms and dyskinesia in Parkinson's mouse models
]]>
https://biorxiv.org/cgi/content/short/2026.01.20.700641v1?rss=1"
Chowdhury, A.Fraser, A.Departee, M.Taskin, N.Quinlan, M. A.Mich, J. K.Omstead, V.Lerma, N.Opitz-Araya, X.Hughes, A. C.Kussick, E.Martinez, R.Reding, M.Liang, E.Shulga, L.Rette, D.Huang, C.Casian, B.Leibly, M.Helback, O.Barcelli, T.Wood, T.Uribe, N.Bacon, C.Bowlus, J.Newman, D.Kutsal, R.Khem, S.Donadio, N.Yao, S.Ronellenfitch, K.Wright, V.Gudsnuk, K.Horwitz, G. D.Levi, B. P.Lein, E. S.Ting, J. T.Daigle, T. L.2026-01-21doi:10.64898/2026.01.20.700641Cold Spring Harbor Laboratory Press2026-01-21
<![CDATA[
The Caudate Nucleus Exhibits Distinct Pathology and Cell Type-Specific Responses Across Alzheimer's Disease
]]>
https://biorxiv.org/cgi/content/short/2026.01.10.694705v1?rss=1"
Kana, O. Z.Postupna, N.Agrawal, A.Long, B.Travaglini, K.Gabitto, M.Lai, H.-Y.Mahoney, J. T.Xiao, M.Bajwa, T.Hulsey-Vincent, H.Oyaizu, S. L.Mena, G. E.Hong, J.Gelfand, E. C.Kaplan, E. S.Ariza, J.Smith, K. A.McMillen, D. A.Chakka, A. B.Goldy, J.Melief, E. J.Barta, S.Oyama, A.Ruiz, A.Pom, C. A.Ayala, A.Bixby, M.Huang, A.Martin, N.Cuevas, N. V.Olsen, P.Nagra, J.Chakrabarty, R.Tieu, M.Cardenas, T.Torkelson, A.Bertagnolli, D.Guzman, J.Ferrer, R.Waters, J.Grabowski, T. J.Crane, P. K.Gatto, N. M.Miller, J. A.Hodg2026-01-10doi:10.64898/2026.01.10.694705Cold Spring Harbor Laboratory Press2026-01-10
<![CDATA[
Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism
]]>
https://biorxiv.org/cgi/content/short/2025.11.05.686845v1?rss=1"
Yuan, G.Suresh, V.Wigdor, E.Hao, Y.Leonard, R.Steyert, M.Griffiths, M.Evans, C.Rohani, N.Weiss, J.Lassen, F. H.Schafer, N.Dong, S.Palmer, D. S.Sanders, S. J.Nowakowski, T. J.2025-11-07doi:10.1101/2025.11.05.686845Cold Spring Harbor Laboratory Press2025-11-07
<![CDATA[
Progenitor Diversity and Architecture of the Human Ganglionic Eminences Shaping the Basal Ganglia
]]>
https://biorxiv.org/cgi/content/short/2025.12.31.697063v1?rss=1"
Siebert, C. V.Song, M.Moriano, J. A.Li, Z.Silla, A. C.Walker, M.Chen, S.Baltazar, J.Oliveira, L. G. d.Shankar, M.Xie, Y.Suraparaju, P.Wang, S.Bi, Q.Xie, Y.Ren, Y.Garcia, M. T.Wang, L.Zuo, G.Smidt, M. P.Hoekman, M. F. M.Harwell, C.Parent, J.Rubenstein, J.Alvarez-Buylla, A.Kriegstein, A.2026-01-02doi:10.64898/2025.12.31.697063Cold Spring Harbor Laboratory Press2026-01-02
<![CDATA[
A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons
]]>
https://biorxiv.org/cgi/content/short/2026.01.28.702385v1?rss=1"
Heffel, M. G.Xu, H.Pastor-Alonso, O.Li, X.Baig, M. S.Irfan Ghoor, R.Li, R.Kern, C.Kum, J.Zhang, Y.Paino, J.Tsai, M. J.Tai, C.-Y.Tucker, G.Zhao, Z.Hou, A.von Behren, Z.Bhade, M.Li, S.Sandoval, K.Scholes, J.Codrea, F.Calimlim, J.Liao, E. K.Leung, G.Kim, J.Eskin, E.Flint, J.Cotter, J. A.Pasaniuc, B.Bintu, B.Zhu, Q.Mukamel, E. A.Ernst, J.Paredes, M. F.Luo, C.2026-01-29doi:10.64898/2026.01.28.702385Cold Spring Harbor Laboratory Press2026-01-29
<![CDATA[
UC Irvine Brain Initiative Cell Atlas Network (BICAN) Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas Project
]]>
https://biorxiv.org/cgi/content/short/2025.12.23.696304v1?rss=1"
Xu, X.Berry, J. V.Tran, B. M.Wu, G.Tan, Z.Mendoza, E.Kim, M.Arat, Z.Lin, P. S. H.Valenzuela, L.Holmes, T. C.Virovka, A.Thaxton, M.Nguyen, M.Stein, S.Sigaroudi, V. R.De La Rosa, A.Gawronski, B.Silva, J.Gonzalez, L.Wright, S.Wood, K.Hui, G. K.Anousaya, D.Gangeddula, V. R.Gama, N.Gama, J.Gross, T.Bunney, B.Stein, R.Sequeira, P. A.Mamdani, F.Cartagena, P.Bunney, W. E.Lou, J.Park, H. L.Wilson, A.Brooks, H. M.Allhusen, V.Crawford, J.Knight, J. M.Ren, B.Ecker, J.Behrens, M. M.Keene, C. D.Stark, C.Head, E.Yon2025-12-26doi:10.64898/2025.12.23.696304Cold Spring Harbor Laboratory Press2025-12-26
<![CDATA[
Tissue-to-Bytes: A Catalytic Digital Twin Platform for Consortium-Scale Integration of Single-Cell Omics Data in BRAIN Initiative Cell Atlas Network
]]>
https://biorxiv.org/cgi/content/short/2025.12.06.692733v1?rss=1"
Tao, S.Li, X.Huang, Y.Abeysinghe, R.Tong, L.Lin, S.Chou, W.-C.Edgu-Fry, E.Smith, K. A.Ng, L.Cui, L.ZHANG, G.-Q.2025-12-09doi:10.64898/2025.12.06.692733Cold Spring Harbor Laboratory Press2025-12-09
<![CDATA[
An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia
]]>
https://biorxiv.org/cgi/content/short/2026.01.29.702575v1?rss=1"
Zhang, W.Ding, W.Li, K.Chang, L.Klein, A.Baez-Becerra, C. T.Rink, J. A.Bartlett, A.Chen, H.Schenker, N.Johansen, N.Mollenkopf, T.Fu, Y.Yang, X.Liu, S.Seng, C.Miao, B.Liu, T.Zhu, Q.Hodge, R. D.Bakken, T. E.Lein, E. S.Hawrylycz, M.Xu, X.Behrens, M. M.Ren, B.Ecker, J. R.Wang, T.Li, D.2026-01-30doi:10.64898/2026.01.29.702575Cold Spring Harbor Laboratory Press2026-01-30
<![CDATA[
multiVIB: A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data
]]>
https://biorxiv.org/cgi/content/short/2025.11.29.691308v1?rss=1"
Xu, Y.Fleming, S. J.Wang, B.Schoenbeck, E. G.Babadi, M.Huo, B.-X.2025-12-01doi:10.1101/2025.11.29.691308Cold Spring Harbor Laboratory Press2025-12-01
<![CDATA[
A consensus spinal cord cell type atlas across mouse, macaque, and human
]]>
https://biorxiv.org/cgi/content/short/2026.02.04.703852v1?rss=1"
Schmitz, M. T.Johansen, N. J.Kempynck, N.Kapen, I.Fu, Y.Hewitt, M.Seeman, S. C.Kussick, E.Gautier, O.Leone, M. J.Ding, S.-L.Gao, Y.Bhandiwad, A.Ariza, J.Ayala, A.Barta, S.Blum, J. A.Cano-Gomez, L.Cardenas, T.Chakka, A. B.Cuevas, N. V.Donadio, N.Fancher, K.Ferrer, R.Goldy, J.Hastings, S. D.Hirschstein, D.Ho, W.Huang, C.Juneau, Z. C.Kim, S. R.Lewis, Z. R.Liang, E.Martin, N. X.Nagra, J.Newman, D.Noh, M.-C.Olsen, P.Oyama, A.Pena, N.Poldsam, H.Ray, P. L.Reding, M.Rimorin, C.Ruiz, A.Shapovalova, N. V.Shulga,2026-02-05doi:10.64898/2026.02.04.703852Cold Spring Harbor Laboratory Press2026-02-05
<![CDATA[
Human Neocortical Glutamatergic Neurons Revealed Through Multimodal Profiling
]]>
https://biorxiv.org/cgi/content/short/2026.01.08.698257v1?rss=1"
Dalley, R.Walling-Bell, S.Miller, J. A.Waleboer, F.Thijssen, J.McCutcheon, A.Gelfand, E.Mallory, M.Radaelli, C.Liu, X.-P.Sawchuk, S.Alfiler, L.Andrade, J.Ariza, J.Ayala, A.Baker, K.Barkan, E.Barta, S.Berry, K.Bertagnolli, D.Bickley, K.Bixby, M.Blake, K.Bomben, J.Brouner, K.Budzillo, A.Campos, J.Cardenas, T.Carey, D.Casper, T.Chakka, A. B.Clark, M.Coopmans, T. V.Crichton, K.Dee, N.Dotson, N. I.Driessens, S. L. W.Egdorf, T.Ellingwood, L.English, C.Enstrom, R.de Frates, R.Galakhova, A. A.Gary, A.Gloe, J.Gold2026-01-08doi:10.64898/2026.01.08.698257Cold Spring Harbor Laboratory Press2026-01-08
<![CDATA[
Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics
]]>
https://biorxiv.org/cgi/content/short/2025.11.16.686778v1?rss=1"
Wang, N.Turner, D.Feinberg, H.Nieto Caballero, V. E.Yuan, D.Scott, N.Cardenas, C.DeBerardine, M.Dan, S.Caceres, L.Schembri, J.Yao, Z.Lee, C.Pillow, J. W.Krienen, F. M.2025-11-16doi:10.1101/2025.11.16.686778Cold Spring Harbor Laboratory Press2025-11-16
<![CDATA[
A Meta-Atlas of the Developing Human Cortex Identifies Modules Driving Cell Subtype Specification
]]>
https://biorxiv.org/cgi/content/short/2023.09.12.557406v1?rss=1"
Nano, P. R.Fazzari, E.Azizad, D.Nguyen, C. V.Wang, S.Kan, R. L.Wick, B.Haeussler, M.Bhaduri, A.2023-09-13doi:10.1101/2023.09.12.557406Cold Spring Harbor Laboratory Press2023-09-13
<![CDATA[
Mesoscale molecular architecture of the human striatum across cell types and lifespan
]]>
https://biorxiv.org/cgi/content/short/2026.03.04.709715v1?rss=1"
Kraft, A. W.Lee, M.Rayan, N.Gao, H.Milidantri, J.Vanderburg, C.Balderrama, K.Nadaf, N.Kumar, V.Flowers, K.Finn, E.Shabet, M.Muratoglu, E.Yoo, O.Shakir, K.Nemesh, J.Burger, S.Drouin, S.Catalini, O.Raj, M.Mohsin, A.Budnik, N.Reese, L.McCarroll, S. A.Ichihara, K.Macosko, E. Z.2026-03-05doi:10.64898/2026.03.04.709715Cold Spring Harbor Laboratory Press2026-03-05
<![CDATA[
MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomies
]]>
https://biorxiv.org/cgi/content/short/2026.03.06.710160v1?rss=1"
Daniel, S. F.Lee, C.Mollenkopf, T.Lee, M.Arbuckle, J.Fiabane, E.Gabitto, M. I.Johansen, N.Kapen, I.Kraft, A. W.Lai, J.Li, S. Y.McGinty, R.Miller, J. A.Welch-Moosman, S.Otto, S.Sawyer, L.Shepard, N.Thompson, C. L.Tjaernberg, A.Waters, J.Zhen, X.Macosko, E.Lein, E.Ng, L.Zeng, H.Mufti, S.Yao, Z.Hawrylycz, M.2026-03-09doi:10.64898/2026.03.06.710160Cold Spring Harbor Laboratory Press2026-03-09
<![CDATA[
Connecting single neuron transcriptomes to the projectome in mouse visual cortex
]]>
https://biorxiv.org/cgi/content/short/2023.11.25.568393v1?rss=1"
Sorensen, S. A.Gouwens, N. W.Wang, Y.Mallory, M.Budzillo, A.Dalley, R.Lee, B. R.Gliko, O.Kuo, H.Kuang, X.Mann, R.Ahmadinia, L.Alfiler, L.Baftizadeh, F.Baker, K. S.Bannick, S.Bertagnolli, D.Bickley, K.Bohn, P.Bomben, J.Boyer, G.Brouner, K.Cahoon, A.Chen, N.Chen, C.Chen, K.Chvilicek, M.Collman, F.Daigle, T. L.Dawes, T.de Frates, R.Dee, N.DePartee, M.Egdorf, T.El-Hifnawi, L.Esposito, L.Farrell, C.Gala, R.Gamlin, C.Gary, A.Goldy, J.Gu, H.Hadley, K.Hawrylycz, M.Henry, A.Hill, D.Hirokawa, K. E.Huang, Z.Jo2023-11-27doi:10.1101/2023.11.25.568393Cold Spring Harbor Laboratory Press2023-11-27
<![CDATA[
Inter-individual variation of cellular and gene-expression properties of the human striatum
]]>
https://biorxiv.org/cgi/content/short/2026.03.20.713160v1?rss=1"
Burger, S.Yoo, O.Nemesh, J.Muratoglu, E.Vanderburg, C.Yuan, J.Shakir, K.Mello, C. J.Rayan, N. A.Milidantri, J.Kim, K.Drouin, S.Finn, E.Gao, H.Budnik, N.Goldman, M.Fritch, H.Genovese, G.Hogan, M.Catalini, O.Kashin, S.Rockweiler, N.Wysoker, A.Macaisa, L.Reese, L.Flowers, K.Kraft, A. W.Fleming, S. J.Coe, M.Gunaratne, R.Spina, L.Crombie, C.Mohsin, A.Kamitaki, N.Macosko, E. Z.Ichihara, K.McCarroll, S. A.2026-03-23doi:10.64898/2026.03.20.713160Cold Spring Harbor Laboratory Press2026-03-23