Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex
Open accessAbstract
Building a brain: The human brain is built in an inside-out manner as a series of layers. Although progenitor cells spin off new neurons in a seemingly organized fashion, the devil is in the details. Nowakowski et al. analyzed the transcriptomes of single cells from the developing brain to elucidate the hidden complexity of brain construction. For each cell, its position within the brain matters, as well as what type of neuron is being made at what point during overall development. These individual expression patterns result in organized diversity in the brain's cortex. Science , this issue p. 1318
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
NPAS3 is expressed in different cell types across human brain development.
“Additionally, the analysis of different databases of single-cell RNAseq in the human developing brain indicates that NPAS3 is expressed in different cell types across development (Nowakowski et al. 2017; Velmeshev et al. 2023; supplementary fig. S13e and f, Supplementary Material online).”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Nowakowski et al. 2017
The paper’s account of its single-cell RNA-seq analysis describes multiple cell types and developmental stages, but it does not report NPAS3 expression in those cells. Searches of our copy for “NPAS3” and for NPAS3 expression across developing-brain cell types found no passage addressing the gene-specific claim. (LLM, conf=0.72)
Experimental — accuracy not yet measuredIn the first postconceptional weeks, NPAS3 is expressed in radial glia cells, interneurons derived from ganglionic eminence, astrocytes, and intermediate progenitors; during later stages it is expressed in astrocytes, excitatory and inhibitory neurons.
“However, in the first postconceptional weeks, it is expressed in radial glia cells (RG), interneurons derived from ganglionic eminence (INT-CTX-GE), astrocytes, and Intermediate Progenitors (IPC [supplementary fig. S13e, Supplementary Material online; Nowakowski et al. 2017]); during later stages it is expressed in astrocytes, excitatory and inhibitory neurons (supplementary fig. S11f, Supplementa”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Nowakowski et al. 2017
Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredContinuous trajectories appear in brain development and in adult differentiating populations, including oligodendrocyte lineage cells and newborn dentate gyrus granule cells.
“Continuous trajectories occur during brain development (Nowakowski et al., 2017) and in differentiating cell populations in the adult, such as oligodendrocyte lineage cells (Marques et al., 2016) or newborn granule cells in the dentate gyrus of the hippocampus (Habib et al., 2016).”
From Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes (2021) · cites this paper as Nowakowski et al., 2017
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
WGCNA: an R package for weighted correlation network analysis
Langfelder, P., & Horvath, S. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-559 · Cited by 27,252 · see citing works
Specification of Cerebral Cortical Areas
Rakic, P. (1988) · Science · doi:10.1126/science.3291116 · Cited by 3,127 · see citing works
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124 · see citing works
Adult mouse cortical cell taxonomy revealed by single cell transcriptomics
Tasic, B., Menon, V., Nguyen, T. N., Kim, T. K., Jarsky, T., Yao, Z., Levi, B., Gray, L. T., Sorensen, S. A., Dolbeare, T., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4216 · Cited by 1,714 · see citing works
Transcriptional landscape of the prenatal human brain
Miller, J. A., Ding, S.-L., Sunkin, S. M., Smith, K. A., Ng, L., Szafer, A., Ebbert, A., Riley, Z. L., Royall, J. J., Aiona, K., et al. (2014) · Nature · doi:10.1038/nature13185 · Cited by 1,325 · see citing works
Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics
Shekhar, K., Lapan, S. W., Whitney, I. E., Tran, N. M., Macosko, E. Z., Kowalczyk, M., Adiconis, X., Levin, J. Z., Nemesh, J., Goldman, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.07.054 · Cited by 1,176 · see citing works
Rakic, P. (1974) · Science · doi:10.1126/science.183.4123.425 · Cited by 1,161 · see citing works
Development of the human cerebral cortex: Boulder Committee revisited
Bystron, I., Blakemore, C., & Rakic, P. (2008) · Nature Reviews Neuroscience · doi:10.1038/nrn2252 · Cited by 977 · see citing works
Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain
Lake, B. B., Ai, R., Kaeser, G. E., Salathia, N. S., Yung, Y. C., Liu, R., Wildberg, A., Gao, D., Fung, H.-L., Chen, S., et al. (2016) · Science · doi:10.1126/science.aaf1204 · Cited by 957 · see citing works
Pollen, A. A., Nowakowski, T. J., Shuga, J., Wang, X., Leyrat, A. A., Lui, J. H., Li, N., Szpankowski, L., Fowler, B., Chen, P., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2967 · Cited by 920 · see citing works
Self-citationMolecular Identity of Human Outer Radial Glia during Cortical Development
Pollen, A. A., Nowakowski, T. J., Chen, J., Retallack, H., Sandoval-Espinosa, C., Nicholas, C. R., Shuga, J., Liu, S. J., Oldham, M. C., Diaz, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.004 · Cited by 908 · see citing works
Self-citationThe origin and evolution of cell types
Arendt, D., Musser, J. M., Baker, C. V. H., Bergman, A., Cepko, C., Erwin, D. H., Pavlicev, M., Schlosser, G., Widder, S., Laubichler, M. D., et al. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.127 · Cited by 764 · see citing works
Johnson, M. B., Kawasawa, Y. I., Mason, C. E., Krsnik, Ž., Coppola, G., Bogdanović, D., Geschwind, D. H., Mane, S. M., State, M. W., & Šestan, N. (2009) · Neuron · doi:10.1016/j.neuron.2009.03.027 · Cited by 603 · see citing works
Weissman, T. A., Riquelme, P. A., Ivic, L., Flint, A. C., & Kriegstein, A. R. (2004) · Neuron · doi:10.1016/j.neuron.2004.08.015 · Cited by 579 · see citing works
Self-citationREGIONALIZATION OF THE PROSENCEPHALIC NEURAL PLATE
Rubenstein, J. L. R., Shimamura, K., Martı́nez, S., & Puelles, L. (1998) · Annual Review of Neuroscience · doi:10.1146/annurev.neuro.21.1.445 · Cited by 546 · see citing works
Do cortical areas emerge from a protocortex?
O'Leary, D. D. M. (1989) · Trends in Neurosciences · doi:10.1016/0166-2236(89)90080-5 · Cited by 536 · see citing works
Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells
Nowakowski, T. J., Pollen, A. A., Di Lullo, E., Sandoval-Espinosa, C., Bershteyn, M., & Kriegstein, A. R. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.03.012 · Cited by 529 · see citing works
Self-citationThe Postnatal Development of the Human Cerebral Cortex
Conel, J. L. (1960) · The American Journal of the Medical Sciences · doi:10.1097/00000441-196001000-00020 · Cited by 472 · see citing works
Zeng, H., Shen, E. H., Hohmann, J. G., Oh, S. W., Bernard, A., Royall, J. J., Glattfelder, K. J., Sunkin, S. M., Morris, J. A., Guillozet-Bongaarts, A. L., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.052 · Cited by 426 · see citing works
Rice, D. S., Sheldon, M., D’Arcangelo, G., Nakajima, K., Goldowitz, D., & Curran, T. (1998) · Development · doi:10.1242/dev.125.18.3719 · Cited by 378 · see citing works
A comprehensive transcriptional map of primate brain development
Bakken, T. E., Miller, J. A., Ding, S., Sunkin, S. M., Smith, K. A., Ng, L., Szafer, A., Dalley, R. A., Royall, J. J., Lemon, T. A., et al. (2016) · Nature · doi:10.1038/nature18637 · Cited by 376 · see citing works
Nowakowski, T. J., Pollen, A. A., Sandoval-Espinosa, C., & Kriegstein, A. R. (2016) · Neuron · doi:10.1016/j.neuron.2016.09.005 · Cited by 346 · see citing works
Self-citationSingle-cell analysis of long non-coding RNAs in the developing human neocortex
Liu, S. J., Nowakowski, T. J., Pollen, A. A., Lui, J. H., Horlbeck, M. A., Attenello, F. J., He, D. X., Weissman, J. S., Kriegstein, A. R., Diaz, A. A., et al. (2016) · Genome biology · doi:10.1186/s13059-016-0932-1 · Cited by 345 · see citing works
Self-citationTelley, L., Govindan, S., Prados, J., Stévant, I., Nef, S., Dermitzakis, E. T., Dayer, A. G., & Jabaudon, D. (2016) · Science · doi:10.1126/science.aad8361 · Cited by 330 · see citing works
Mirzaa, G., Campbell, C., Solovieff, N., Goold, C. P., Jansen, L., Menon, S., Timms, A., Conti, V., Biag, J., Adams, C., et al. (2016) · JAMA Neurology · doi:10.1001/jamaneurol.2016.0363 · Cited by 246 · see citing works
Self-citationBrain Mechanisms for Directed Attention
Mountcastle, V. B. (1978) · Journal of the Royal Society of Medicine · doi:10.1177/014107687807100105 · Cited by 237 · see citing works
Fixed single-cell transcriptomic characterization of human radial glial diversity
Thomsen, E. R., Mich, J. K., Yao, Z., Hodge, R. D., Doyle, A. M., Jang, S., Shehata, S. I., Nelson, A. M., Shapovalova, N. V., Levi, B. P., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3629 · Cited by 227 · see citing works
Generality of the functional structure of the neocortex
Creutzfeldt, O. D. (1977) · Die Naturwissenschaften · doi:10.1007/bf00483547 · Cited by 206 · see citing works
Hedgehog signaling promotes basal progenitor expansion and the growth and folding of the neocortex
Wang, L., Hou, S., & Han, Y.-G. (2016) · Nature Neuroscience · doi:10.1038/nn.4307 · Cited by 190 · see citing works
Cntnap4 differentially contributes to GABAergic and dopaminergic synaptic transmission
Karayannis, T., Au, E., Patel, J. C., Kruglikov, I., Markx, S., Delorme, R., Héron, D., Salomon, D., Glessner, J., Restituito, S., et al. (2014) · Nature · doi:10.1038/nature13248 · Cited by 183 · see citing works
A role for Sonic hedgehog in axon-to-astrocyte signalling in the rodent optic nerve
Wallace, V. A., & RAFF, M. C. (1999) · Development · doi:10.1242/dev.126.13.2901 · Cited by 177 · see citing works
Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex
Lui, J. H., Nowakowski, T. J., Pollen, A. A., Javaherian, A., Kriegstein, A. R., & Oldham, M. C. (2014) · Nature · doi:10.1038/nature13973 · Cited by 166 · see citing works
Self-citationInactivation of mTORC1 in the Developing Brain Causes Microcephaly and Affects Gliogenesis
Cloëtta, D., Thomanetz, V., Baranek, C., Lustenberger, R. M., Lin, S., Oliveri, F., Atanasoski, S., & Rüegg, M. A. (2013) · Journal of Neuroscience · doi:10.1523/jneurosci.3294-12.2013 · Cited by 145 · see citing works
A network of heterochronic genes including Imp1 regulates temporal changes in stem cell properties
Nishino, J., Kim, S., Zhu, Y., Zhu, H., & Morrison, S. J. (2013) · eLife · doi:10.7554/elife.00924 · Cited by 123 · see citing works
Selective cortical interneuron and GABA deficits in cyclin D2-null mice
Glickstein, S. B., Moore, H., Slowinska, B., Racchumi, J., Suh, M., Chuhma, N., & Ross, M. E. (2007) · Development · doi:10.1242/dev.008524 · Cited by 89 · see citing works
Ten-m2 Is Required for the Generation of Binocular Visual Circuits
Young, T. R., Bourke, M. J., Zhou, X., et al. (2013) · Journal of Neuroscience · doi:10.1523/jneurosci.4708-12.2013 · Cited by 71 · see citing works
Lmo4 Establishes Rostral Motor Cortex Projection Neuron Subtype Diversity
Cederquist, G., Azim, E., Shnider, S. J., Padmanabhan, H. K., & Macklis, J. D. (2013) · Journal of Neuroscience · doi:10.1523/jneurosci.5140-12.2013 · Cited by 71 · see citing works
Conel, J. L. (1939) · Harvard University Press eBooks · doi:10.4159/harvard.9780674187641 · Cited by 37 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [11]Bayer SA Altman J Neocortical Development Raven Press 1991
Cited by
Sorted by citations
Satterstrom, F. K., Kosmicki, J. A., Wang, J., Breen, M. S., De Rubeis, S., An, J.-Y., Peng, M., Collins, R., Grove, J., Klei, L., et al. (2020) · Cell · doi:10.1016/j.cell.2019.12.036 · Cited by 2,321 · see citing works
“(D) The cumulative number of ASD-associated genes expressed in RNA-seq dat (Nowakowski et al., 2017).”
BackgroundMethodInfluentialSelf-citationTranscriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Maynard, K. R., Collado-Torres, L., Weber, L. M., Uytingco, C., Barry, B. K., Williams, S. R., Catallini, J. L., Tran, M. N., Besich, Z., Tippani, M., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00787-0 · Cited by 1,222 · see citing works
Individual brain organoids reproducibly form cell diversity of the human cerebral cortex
Velasco, S., Kedaigle, A. J., Simmons, S. K., Nash, A., Rocha, M., Quadrato, G., Paulsen, B., Nguyen, L., Adiconis, X., Regev, A., et al. (2019) · Nature · doi:10.1038/s41586-019-1289-x · Cited by 1,094 · see citing works
Single-cell genomics identifies cell type–specific molecular changes in autism
Velmeshev, D., Schirmer, L., Jung, D., Haeussler, M., Perez, Y., Mayer, S., Bhaduri, A., Goyal, N., Rowitch, D. H., & Kriegstein, A. R. (2019) · Science · doi:10.1126/science.aav8130 · Cited by 927 · see citing works
Self-citationIntegrative functional genomic analysis of human brain development and neuropsychiatric risks
Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., et al. (2018) · Science · doi:10.1126/science.aat7615 · Cited by 810 · see citing works
Self-citationEstablishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Pollen, A. A., Bhaduri, A., Andrews, M. G., Nowakowski, T. J., Meyerson, O. S., Mostajo-Radji, M. A., Di Lullo, E., Alvarado, B., Bedolli, M., Dougherty, M. L., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.017 · Cited by 600 · see citing works
Self-citationHuman-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis
Fiddes, I. T., Lodewijk, G. A., Mooring, M., Bosworth, C. M., Ewing, A. D., Mantalas, G. L., Novak, A. M., van den Bout, A., Bishara, A., Rosenkrantz, J. L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.051 · Cited by 595 · see citing works
Self-citationA Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation
Polioudakis, D., de la Torre-Ubieta, L., Langerman, J., Elkins, A. G., Shi, X., Stein, J. L., Vuong, C. K., Nichterwitz, S., Gevorgian, M., Opland, C. K., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.06.011 · Cited by 513 · see citing works
Molecular architecture of the developing mouse brain
La Manno, G., Siletti, K., Furlan, A., Gyllborg, D., Vinsland, E., Mossi Albiach, A., Mattsson Langseth, C., Khven, I., Lederer, A. R., Dratva, L. M., et al. (2021) · Nature · doi:10.1038/s41586-021-03775-x · Cited by 563 · see citing works
Trevino, A. E., Müller, F., Andersen, J., Sundaram, L., Kathiria, A., Shcherbina, A., Farh, K., Chang, H. Y., Pașca, A. M., Kundaje, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.07.039 · Cited by 478 · see citing works
Inherited and de novo genetic risk for autism impacts shared networks
Ruzzo, E. K., Pérez-Cano, L., Jung, J.-Y., Wang, L.-K., Kashef-Haghighi, D., Hartl, C., Singh, C., Xu, J., Hoekstra, J. N., Leventhal, O., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.015 · Cited by 457 · see citing works
Maturation and circuit integration of transplanted human cortical organoids
Revah, O., Gore, F., Kelley, K. W., Andersen, J., Sakai, N., Chen, X., Li, M.-Y., Birey, F., Yang, X., Saw, N. L., et al. (2022) · Nature · doi:10.1038/s41586-022-05277-w · Cited by 504 · see citing works
Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex
Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., Bartolini, G., Vitali, I., Cadilhac, C., Hippenmeyer, S., et al. (2019) · Science · doi:10.1126/science.aav2522 · Cited by 423 · see citing works
Development and arealization of the cerebral cortex
Cadwell, C. R., Bhaduri, A., Mostajo-Radji, M. A., Keefe, M. G., & Nowakowski, T. J. (2019) · Neuron · doi:10.1016/j.neuron.2019.07.009 · Cited by 408 · see citing works
Self-citationDevelopment of prefrontal cortex
Kolk, S. M., & Rakic, P. (2022) · Neuropsychopharmacology · doi:10.1038/s41386-021-01137-9 · Cited by 378 · see citing works
Innovations present in the primate interneuron repertoire
Krienen, F. M., Goldman, M., Zhang, Q., C. H. del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2781-z · Cited by 381 · see citing works
Innovations in Primate Interneuron Repertoire
Krienen, F. M., Goldman, M., Zhang, Q., del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2019) · doi:10.1101/709501 · Cited by 372 · see citing works
Corces, M. R., Shcherbina, A., Kundu, S., Gloudemans, M. J., Frésard, L., Granja, J. M., Louie, B. H., Eulalio, T., Shams, S., Bagdatli, S. T., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-00721-x · Cited by 358 · see citing works
In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes
Jin, X., Simmons, S. K., Guo, A., Shetty, A. S., Ko, M., Nguyen, L., Jokhi, V., Robinson, E., Oyler, P., Curry, N., et al. (2020) · Science · doi:10.1126/science.aaz6063 · Cited by 317 · see citing works
Inferring and perturbing cell fate regulomes in human brain organoids
Fleck, J. S., Jansen, S. M. J., Wollny, D., Zenk, F., Seimiya, M., Jain, A., Okamoto, R., Santel, M., He, Z., Camp, J. G., et al. (2023) · Nature · doi:10.1038/s41586-022-05279-8 · Cited by 315 · see citing works
Sey, N. Y. A., Hu, B., Mah, W., Fauni, H., McAfee, J. C., Rajarajan, P., Brennand, K. J., Akbarian, S., & Won, H. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0603-0 · Cited by 297 · see citing works
Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes
Armand, E. J., Li, J., Xie, F., Luo, C., & Mukamel, E. A. (2021) · Neuron · doi:10.1016/j.neuron.2020.12.010 · Cited by 241 · see citing works
Chromatin accessibility dynamics in a model of human forebrain development
Trevino, A. E., Sinnott-Armstrong, N., Andersen, J., Yoon, S.-J., Huber, N., Pritchard, J. K., Chang, H. Y., Greenleaf, W. J., & Pașca, S. P. (2020) · Science · doi:10.1126/science.aay1645 · Cited by 251 · see citing works
Deconstructing cortical folding: genetic, cellular and mechanical determinants
Llinares-Benadero, C., & Borrell, V. (2019) · Nature Reviews Neuroscience · doi:10.1038/s41583-018-0112-2 · Cited by 243 · see citing works
Single-cell analysis of prenatal and postnatal human cortical development
Velmeshev, D., Perez, Y., Yan, Z., Valencia, J. E., Castaneda-Castellanos, D. R., Wang, L., Schirmer, L., Mayer, S., Wick, B., Wang, S., et al. (2023) · Science · doi:10.1126/science.adf0834 · Cited by 204 · see citing works
Self-citationLong, K. R., Newland, B., Florio, M., Kalebic, N., Langen, B., Kolterer, A., Wimberger, P., & Huttner, W. B. (2018) · Neuron · doi:10.1016/j.neuron.2018.07.013 · Cited by 196 · see citing works
Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development
Nowakowski, T. J., Rani, N., Golkaram, M., Zhou, H. R., Alvarado, B., Huch, K., West, J. A., Leyrat, A., Pollen, A. A., Kriegstein, A. R., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0265-3 · Cited by 166 · see citing works
Self-citationDevelopmental mechanisms underlying the evolution of human cortical circuits
Vanderhaeghen, P., & Polleux, F. (2023) · Nature Reviews Neuroscience · doi:10.1038/s41583-023-00675-z · Cited by 173 · see citing works
Tropism of SARS-CoV-2 for human cortical astrocytes
Andrews, M. G., Mukhtar, T., Eze, U. C., Simoneau, C. R., Ross, J., Parikshak, N., Wang, S., Zhou, L., Koontz, M., Velmeshev, D., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2122236119 · Cited by 159 · see citing works
Self-citationAmplification of human interneuron progenitors promotes brain tumors and neurological defects
Eichmüller, O. L., Corsini, N. S., Vértesy, Á., Morassut, I., Scholl, T., Gruber, V.-E., Peer, A. M., Chu, J., Novatchkova, M., Hainfellner, J. A., et al. (2022) · Science · doi:10.1126/science.abf5546 · Cited by 163 · see citing works
Notaras, M., Lodhi, A., Dündar, F., Collier, P., Sayles, N. M., Tilgner, H., Greening, D., & Colak, D. (2022) · Molecular Psychiatry · doi:10.1038/s41380-021-01316-6 · Cited by 150 · see citing works
Sestan, N., & State, M. W. (2018) · Neuron · doi:10.1016/j.neuron.2018.10.015 · Cited by 127 · see citing works
Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases
Fleck, J. S., Sanchís-Calleja, F., He, Z., Santel, M., Boyle, M. J., Camp, J. G., & Treutlein, B. (2021) · Cell Stem Cell · doi:10.1016/j.stem.2021.02.015 · Cited by 118 · see citing works
Three-dimensional genome rewiring in loci with human accelerated regions
Keough, K. C., Whalen, S., Inoue, F., Przytycki, P. F., Fair, T., Deng, C., Steyert, M., Ryu, H., Lindblad-Toh, K., Karlsson, E., et al. (2023) · Science · doi:10.1126/science.abm1696 · Cited by 113 · see citing works
Self-citationHerrero-Navarro, Á., Puche-Aroca, L., Moreno-Juan, V., Sempere-Ferràndez, A., Espinosa, A., Susín, R., Torres-Masjoan, L., Leyva-Díaz, E., Karow, M., Figueres-Oñate, M., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe8978 · Cited by 117 · see citing works
Single cell transcriptomics in neuroscience: cell classification and beyond
Tasic, B. (2018) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2018.04.021 · Cited by 83 · see citing works
Rosebrock, D., Arora, S., Mutukula, N., Volkman, R., Gralinska, E., Balaskas, A., Aragonés Hernández, A., Buschow, R., Brändl, B., Müller, F.-J., et al. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00929-5 · Cited by 89 · see citing works
Cellular and Molecular Mechanisms Linking Human Cortical Development and Evolution
Libé-Philippot, B., & Vanderhaeghen, P. (2021) · Annual Review of Genetics · doi:10.1146/annurev-genet-071719-020705 · Cited by 78 · see citing works
Peng, T., Ma, X., Hua, W., Wang, C., Chu, Y., Sun, M., Fermi, V., Hamelmann, S., Lindner, K., Shao, C., et al. (2025) · Cell Stem Cell · doi:10.1016/j.stem.2025.01.002 · Cited by 86 · see citing works
Satterstrom, F. K., Kosmicki, J. A., Wang, J., Breen, M. S., De Rubeis, S., An, J.-Y., Peng, M., Collins, R., Grove, J., Klei, L., et al. (2018) · doi:10.1101/484113 · Cited by 2,323 · see citing works
“Here, we exploit the 99 ASD-associated genes to perform a more 8 direct assessment, leveraging existing single-cell RNA-seq data from 4,261 cells collected from 9 the prenatal human cortex (82), ranging from 6 to 37 post-conception weeks (pcw) with an 10 average of 16.”
BackgroundMethodInfluentialSelf-citationReview of multi-omics data resources and integrative analysis for human brain disorders
Dong, X., Liu, C., & Dozmorov, M. (2021) · Briefings in Functional Genomics · doi:10.1093/bfgp/elab024 · Cited by 47 · see citing works
Zimmer, T. S., Broekaart, D. W. M., Gruber, V.-E., van Vliet, E. A., Mühlebner, A., & Aronica, E. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.01028 · Cited by 48 · see citing works
Micali, N., Kim, S.-K., Diaz-Bustamante, M., Stein-O’Brien, G., Seo, S., Shin, J.-H., Rash, B. G., Ma, S., Wang, Y., Olivares, N. A., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107599 · Cited by 31 · see citing works
Funk, O. H., Qalieh, Y., Doyle, D. Z., Lam, M. M., & Kwan, K. Y. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2116956119 · Cited by 33 · see citing works
Single cell epigenomic atlas of the developing human brain and organoids
Ziffra, R. S., Kim, C. N., Wilfert, A., Turner, T. N., Haeussler, M., Casella, A. M., Przytycki, P. F., Kreimer, A., Pollard, K. S., Ament, S. A., et al. (2019) · doi:10.1101/2019.12.30.891549 · Cited by 33 · see citing works
Self-citationA community-based transcriptomics classification and nomenclature of neocortical cell types
Yuste, R., Hawrylycz, M., Aalling, N., Aguilar-Valles, A., Arendt, D., Armañanzas, R., Ascoli, G. A., Bielza, C., Bokharaie, V., Bergmann, T. B., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0685-8 · Cited by 32 · see citing works
García-Cabezas, M. Á., Barbas, H., & Zikopoulos, B. (2018) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2018.00070 · Cited by 30 · see citing works
Molecular Logic of Cellular Diversification in the Mammalian Cerebral Cortex
Di Bella, D. J., Habibi, E., Yang, S.-M., Stickels, R. R., Brown, J., Yadollahpour, P., Chen, F., Macosko, E. Z., Regev, A., & Arlotta, P. (2020) · doi:10.1101/2020.07.02.185439 · Cited by 20 · see citing works
Caporale, A. L., Cinalli, A. R., Rubinstein, M., & Franchini, L. F. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae186 · Cited by 7 · see citing works
“Additionally, the analysis of different databases of single-cell RNAseq in the human developing brain indicates that NPAS3 is expressed in different cell types across development (Nowakowski et al. 2017; Velmeshev et al. 2023; supplementary fig.”
BackgroundHuman-specific genetic hallmarks in neocortical development: focus on neural progenitors
Tynianskaia, L., & Heide, M. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102267 · Cited by 8 · see citing works
- Authors
- Nowakowski, T. J., Bhaduri, A., Pollen, A. A., Alvarado, B., Mostajo-Radji, M. A., Di Lullo, E., Haeussler, M., Sandoval-Espinosa, C., Liu, S. J., Velmeshev, D., Ounadjela, J. R., Shuga, J., Wang, X., Lim, D. A., West, J. A., Leyrat, A. A., Kent, W. J., & Kriegstein, A. R.
- Affiliations
- University of California, San Francisco (US)
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
- University of California, Santa Cruz (US)
- Standard BioTools (United States) (US)
- Corresponding author
- Nowakowski, Tomasz J.
- Bhaduri, Aparna
- Pollen, Alex A.
- Kriegstein, Arnold R.
- ORCID
- Venue
- Science
- Published
- 2017-12-08
- Volume
- 358
- Issue
- 6368
- Pages
- 1318-1323
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC5991609
- OpenAlex
- W2772624269
- Semantic Scholar
- f6dfb471168febb2c0e2eeb9f9852360047e19ae
- Cited by
- 964
- References
- 38
- Citations by year
- 2026: 88 · 2025: 94 · 2024: 102 · 2023: 139 · 2022: 110 · 2021: 153 · 2020: 128 · 2019: 96 · 2018: 53
- FWCI
- 32.07
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health (R01NS091544)
- Damon Runyon Cancer Research Foundation (DRG-2166-13)
- NIH (U01MH105989, R35NS097305)
- Topics
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- cortical development, neurogenesis, cell type diversity, mTOR signaling, outer radial glia, cortical topography, lineage-specific gene expression
- MeSH terms
- Cerebral Cortex, Humans, Neuroglia, Neurons, Telencephalon, Gene Expression Regulation, Developmental, Neurogenesis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
