Preprints
Wang, B.; Vartak, R.; Zaltsman, Y.; Naing, Z. Z. C.; Hennick, K. M.; Polacco, B. J.; Bashir, A.; Eckhardt, M.; Bouhaddou, M.; Xu, J.; Sun, N.; Lasser, M.; Zhou, Y.; Guiley, K. Z.; Chan, U.; Kaye, J. A.; Khare, P.; Drake, S.; Drury, V.; Burke, D. F.; Gonzalez, S.; Alkhairy, S.; Morris, M.; Baum, T.; Krasnoff, R.; Wang, S.; Pham, P.; Arbalaez, J.; Pratt, D.; Chag, S.; Rolland, T.; Bourgeron, T.; Finkbeiner, S.; Bandyopadhay, S.; Ideker, T.; Beltrao, P.; Willsey, H. R.; Obernier, K.; Nowakowski, T. J.; Huttenhain, R.; State, M. W.; Willsey, A. J.; Krogan, N. J. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv https://doi.org/10.1101/2023.12.03.569805
Deng, Chengyu, Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F. Przytycki, Fumitaka Inoue, Daniela Alves Pereira, et al. 2023. “Massively Parallel Characterization of Psychiatric Disorder-Associated and Cell-Type-Specific Regulatory Elements in the Developing Human Cortex.” bioRxiv. https://doi.org/10.1101/2023.02.15.528663.
Heffel MG, Zhou J, Zhang Y, Lee DL, Hou K, Pastor O, Abuhanna K, Schmitt AD, Li T, Haeussler M, Wick B, Zhang M, Xie F, Ziffra RS, Mukamel EA, Eskin E, Pasaniuc B, Ecker JR, Dixon J, Nowakowski TJ, Paredes MF, Luo C. Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus. doi: https://doi.org/10.1101/2022.10.07.511350
2024
Shin D, Kim CN, Ross J, Hennick KM, Wu SR, Paranjape N, Leonard R, Wang JC, Keefe MG, Pavlovic BJ, Donohue KC, Moreau C, Wigdor EM, Larson HH, Allen DE, Cadwell CR, Bhaduri A, Popova G, Bearden CE, Pollen AA, Jacquemont S, Sanders SJ, Haussler D, Wiita AP, Frost NA, Sohal VS, Nowakowski TJ. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell 2024 Feb 13:S1934-5909(24)00040-7. doi: 10.1016/j.stem.2024.01.010. PMID: 38382530 Preview by Leyva-Díaz E., Wilson ES., López-Bendito G. Development has the answer: Unraveling psychiatric disorders via thalamocortical organoids. Cell Stem Cell 2024 DOI:https://doi.org/10.1016/j.stem.2024.02.008
Zhu D, Brookes DH, Busia A, Carneiro A, Fannjiang C, Popova G, Shin D, Donohue KC, Lin LF, Miller ZM, Williams ER, Chang EF, Nowakowski TJ, Listgarten J, Schaffer DV. Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy. Sci Adv. 2024 Jan 26;10(4):eadj3786. doi: 10.1126/sciadv.adj3786. Epub 2024 Jan 24. PMID: 38266077
2023
Kim CN, Shin D, Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. Science 2023 Oct 13;382(6667):eadf9941. doi: 10.1126/science.adf9941.
Popova G, Retallack H, Kim CN, Shin D, Wang A, DeRisi JJ, Nowakowski TJ. Rubella virus tropism and single cell responses in human primary tissue and microglia-containing organoids. eLife 12:RP87696 (2023) doi: https://doi.org/10.1101/2022.10.24.513565; PMID: 37470786
Preview by Epifanova E. and Nguyen L. Brain Development: The dangers of rubella virus. eLife https://doi.org/10.7554/eLife.89265
Schneider A, Azabou M, McDougall-Vigier L, Parks DF, Ensley S, Bhaskaran-Nair K, Nowakowski T, Dyer EL, Hengen KB. Transcriptomic cell type structures in vivo neuronal activity across multiple timescales. Cell Rep. 2023 Mar 29; 42(4):112318. doi: 10.1016/j.celrep.2023.112318.
2022
Nowakowski TJ, Salama SR. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells. 2022 DOI: https://doi.org/10.3390/cells11182803
Allen DE, Donohue KC, Cadwell CR, Shin D, Keefe MG, Sohal VS, Nowakowski TJ. Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes. Science 2022 DOI: 10.1126/science.abm5224
Wu Z*, Chhun BB*, Popova G*, Kim CN, Yeh LH, Nowakowski TJ**, Zou J**, Mehta SB**. DynaMorph: learning morphodynamic states of human cells with live imaging and sc-RNAseq. Molecular Biology of the Cell 2022 DOI: 10.1091/mbc.E21-11-0561
Winkler EA, Kim CN, Ross JM, Garcia JH, Gil E, Oh I, Chen LQ, Wu D, Catapano JS, Raygor K, Narsinh K, Kim H, Weinsheimer S, Coole DL, Walcott BP, Lawton MT, Gupta N, Zlokovic BV, Chang EF, Abla AA, Lim DA, Nowakowski TJ. Single cell atlas of the normal and malformed human brain vasculature. Science 2022. eabi7377. doi: 10.1126/science.abi7377.
Delgado RN, Allen DE, Keefe MG, Mancia Leon WR, Ziffra RS, Crouch EE, Alvarez-Buylla A, Nowakowski TJ. Individual human cortical progenitors can produce excitatory and inhibitory neurons. Nature. 2022; PMID: 34912114
Bandler RC, Vitali I, Delgado RN, Ho MC, Dvoretskova E, Ibarra Molinas JS, Frazel PW, Mohammadkhani M, Machold R, Maedler S, Liddelow SA, Nowakowski TJ, Fishell G, Mayer C. Single-cell delineation of lineage and genetic identity in the mouse brain. Nature. 2022 PMID: 34912118
STICR Libraries are now on Addgene - Pooled Library #180483, #186334, #186335
2021
Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021 Oct;598(7879):205-213. PMID: 34616060
Popova G, Soliman SS, Kim CN, Keefe MG, Hennick KM, Jain S, Li T, Tejera D, Shin D, Chhun BB, McGinnis CS, Speir M, Gartner ZJ, Mehta SB, Haeussler M, Hengen KB, Ransohoff RR, Piao X, Nowakowski TJ. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids Cell Stem Cell. 2021 Sep 16;S1934-5909(21)00376-3. PMID: 34536354
Preview by Bennett ML, Song H, Ming GL. Microglia modulate neurodevelopment in human neuroimmune organoids. Cell Stem Cell 28, December 2, 2021; https://doi.org/10.1016/j.stem.2021.11.005
Ly VT, Baudin PV, Pansodtee P, Jung EA, Voitiuk K, Rosen YM, Willsey HR, Mantalas GL, Seiler ST, Selberg JA, Cordero SA, Ross JM, Rolandi M, Pollen AA, Nowakowski TJ, Haussler D, Mostajo-Radji MA, Salama SR, Teodorescu M. Picroscope: low-cost system for simultaneous longitudinal biological imaging. Commun Biol. 2021 Nov 4;4(1):1261
Voitiuk K, Geng J, Keefe MG, Parks DF, Sanso SE, Hawthorne N, Freeman DB, Currie R, Mostajo-Radji MA, Pollen AA, Nowakowski TJ, Salama SR, Teodorescu M, Haussler D. Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments. J Neural Eng. 2021 Nov 12;18(6).
Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M. UCSC Cell Browser: Visualize Your Single-Cell Data. Bioinformatics. 2021 Jul 9:btab503. doi: 10.1093/bioinformatics/btab503. Online ahead of print.PMID: 34244710
Coll-Tané M, Gong NN, Belfer SJ, van Renssen LV, Kurtz-Nelson EC, Szuperak M, Eidhof I, van Reijmersdal B, Terwindt I, Durkin J, Verheij MMM, Kim CN, Hudac CM, Nowakowski TJ, Bernier RA, Pillen S, Earl RK, Eichler EE, Kleefstra T, Kayser MS, Schenck A. The CHD8/CHD7/Kismet family links blood-brain barrier glia and serotonin to ASD-associated sleep defects. Sci Adv. 2021 Jun 4;7(23):eabe2626. doi: 10.1126/sciadv.abe2626. Print 2021 Jun.PMID: 34088660
Willsey HR, Exner CRT, Xu Y, Everitt A, Sun N, Wang B, Dea J, Schmunk G, Zaltsman Y, Teerikorpi N, Kim A, Anderson AS, Shin D, Seyler M, Nowakowski TJ, Harland RM, Willsey AJ, State MW. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron. 2021 Apr 21;109(8):1409. doi: 10.1016/j.neuron.2021.03.030.PMID: 33887193
2020
Ross JM, Kim C, Allen D, Crouch EE, Narsinh K, Cooke DL, Abla AA, Nowakowski TJ, Winkler EA, The Expanding Cell Diversity of the Brain Vasculature Front Physiol. 2020 Dec 3;11:600767; PMID: 33343397
Guo SM, Yeh LH, Folkesson J, Ivanov IE, Krishnan AP, Keefe MG, Hashemi E, Shin D, Chhun BB, Cho NH, Leonetti MD, Han MH, Nowakowski TJ, Mehta SB Revealing architectural order with quantitative label-free imaging and deep learning Elife 2020 Jul 27;9:e55502; PMID: 32716843
Keefe MG, Nowakowski TJ. Evolutionary Expansion of Human Cerebellar Germinal Zones. Trends Neurosci. 2020; PMID: 31954525
2019
Cadwell CR, Bhaduri A, Mostajo-Radji M, Keefe MG, Nowakowski TJ. Development and Arealization of the Cerebral Cortex., Neuron 2019. PMID: 31557462
Keefe MG, Nowakowski TJ. A cookbook for neuronal flavors. Nature. 2019; 573:36-37; PMID:31481767
Linsley JW, Tripathi A, Epstein I, Schmunk G, Mount E, Campioni M, Oza V, Barch M, Javaherian A, Nowakowski TJ, Samsi S, Finkbeiner S. Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration. Commun Biol. 2019. PMID: 31069265
Andrews MG, Nowakowski TJ Human brain development through the lens of cerebral organoid models Brain Research 2019, 1725:146470; PMID: 31542572
2018
Bhaduri A, Nowakowski TJ Single-cell sequencing paints diverse pictures of the brain. Nature 2018 563(7729):38-39. PMID:30382219
Nowakowski TJ. Building blocks of the human brain. Science 2018 362(6411):169 PMID:30309940
Kosik KS, Nowakowski T. Evolution of New miRNAs and Cerebro-Cortical Development. Annu Rev Neurosci 2018 Apr 4. PMID:29618285
Other Publications
Pratt T., Nowakowski TJ., Price DJ. MicroRNA and neocortical evolution. in Essentials of Noncoding RNA in Neuroscience: Ontogenetics, Plasticity of the Vertebrate Brain. Edition: 1st, Publisher: Elsevier; Imprint Academic Press, Editor: Davide De Pietri Tonelli, ISBN: 9780128044025