Publications | Nowakowski Lab

For a complete list, see UCSF Profile or PubMed.

Preprints

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
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
Wang, B.; Vartak, R.; Zaltsman, Y.; Naing, Z. Z. C.; Hennick, K. M., et al. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv https://doi.org/10.1101/2023.12.03.569805

Jeong D, et al. Multidimensional profiling of heterogeneity in supratentorial ependymomas. Nature. 2026 Mar 11. doi: 10.1038/s41586-026-10214-2. Online ahead of print. PMID: 41813893
Graham AJ, et al. Stress-relaxing granular bioprinting materials enable complex and uniform organoid self-organization. Nat Mater. 2026 Mar 10. doi: 10.1038/s41563-026-02519-4. Online ahead of print. PMID: 41807773
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
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. Epub 2026 Jan 21. PMID: 41565813

Keefe MG*, Steyert MR*, Nowakowski TJ. Lineage-resolved atlas of the developing human cortex. Nature. 2025. PMID: 41193842
Nowakowski TJ, et al. The new frontier in understanding human and mammalian brain development. Nature. 2025. PMID: 41193845
Yu D, Jain S, et al. Microglia regulate GABAergic neurogenesis in prenatal human brain through IGF1. Nature. 2025. PMID: 40770097
Steyert MR, Li T, Piao X, Nowakowski TJ. Molecular Signatures in Cortical Development. Annu Rev Neurosci. 2025. PMID: 40670292
Furlanis E, et al. An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes. Neuron. 2025. PMID: 40403705
Wu SR, Nowakowski TJ. Exploring human brain development and disease using assembloids. Neuron. 2025. PMID: 40107269
Teter OM, et al. CRISPRi-based screen of autism spectrum disorder risk genes in microglia. Mol Psychiatry. 2025. PMID: 40188316
Teerikorpi N, et al. Ciliary biology intersects autism and congenital heart disease. Development. 2025. PMID: 40552535
Elliott MAT, Andrews JP, et al. Microscale maps of bursting dynamics across human hippocampal slices. J Neurophysiol. 2025. PMID: 41385612

Andrews JP, et al. Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices. Nature Neuroscience. 2024. PMID: 39548326
Lee AT, Chang EF, Paredes MF, Nowakowski TJ. Large-scale neurophysiology and single-cell profiling in human neuroscience. Nature. 2024. PMID: 38898291
Heffel MG, et al. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature. 2024. doi: 10.1038/s41586-024-08030-7
Deng C, et al. Massively parallel characterization of regulatory elements in the developing human cortex. Science. 2024. PMID: 38781390
Shin D, Kim CN, et al. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion. Cell Stem Cell. 2024. PMID: 38382530
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
Escoubas CC, et al. Type-I-interferon-responsive microglia shape cortical development and behavior. Cell. 2024. doi: 10.1016/j.cell.2024.02.020
Adameyko I, et al. Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity in the nervous system. Nat Neurosci. 2024. PMID: 39627588
Barnett SN, et al. An organotypic atlas of human vascular cells. Nat Med. 2024. PMID: 39566559

Kim CN, Shin D, Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. Science. 2023. doi: 10.1126/science.adf9941
Popova G, et al. Rubella virus tropism and single cell responses in human primary tissue and microglia-containing organoids. eLife. 2023. PMID: 37470786
Schneider A, et al. Transcriptomic cell type structures in vivo neuronal activity across multiple timescales. Cell Rep. 2023. doi: 10.1016/j.celrep.2023.112318

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
Delgado RN, et al. Individual human cortical progenitors can produce excitatory and inhibitory neurons. Nature. 2022. PMID: 34912114
Wu Z*, Chhun BB*, Popova G*, Kim CN, et al. DynaMorph: learning morphodynamic states of human cells. Mol Biol Cell. 2022.
Nowakowski TJ, Salama SR. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells. 2022.

Ziffra RS, Kim CN, et al. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021. PMID: 34616060
Popova G, et al. Human microglia states are conserved across experimental models and regulate neural stem cell responses. Cell Stem Cell. 2021. PMID: 34536354
Willsey HR, et al. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis. Neuron. 2021. PMID: 33887193
Speir ML, et al. UCSC Cell Browser: Visualize Your Single-Cell Data. Bioinformatics. 2021. PMID: 34244710

Ross JM, Kim C, et al. The Expanding Cell Diversity of the Brain Vasculature. Front Physiol. 2020. PMID: 33343397
Guo SM, et al. Revealing architectural order with quantitative label-free imaging and deep learning. Elife. 2020. PMID: 32716843
Keefe MG, Nowakowski TJ. Evolutionary Expansion of Human Cerebellar Germinal Zones. Trends Neurosci. 2020. PMID: 31954525

Cadwell CR, Bhaduri A, et al. Development and Arealization of the Cerebral Cortex. Neuron. 2019. PMID: 31557462
Andrews MG, Nowakowski TJ. Human brain development through the lens of cerebral organoid models. Brain Research. 2019. PMID: 31542572

Bhaduri A, Nowakowski TJ. Single-cell sequencing paints diverse pictures of the brain. Nature. 2018. PMID: 30382219
Nowakowski TJ. Building blocks of the human brain. Science. 2018. PMID: 30309940
Kosik KS, Nowakowski T. Evolution of New miRNAs and Cerebro-Cortical Development. Annu Rev Neurosci. 2018. PMID: 29618285