Preprints
Matthew Elliott, John P. Andrews, Tjitse van der Molen, Jinghui Geng, Alex Spaeth, Kateryna Voitiuk, Cordero Core, Thomas Gillespie, Ari Sinervo, David F. Parks, Ash Robbins, Daniel Solis, Edward F. Chang, Tomasz J Nowakowski, Mircea Teodorescu, David Haussler, Tal Sharf. Pathological microcircuits initiate epileptiform events in patient hippocampal slices. bioRxiv 2024.11.13.623525; doi: https://doi.org/10.1101/2024.11.13.623525
Jinghui Geng, Kateryna Voitiuk, David F. Parks, Ash Robbins, Alex Spaeth, Jessica L. Sevetson, Sebastian Hernandez, Hunter E. Schweiger, John P. Andrews, Spencer T. Seiler, Matthew A. T. Elliott, Edward F. Chang, Tomasz J. Nowakowski, Rob Currie, Mohammed A. Mostajo-Radji, David Haussler, Tal Sharf, Sofie R. Salama, Mircea Teodorescu. Multiscale Cloud-based Pipeline for Neuronal Electrophysiology Analysis and Visualization. bioRxiv 2024.11.14.623530; doi: https://doi.org/10.1101/2024.11.14.623530
Graham AJ, Khoo MWL, Srivastava V, Viragova S, Kim H, Parekh K, Hennick KM, Bird M, Goldhammer N, Yu JZ, Morley CD, Lebel P, Kumar S, Rosenbluth JM, Nowakowski TJ, Klein O, Gómez-Sjöberg R, Gartner ZJ. MAGIC matrices: freeform bioprinting materials to support complex and reproducible organoid morphogenesis. bioRxiv [Preprint]. 2024 Oct 9:2 doi: 10.1101/2024.02.01.578324
David Shin, Madeleine E. Urbanek, H. Hanh Larson, Anthony J. Moussa, Kevin Y. Lee, Donovan L. Baker, Elio Standen-Bloom, Sangeetha Ramachandran, Derek Bogdanoff, Cathryn R. Cadwell, Tomasz J. Nowakowski High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing. doi: https://doi.org/10.1101/2024.10.01.616167
Nia Teerikorpi, Micaela C. Lasser, Sheng Wang, Elina Kostyanovskaya, Ethel Bader, Nawei Sun, Jeanselle Dea, Tomasz J. Nowakowski, A. Jeremy Willsey, Helen Rankin Willsey Ciliary biology intersects autism and congenital heart disease. doi: https://doi.org/10.1101/2024.07.30.602578
Daeun Jeong, Sara G. Danielli, Kendra K. Maaß, David R. Ghasemi, Svenja K. Tetzlaff, Ekin Reyhan, Carlos Alberto Oliveira de Biagi-Junior, Sina Neyazi, Andrezza Nascimento, Rebecca Haase, Costanza Lo Cascio, Bernhard Englinger, Li Jiang, Cuong M. Nguyen, Alicia-Christina Baumgartner, Sophia Castellani, Jacob S. Rozowsky, Olivia A. Hack, McKenzie L. Shaw, Daniela Lotsch-Gojo, Katharina Bruckner, Stefan M. Pfister, Marcel Kool, Tomasz J. Nowakowski, Johannes Gojo, Lissa Baird, Sanda Alexandrescu, Kristian W. Pajtler, Varun Venkataramani, Mariella G. Filbin Single-cell multidimensional profiling of tumor cell heterogeneity in supratentorial ependymomas. doi: https://doi.org/10.1101/2024.08.07.607066
Olivia M Teter, Nina M Dräger, Sydney M Sattler, Amanda McQuade, Brandon B Holmes, Vasileios Papakis, Kun Leng, Steven Boggess, David Shin, Tomasz J Nowakowski, James Wells, Martin Kampmann. CRISPRi-based screen of Autism Spectrum Disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and uptake of synaptic material. doi: https://doi.org/10.1101/2024.06.01.596962
Elisabetta Furlanis, Min Dai, Brenda Leyva Garcia, Josselyn Vergara, Ana Pereira, Kenneth Pelkey, Thien Tran, Bram L. Gorissen, Anna Vlachos, Ariel Hairston, Shuhan Huang, Deepanjali Dwivedi, Sarah Du, Sara Wills, Justin McMahon, Anthony T. Lee, Edward F. Chang, Taha Razzaq, Ahmed Qazi, Geoffrey Vargish, Xiaoqing Yuan, Adam Caccavano, Steven Hunt, Ramesh Chittajallu, Nadiya McLean, Lauren Hewit, Emily Paranzino, Haley Rice, Alex C. Cummins, Anya Plotnikova, Arya Mohanty, Anne Claire Tangen, Jung Hoon Shin, Reza Azadi, Mark A.G. Eldridge, Veronica A. Alvarez, Bruno B. Averbeck, Mansour Alyahyay, Tania Reyes Vallejo, Mohammed Soheib, Lucas G. Vattino, Cathryn P. MacGregor, Emmie Banks, Viktor Janos Olah, Shovan Naskar, Sophie Hill, Sophie Liebergall, Rohan Badiani, Lili Hyde, Qing Xu, Kathryn C. Allaway, Ethan M. Goldberg, Tomasz J. Nowakowski, Soohyun Lee, Anne E. Takesian, Leena A. Ibrahim, Asim Iqbal, Chris J. McBain, Jordane Dimidschstein, Gord Fishell, Yating Wang. An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes. doi: https://doi.org/10.1101/2024.07.17.603924
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
2024
Adameyko I, Bakken T, Bhaduri A, Chhatbar C, Filbin MG, Gate D, Hochgerner H, Kim CN, Krull J, La Manno G, Li Q, Linnarsson S, Ma Q, Mayer C, Menon V, Nano P, Prinz M, Quake S, Walsh CA, Yang J, Bayraktar OA, Gokce O, Habib N, Konopka G, Liddelow SA, Nowakowski TJ. Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system. Nat Neurosci. 2024 Dec;27(12):2278-2291. doi: 10.1038/s41593-024-01827-9. PMID: 39627588
Bonev B, Gonçalo CB, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Bayraktar O, Habib N, Nowakowski TJ. Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. Nat Neurosci. 2024 Dec;27(12):2292-2309. doi: 10.1038/s41593-024-01806-0. PMID: 39627587
Colonna M, Konopka G, Liddelow SA, Nowakowski T, Awatramani R, Bateup HS, Cadwell CR, Caglayan E, Chen JL, Gillis J, Kampmann M, Krienen F, Marsh SE, Monje M, O'Dea MR, Patani R, Pollen AA, Quintana FJ, Scavuzzo M, Schmitz M, Sloan SA, Tesar PJ, Tollkuhn J, Tosches MA, Urbanek ME, Werner JM, Bayraktar OA, Gokce O, Habib N. Implementation and validation of single-cell genomics experiments in neuroscience. Nat Neurosci. 2024 Dec;27(12):2310-2325. doi: 10.1038/s41593-024-01814-0. PMID: 39627589
Barnett SN, Cujba AM, Yang L, Maceiras AR, Li S, Kedlian V, Pett JP, Polanski K, Miranda AMA, Xu C, Cranley J, Kanemaru K, Lee M, Mach L, Perera S, Tudor C, Joseph PD, Pritchard S, Toscano-Rivalta R, Tuong K, Bolt L, Petryszak R, Prete M, Cakir B, Huseynov A, Sarropoulos I, Chowdhury RA, Elmentaite R, Madissoon E, Oliver A, Campos L, Brazovskaja A, Gomes T, Treutlein B, Kim CN, Nowakowski TJ, Meyer KB, Randi AM, Noseda M, Teichmann SA. An organotypic atlas of human vascular cells. Nat Med. 2024 Nov 20. doi: 10.1038/s41591-024-03376-x. PMID: 39566559
Andrews JP, Geng J, Voitiuk K, Elliott MAT, Shin D, Robbins A, Spaeth A, Wang A, Li L, Solis D, Keefe MG, Sevetson JL, Rivera de Jesús JA, Donohue KC, Larson HH, Ehrlich D, Auguste KI, Salama S, Sohal V, Sharf T, Haussler D, Cadwell CR, Schaffer DV, Chang EF, Teodorescu M, Nowakowski TJ. (2024). Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices. Nature Neuroscience 2024 Nov 15. doi: 10.1038/s41593-024-01782-5. PMID: 39548326.
Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, Haeussler M, Wick B, Zhang MJ, Xie F, Ziffra RS, Mukamel EA, Eskin E, Nowakowski TJ, Dixon JR, Pasaniuc B, Ecker JR, Zhu Q, Bintu B, Paredes MF, Luo C. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature. 2024 Oct 9. doi: 10.1038/s41586-024-08030-7
Lee AT, Chang EF, Paredes MF, Nowakowski TJ. Large-scale neurophysiology and single-cell profiling in human neuroscience. Nature. 2024 Jun;630(8017):587-595. doi: 10.1038/s41586-024-07405-0. Epub 2024 Jun 19. PMID: 38898291
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM; PsychENCODE Consortium‡; Pollen AA, Nowakowski TJ, Ahituv N, Pollard KS; PsychENCODE Consortium. Massively parallel characterization of regulatory elements in the developing human cortex. Science. 2024 May 24;384(6698):eadh0559. doi: 10.1126/science.adh0559. Epub 2024 May 24.PMID: 38781390
Escoubas CC, Dorman LC, Nguyen PT, Lagares-Linares C, Nakajo H, Anderson SR, Barron JJ, Wade SD, Cuevas B, Vainchtein ID, Silva NJ, Guajardo R, Xiao Y, Lidsky PV, Wang EY, Rivera BM, Taloma SE, Kim DK, Kaminskaya E, Nakao-Inoue H, Schwer B, Arnold TD, Molofsky AB, Condello C, Andino R, Nowakowski TJ, Molofsky AV. Type-I-interferon-responsive microglia shape cortical development and behavior. Cell. 2024 Apr 11;187(8):1936-1954.e24. doi: 10.1016/j.cell.2024.02.020
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.
Dataset: https://adult-brain-vasc.cells.ucsc.edu
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