Publications

For a complete list, see UCSF Profile or PubMed.

Preprints

  • Moriano J, Mukhtar T, et al. A multimodal interrogation of Broca's area in the pediatric and adult human brain. bioRxiv [Preprint]. 2026. doi: 10.64898/2026.07.22.739934. PMID: 42539239
  • Liu DD, et al. Isolation of postnatal human neural stem cells. bioRxiv [Preprint]. 2026. doi: 10.64898/2026.06.11.731596. PMID: 42327304
  • Suresh V*, Wigdor EM*, Hao Y*, et al. Molecular dynamics of Brodmann Area 22 in development and autism. bioRxiv [Preprint]. 2026 Apr 3:2026.03.31.715694. doi: 10.64898/2026.03.31.715694. PMCID: PMC13060142
  • Johnson HJ, et al. Optogenetic WNT signaling drives germ layer self-organization in a human gastruloid model. bioRxiv [Preprint]. 2026. doi: 10.64898/2026.02.23.707602. PMID: 42124654
  • Renne T, et al. Genetic and Cortical Cell-Type Liability Architecture of Autism. bioRxiv 2025.
  • Yuan G*, Suresh V*, Wigdor E*, Hao Y*, et al. Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism. bioRxiv 2025.
  • Alexander Aivazidis A, Memi F, et al. A spatial transcriptomic atlas of autism-associated genes identifies convergence in the developing human thalamus. bioRxiv doi: https://doi.org/10.1101/2025.11.05.685843
  • Hennick K*, Sui Y*, et al. Sex differences in the developing human cortex intersect with genetic risk of neurodevelopmental disorders. bioRxiv 2025.
  • Ding JW, Kim CN, Steyert MR, et al. Accelerated Tempo of Cortical Neurogenesis in Down Syndrome. bioRxiv 2025.
  • Schmitz MT, et al. ANTIPODE Provides a Global View of Cell Type Homology and Transcriptomic Divergence in the Developing Mammalian Brain. bioRxiv 2025.
  • David Shin,  Madeleine E. Urbanek, et al. High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing. bioRxiv doi: https://doi.org/10.1101/2024.10.01.616167

Select Publications

2026

  • Yuan et al. Spatiotemporal clonal architecture of the newborn mouse forebrain. Nature 2026 Sep 30. doi: 10.1038/s41586-026-11064-8. PMID: 42816613
  • Wang B, et al. Autism mutations rewire protein interaction networks to drive neurodevelopmental pathology. Science. 2026 Aug 27;393:eady4523. doi: 10.1126/science.ady4523. PMID: 42658940
  • Sui Y, et al. Using the linear references from the pangenome to discover missing autism variants. Nat Commun. 2026 Jan 23;17(1):1681. doi: 10.1038/s41467-026-68378-4. PMID: 41577710, PMCID: PMC12909954
  • Ding JW, et al. Dissecting gene regulatory networks governing human cortical cell fate. Nature. 2026 Mar;651(8106):732-742. doi: 10.1038/s41586-025-09997-7. PMID: 41565813, PMCID: PMC12999477 

2025

  • Keefe MG*, Steyert MR*, Nowakowski TJ. Lineage-resolved atlas of the developing human cortex. Nature. 2025. PMID: 41193842, PMCID: PMC12589122
  • Nowakowski TJ, et al. The new frontier in understanding human and mammalian brain development. Nature. 2025. PMID: 41193845, PMCID: PMC13108688
  • Yu D, Jain S, et al. Microglia regulate GABAergic neurogenesis in prenatal human brain through IGF1. Nature. 2025. PMID: 40770097, PMCID: PMC12527950
  • Steyert MR, Li T, Piao X, Nowakowski TJ. Molecular Signatures in Cortical Development. Annu Rev Neurosci. 2025. DOI: 10.1146/annurev-neuro-091823-014001 PMID: 40670292
  • Wu SR, Nowakowski TJ. Exploring human brain development and disease using assembloids. Neuron. 2025. PMID: 40107269, PMCID: PMC12022838
  • Teerikorpi N, et al. Ciliary biology intersects autism and congenital heart disease. Development. 2025. PMID: 40552535, PMCID: PMC12273630

2024

  • Andrews JP, et al. Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices. Nature Neuroscience. 2024. PMID: 39548326, PMCID: PMC11881784
  • Lee AT, Chang EF, Paredes MF, Nowakowski TJ. Large-scale neurophysiology and single-cell profiling in human neuroscience. Nature. 2024. PMID: 38898291, PMCID: PMC12049086
  • Deng C, et al. Massively parallel characterization of regulatory elements in the developing human cortex. Science. 2024. PMID: 38781390, PMCID: PMC12085231
  • Shin D, Kim CN, et al. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion. Cell Stem Cell. 2024. PMID: 38382530, PMCID: PMC10939828
  • Zhu D, et al. Optimal trade-off control in machine learning-based library design, application to AAV for gene therapy. Sci Adv. 2024. PMID: 38266077, PMCID: PMC10807795
  • Bonev B, et al. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci. 2024. PMID: 39627588, PMCID: PMC11999325

2023

  • Kim CN, Shin D, Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. Science. 2023. doi: 10.1126/science.adf9941, PMID: 37824646, PMCID: PMC10758299
  • Popova G, et al. Rubella virus tropism and single cell responses in human primary tissue and microglia-containing organoids. eLife. 2023. PMID: 37470786, PMCID: PMC10370260

2022

  • Allen DE, et al. Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes. Science. 2022. DOI: 10.1126/science.abm5224
  • Winkler EA, Kim CN, et al. Single cell atlas of the normal and malformed human brain vasculature. Science. 2022. doi: 10.1126/science.abi7377, PMID: 35587512, PMCID: PMC9233096
  • Delgado RN, et al. Individual human cortical progenitors can produce excitatory and inhibitory neurons. Nature. 2022. PMID: 34912114, PMCID: PMC8994470

2021

  • Ziffra RS, Kim CN, et al. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021. PMID: 34616060, PMCID: PMC8494642
  • Popova G, et al. Human microglia states are conserved across experimental models and regulate neural stem cell responses. Cell Stem Cell. 2021. PMID: 34536354, PMCID: PMC8642295

2019

  • Cadwell CR, Bhaduri A, et al. Development and Arealization of the Cerebral Cortex. Neuron. 2019. PMID: 31557462, PMCID: PMC9245854