Tomasz Nowakowski, PhD
Associate Professor
Neurological Surgery
School of Medicine

Websites

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• UCSF Anatomy (anatomy.ucsf.edu)
• Lab website (nowakowski-lab.squarespace.com)

Publications (149)

Top publication keywords:
Atlases as TopicTranscriptomeNeurogenesisNeurosciencesSingle-Cell AnalysisNeocortexNeurogliaOrganoidsNeural Stem CellsEpendymoglial CellsGABAergic NeuronsCerebral CortexNeuronsBrainCell Lineage

• Spatiotemporal analysis of autism gene enrichment implicates cortex, thalamus, and hypothalamus.
  bioRxiv : the preprint server for biology 2026 Wang X, Li Y, Young DM, Ljungdahl A, Dema C, Rohani N, Nowakowski T, Roeder K, Sanders SJ
• A massively parallel reporter assay of MECP2 cis-regulatory elements reveals genetic candidates for male-biased autism.
  bioRxiv : the preprint server for biology 2026 Meyer-Schuman R, Cherry F, Sui Y, Papastathopoulos-Katsaros A, Zhong Y, Li Y, Wang T, Hennick K, Karunakaran D, Berk-Rauch H, Liu Z, Chakravarti A, Nowakowski T, Eichler EE, Zoghbi H
• Author Correction: Multidimensional profiling of heterogeneity in supratentorial ependymomas.
  Nature 2026 Jeong D, Danielli SG, Maaß KK, Ghasemi DR, Tetzlaff SK, Reyhan E, Jiang L, Katiyar S, Sundheimer JK, Lo Cascio C, Neyazi S, de Biagi-Junior CAO, Couvillon E, Castellani S, Pazyra-Murphy M, Mullally M,…
• Linking rare variants to cell-type function in profound autism with brain transcriptomics and foundation models.
  Cell genomics 2026 Dubuc A, Renne T, Huguet G, Jacquemont S, Nowakowski T
• Molecular dynamics of Brodmann Area 22 in development and autism.
  bioRxiv : the preprint server for biology 2026 Suresh V, Wigdor EM, Hao Y, Leonard R, Asfouri J, Griffiths M, Evans C, Yuan G, Rohani N, Weiss J, Dema C, Mukthar T, Lassen FH, Schafer N, Dong S, Palmer DS, Chang EF, Sanders SJ, Nowakowski TJ

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• Multidimensional profiling of heterogeneity in supratentorial ependymomas.
  Nature 2026 Jeong D, Danielli SG, Maaß KK, Ghasemi DR, Tetzlaff SK, Reyhan E, Jiang L, Katiyar S, Sundheimer JK, Lo Cascio C, Neyazi S, de Biagi-Junior CAO, Couvillon E, Castellani S, Pazyra-Murphy M, Mullally M,…
• Stress-relaxing granular bioprinting materials enable complex and uniform organoid self-organization.
  Nature materials 2026 Graham AJ, Khoo MWL, Srivastava V, Viragova S, Kim H, Parekh K, Hennick KM, Bird M, Goldhammer N, Yu JZ, Hu G, Brinkley NT, Pardo L, Amaya JS, Morley CD, Chadha N, Lebel P, Kumar S, Rosenbluth JM, …
• Optogenetic WNT signaling drives germ layer self-organization in a human gastruloid model.
  bioRxiv : the preprint server for biology 2026 Johnson HJ, McMullin DM, Zimmermann JA, Kim CN, Repina NA, Bhalerao R, Nowakowski TJ, Schaffer DV
• Genetic and Cortical Cell-Type Liability Architecture of Autism.
  Research square 2026 Renne T, Benitière F, Poulain C, Dubuc A, Bourque VR, Huguet G, Nowakowski T, Jacquemont S
• Using the linear references from the pangenome to discover missing autism variants.
  Nature communications 2026 Sui Y, Lin J, Noyes MD, Kwon Y, Wong I, Koundinya N, Harvey WT, Wu M, Hoekzema K, Munson KM, Garcia GH, Knuth J, Wertz J, Wang T, Hennick K, Karunakaran D, Polo Prieto RA, Meyer-Schuman R, Cherry F, …
• Dissecting gene regulatory networks governing human cortical cell fate.
  Nature 2026 Ding JW, Kim CN, Ostrowski MS, Abeykoon Y, Pavlovic BJ, Wallace JL, Schaefer NK, Nowakowski TJ, Pollen AA
• Genetic and Cortical Cell-Type Liability Architecture of Autism.
  bioRxiv : the preprint server for biology 2025 Renne T, Benitière F, Poulain C, Dubuc A, Bourque VR, Huguet G, Nowakowski T, Jacquemont S
• Microscale maps of bursting dynamics across human hippocampal slices from patients with epilepsy.
  Journal of neurophysiology 2025 Elliott MAT, Andrews JP, van der Molen T, Geng J, Spaeth A, Toledo A, Voitiuk K, Core C, Gillespie T, Sinervo A, Parks DF, Robbins A, Solís D, Chang EF, Nowakowski TJ, Teodorescu M, Haussler D, Sharf …
• G-protein-coupled receptor ADGRG1 drives a protective microglial state in Alzheimer's disease through MYC activation.
  Neuron 2025 Zhu B, Wangzhou A, Yu D, Li T, Schmidt R, De Florencio SL, Chao L, Thurber AL, Zhou M, Msheik Z, Perez Y, Grinberg LT, Spina S, Ransohoff RM, Kriegstein AR, Seeley WW, Nowakowski T, Piao X
• Disruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism.
  bioRxiv : the preprint server for biology 2025 Yuan G, Suresh V, Wigdor E, Hao Y, Leonard R, Steyert M, Griffiths M, Evans C, Rohani N, Weiss J, Lassen FH, Schafer N, Dong S, Palmer DS, Sanders SJ, Nowakowski TJ
• A spatial transcriptomic atlas of autism-associated genes identifies convergence in the developing human thalamus.
  bioRxiv : the preprint server for biology 2025 Aivazidis A, Memi F, Rademaker K, Koko M, Roberts K, Trinh A, Petryszak R, Kleshchevnikov V, Tuck L, Lisgo S, Li T, Makarchuk S, Prete M, Nowakowski TJ, Martin HC, Bayraktar OA
• Lineage-resolved atlas of the developing human cortex.
  Nature 2025 Keefe MG, Steyert MR, Nowakowski TJ
• The new frontier in understanding human and mammalian brain development.
  Nature 2025 Nowakowski TJ, Nano PR, Matho KS, Chen X, Corrigan EK, Ding W, Gao Y, Heffel M, Jayakumar J, Kaplan HS, Kronman FN, Kovner R, Mannens CCA, Song M, Steyert MR, Venkatesan S, Wallace JL, Wang L, Werner …
• ANTIPODE Provides a Global View of Cell Type Homology and Transcriptomic Divergence in the Developing Mammalian Brain.
  bioRxiv : the preprint server for biology 2025 Schmitz MT, Ding JW, Nolbrant S, McMullen R, Kim CN, Pavlovic BJ, Nowakowski TJ, Bakken TE, Ye CJ, Pollen AA
• Accelerated Tempo of Cortical Neurogenesis in Down Syndrome.
  bioRxiv : the preprint server for biology 2025 Ding JW, Kim CN, Steyert MR, Yuan AT, Shin D, Ivanov D, Nowakowski TJ, Pollen AA
• Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate.
  bioRxiv : the preprint server for biology 2025 Ding JW, Kim CN, Ostrowski MS, Abeykoon Y, Pavlovic BJ, Wallace JL, Nowakowski TJ, Pollen AA
• Sex differences in the developing human cortex intersect with genetic risk of neurodevelopmental disorders.
  bioRxiv : the preprint server for biology 2025 Hennick K, Sui Y, Karunakaran D, Nicollela A, Leonard R, Meyer-Schuman R, Berk-Rauch H, Wang T, Chakravarti A, Zoghbi HY, Eichler EE, Nowakowski TJ
• Stress relaxing granular bioprinting materials enable complex and uniform organoid self-organization.
  bioRxiv : the preprint server for biology 2025 Graham AJ, Khoo MWL, Srivastava V, Viragova S, Kim H, Parekh K, Hennick KM, Bird M, Goldhammer N, Yu JZ, Hu G, Brinkley NT, Pardo L, Amaya JS, Morley CD, Chadha N, Lebel P, Kumar S, Rosenbluth JM, …
• Microglia regulate GABAergic neurogenesis in prenatal human brain through IGF1.
  Nature 2025 Yu D, Jain S, Wangzhou A, Zhu B, Shao W, Coley-O'Rourke EJ, De Florencio S, Kim J, Choi JJ, Paredes MF, Nowakowski TJ, Huang EJ, Piao X
• G-protein-coupled receptor ADGRG1 drives a protective microglial state in Alzheimer's disease through MYC activation.
  Neuron 2025 Zhu B, Wangzhou A, Yu D, Li T, Schmidt R, De Florencio SL, Chao L, Thurber AL, Zhou M, Msheik Z, Perez Y, Grinberg LT, Spina S, Ransohoff RM, Kriegstein AR, Seeley WW, Nowakowski T, Piao X
• Pangenome discovery of missing autism variants.
  medRxiv : the preprint server for health sciences 2025 Sui Y, Lin J, Noyes MD, Kwon Y, Wong I, Koundinya N, Harvey WT, Wu M, Hoekzema K, Munson KM, Garcia GH, Knuth J, Wertz J, Wang T, Hennick K, Karunakaran D, Polo Prieto RA, Meyer-Schuman R, Cherry F, …
• Molecular Signatures in Cortical Development.
  Annual review of neuroscience 2025 Steyert MR, Li T, Piao X, Nowakowski TJ
• Engrafted nitrergic neurons derived from hPSCs improve gut dysmotility in mice.
  Nature 2025 Majd H, Samuel RM, Cesiulis A, Ramirez JT, Kalantari A, Barber K, Farahvashi S, Ghazizadeh Z, Majd A, Chemel AK, Richter MN, Das S, Bendrick JL, Keefe MG, Wang J, Shiv RK, Bhat S, Khoroshkin M, Yu J, …
• Ciliary biology intersects autism and congenital heart disease.
  Development (Cambridge, England) 2025 Teerikorpi N, McCluskey KE, Bader E, Lasser MC, Wang S, Nguyen CH, Schmidt JD, Kostyanovskaya E, Sun N, Dea J, Nowakowski TJ, Willsey AJ, Willsey HR
• Neutrophil extracellular traps-related markers in chronic limb threatening ischemia - a relation with progression and prognosis.
  Thrombosis research 2025 Nowakowski T, Malinowski K, Natorska J, Undas A
• An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes.
  Neuron 2025 Furlanis E, Dai M, Leyva Garcia B, Tran T, Vergara J, Pereira A, Gorissen BL, Wills S, Vlachos A, Hairston A, Dwivedi D, Du S, McMahon J, Huang S, Morabito A, Vazquez A, Kim S, Lee AT, Chang EF, …
• An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes.
  bioRxiv : the preprint server for biology 2025 Furlanis E, Dai M, Garcia BL, Tran T, Vergara J, Pereira A, Gorissen BL, Vlachos A, Hairston A, Dwivedi D, Du S, McMahon J, Huang S, Morabito A, Vazquez A, Kim S, Lee AT, Chang EF, Razzaq T, Qazi A, …
• CRISPRi-based screen of autism spectrum disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning.
  Molecular psychiatry 2025 Teter OM, McQuade A, Hagan V, Liang W, Dräger NM, Sattler SM, Holmes BB, Castillo VC, Papakis V, Leng K, Boggess S, Nowakowski TJ, Wells J, Kampmann M
• Exploring human brain development and disease using assembloids.
  Neuron 2025 Wu SR, Nowakowski TJ
• Pathological microcircuits and epileptiform events in patient hippocampal slices.
  bioRxiv : the preprint server for biology 2025 Elliott MAT, Andrews JP, van der Molen T, Geng J, Spaeth A, Toledo A, Voitiuk K, Core C, Gillespie T, Sinervo A, Parks DF, Robbins A, Solís D, Chang EF, Nowakowski TJ, Teodorescu M, Haussler D, Sharf …
• Low-dose rivaroxaban added to aspirin decreases thrombin generation but does not affect fibrin clot properties: a preliminary study.
  Polish archives of internal medicine 2025 Nowakowski T, Undas KW, Undas A
• Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
  Nature neuroscience 2025 Bonev B, Castelo-Branco G, 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, …
• Multiscale Cloud-Based Pipeline for Neuronal Electrophysiology Analysis and Visualization.
  bioRxiv : the preprint server for biology 2024 Geng J, Voitiuk K, Parks DF, Robbins A, Spaeth A, Sevetson JL, Hernandez S, Schweiger HE, Andrews JP, Seiler ST, Elliott MAT, Chang EF, Nowakowski TJ, Currie R, Mostajo-Radji MA, Haussler D, Sharf T, …
• High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing.
  bioRxiv : the preprint server for biology 2024 Shin D, Urbanek ME, Larson HH, Moussa AJ, Lee KY, Baker DL, Standen-Bloom E, Ramachandran S, Bogdanoff D, Cadwell CR, Nowakowski TJ
• Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system.
  Nature neuroscience 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, …
• Implementation and validation of single-cell genomics experiments in neuroscience.
  Nature neuroscience 2024 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 …
• Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
  Nature neuroscience 2024 Bonev B, Castelo-Branco G, 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, …
• An organotypic atlas of human vascular cells.
  Nature medicine 2024 Barnett SN, Cujba AM, Yang L, Maceiras AR, Li S, Kedlian VR, 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,…
• CRISPRi-based screen of Autism Spectrum Disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning.
  bioRxiv : the preprint server for biology 2024 Teter OM, McQuade A, Hagan V, Liang W, Dräger NM, Sattler SM, Holmes BB, Castillo VC, Papakis V, Leng K, Boggess S, Nowakowski TJ, Wells J, Kampmann M
• Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices.
  Nature neuroscience 2024 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…
• Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior.
  Science (New York, N.Y.) 2024 Barron JJ, Mroz NM, Taloma SE, Dahlgren MW, Ortiz-Carpena JF, Keefe MG, Escoubas CC, Dorman LC, Vainchtein ID, Chiaranunt P, Kotas ME, Nowakowski TJ, Bender KJ, Molofsky AB, Molofsky AV
• Microglia regulate GABAergic neurogenesis in prenatal human brain through IGF1.
  bioRxiv : the preprint server for biology 2024 Yu D, Jain S, Wangzhou A, De Florencio S, Zhu B, Kim JY, Choi JJ, Paredes MF, Nowakowski TJ, Huang EJ, Piao X
• Adhesion G protein-coupled receptor ADGRG1 promotes protective microglial response in Alzheimer's disease.
  bioRxiv : the preprint server for biology 2024 Zhu B, Wangzhou A, Yu D, Li T, Schmidt R, De Florencio SL, Chao L, Perez Y, Grinberg LT, Spina S, Ransohoff RM, Kriegstein AR, Seeley WW, Nowakowski T, Piao X
• Temporally distinct 3D multi-omic dynamics in the developing human brain.
  Nature 2024 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 …
• Single-cell multidimensional profiling of tumor cell heterogeneity in supratentorial ependymomas.
  bioRxiv : the preprint server for biology 2024 Jeong D, Danielli SG, Maaß KK, Ghasemi DR, Tetzlaff SK, Reyhan E, Oliveira de Biagi-Junior CA, Neyazi S, Nascimento A, Haase R, Lo Cascio C, Englinger B, Jiang L, Nguyen CM, Baumgartner AC, Castellani…
• Ciliary biology intersects autism and congenital heart disease.
  bioRxiv : the preprint server for biology 2024 Teerikorpi N, Lasser MC, Wang S, Kostyanovskaya E, Bader E, Sun N, Dea J, Nowakowski TJ, Willsey AJ, Willsey HR
• Elevated plasma factor XI is associated with postthrombotic syndrome.
  Thrombosis research 2024 Stepien K, Siudut J, Zalewski J, Nowakowski T, Undas A
• Large-scale neurophysiology and single-cell profiling in human neuroscience.
  Nature 2024 Lee AT, Chang EF, Paredes MF, Nowakowski TJ
• A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex.
  Science (New York, N.Y.) 2024 Huuki-Myers LA, Spangler A, Eagles NJ, Montgomery KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, PsychENCODE Consortium†, Hyde…
• Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.
  Science (New York, N.Y.) 2024 Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, PsychENCODE Consortium†, …
• Massively parallel characterization of regulatory elements in the developing human cortex.
  Science (New York, N.Y.) 2024 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 …
• Single-cell genomics and regulatory networks for 388 human brains.
  Science (New York, N.Y.) 2024 Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, PsychENCODE Consortium‡, Bakken TE, Bendl J, …
• Single-cell multi-cohort dissection of the schizophrenia transcriptome.
  Science (New York, N.Y.) 2024 Ruzicka WB, Mohammadi S, Fullard JF, Davila-Velderrain J, Subburaju S, Tso DR, Hourihan M, Jiang S, Lee HC, Bendl J, PsychENCODE Consortium§, Voloudakis G, Haroutunian V, Hoffman GE, Roussos P, Kellis…
• Type-I-interferon-responsive microglia shape cortical development and behavior.
  Cell 2024 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…
• Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders.
  Cell stem cell 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, …
• A foundational atlas of autism protein interactions reveals molecular convergence.
  bioRxiv : the preprint server for biology 2024 Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M,…
• Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy.
  Science advances 2024 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
• Improving cellular diversity in human cerebellar organoids.
  Cell stem cell 2024 Steyert M, Nowakowski T
• Single-cell analysis of prenatal and postnatal human cortical development.
  Science (New York, N.Y.) 2023 Velmeshev D, Perez Y, Yan Z, Valencia JE, Castaneda-Castellanos DR, Wang L, Schirmer L, Mayer S, Wick B, Wang S, Nowakowski TJ, Paredes M, Huang EJ, Kriegstein AR
• Spatiotemporal molecular dynamics of the developing human thalamus.
  Science (New York, N.Y.) 2023 Kim CN, Shin D, Wang A, Nowakowski TJ
• Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids.
  eLife 2023 Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T
• Three-dimensional genome rewiring in loci with human accelerated regions.
  Science (New York, N.Y.) 2023 Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Zoonomia Consortium§, Nowakowski T, Ahituv N, Pollen A, Pollard KS
• 385 A Cell Resolution Atlas of the Human Cerebrovasculature Reveals Angiogenic and Inflammatory Cell Programs in Arteriovenous Malformations.
  Neurosurgery 2023 Ethan A. Winkler, Chang Kim, Jayden Ross, Joseph Garcia, Eugene Gil, Irene Oh, Lindsay Chen, David Wu, Joshua Catapano, Kunal P. Raygor, Kazim Narsinh, Helen Kim, Shantel Weinsheimer, Daniel Cooke, …
• Transcriptomic cell type structures in vivo neuronal activity across multiple timescales.
  Cell reports 2023 Schneider A, Azabou M, McDougall-Vigier L, Parks DF, Ensley S, Bhaskaran-Nair K, Nowakowski T, Dyer EL, Hengen KB
• Type I interferon responsive microglia shape cortical development and behavior.
  bioRxiv : the preprint server for biology 2023 Escoubas CC, Dorman LC, Nguyen PT, Lagares-Linares C, Nakajo H, Anderson SR, Cuevas B, Vainchtein ID, Silva NJ, Xiao Y, Lidsky PV, Wang EY, Taloma SE, Nakao-Inoue H, Schwer B, Andino R, Nowakowski TJ,…
• Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex.
  bioRxiv : the preprint server for biology 2023 Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen A, Nowakowski TJ, Ahituv N, Pollard KS
• Abstract 52: Prevalence Of Somatic Activating Kras Mutations In Pediatric And Adult Sporadic Brain Arteriovenous Malformations.
  Stroke 2023 Ethan A Winkler, Joseph Garcia, Cynthia Tsang, Jeffrey Nelson, Charles McCulloch, Shantel Weinsheimer, Christine K Fox, Heather Fullerton, Nerissa Ko, Hua Su, Tomasz Nowakowski, Daniel L Cooke, Steven…
• New York Stem Cell Foundation Robertson Investigators.
  Cell stem cell 2022 McKinley KL, van Boxtel R, Finley LWS, Peña CJ, Nowakowski TJ
• In preprints: new insights into truncated radial glia.
  Development (Cambridge, England) 2022 Steyert M, Nowakowski TJ
• Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Wang T, Kim CN, Bakken TE, Gillentine MA, Henning B, Mao Y, Gilissen C, SPARK Consortium, Nowakowski TJ, Eichler EE
• IoT cloud laboratory: Internet of Things architecture for cellular biology.
  Internet of things (Amsterdam, Netherlands) 2022 Parks DF, Voitiuk K, Geng J, Elliott MAT, Keefe MG, Jung EA, Robbins A, Baudin PV, Ly VT, Hawthorne N, Yong D, Sanso SE, Rezaee N, Sevetson JL, Seiler ST, Currie R, Pollen AA, Hengen KB, Nowakowski TJ…
• Cerebral Organoids as an Experimental Platform for Human Neurogenomics.
  Cells 2022 Nowakowski TJ, Salama SR
• Tropism of SARS-CoV-2 for human cortical astrocytes.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Andrews MG, Mukhtar T, Eze UC, Simoneau CR, Ross J, Parikshak N, Wang S, Zhou L, Koontz M, Velmeshev D, Siebert CV, Gemenes KM, Tabata T, Perez Y, Wang L, Mostajo-Radji MA, de Majo M, Donohue KC, Shin…
• Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes.
  Science (New York, N.Y.) 2022 Allen DE, Donohue KC, Cadwell CR, Shin D, Keefe MG, Sohal VS, Nowakowski TJ
• Dissecting cellular diversity of cortical GABAergic cells across multiple modalities: A turning point in neuronal taxonomy.
  Faculty reviews 2022 Arlotta P, Chen F, Lodato S, Margrie TW, Nowakowski TJ, Pederson T, Rico B
• Microglial GPR56 is the molecular target of maternal immune activation-induced parvalbumin-positive interneuron deficits.
  Science advances 2022 Yu D, Li T, Delpech JC, Zhu B, Kishore P, Koshi T, Luo R, Pratt KJB, Popova G, Nowakowski TJ, Villeda SA, Piao X
• The development and evolution of inhibitory neurons in primate cerebrum.
  Nature 2022 Schmitz MT, Sandoval K, Chen CP, Mostajo-Radji MA, Seeley WW, Nowakowski TJ, Ye CJ, Paredes MF, Pollen AA
• A single-cell atlas of the normal and malformed human brain vasculature.
  Science (New York, N.Y.) 2022 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, Cooke DL, Walcott BP, Lawton MT, Gupta N, Zlokovic BV, Chang EF, Abla AA, …
• Endoluminal Biopsy for Molecular Profiling of Human Brain Vascular Malformations.
  Neurology 2022 Winkler E, Wu D, Gil E, McCoy D, Narsinh K, Sun Z, Mueller K, Ross J, Kim H, Weinsheimer S, Berger M, Nowakowski T, Lim D, Abla A, Cooke D
• DynaMorph: self-supervised learning of morphodynamic states of live cells.
  Molecular biology of the cell 2022 Wu Z, Chhun BB, Popova G, Guo SM, Kim CN, Yeh LH, Nowakowski T, Zou J, Mehta SB
• Nests of dividing neuroblasts sustain interneuron production for the developing human brain.
  Science (New York, N.Y.) 2022 Paredes MF, Mora C, Flores-Ramirez Q, Cebrian-Silla A, Del Dosso A, Larimer P, Chen J, Kang G, Gonzalez Granero S, Garcia E, Chu J, Delgado R, Cotter JA, Tang V, Spatazza J, Obernier K, Ferrer Lozano …
• Individual human cortical progenitors can produce excitatory and inhibitory neurons.
  Nature 2021 Delgado RN, Allen DE, Keefe MG, Mancia Leon WR, Ziffra RS, Crouch EE, Alvarez-Buylla A, Nowakowski TJ
• Single-cell delineation of lineage and genetic identity in the mouse brain.
  Nature 2021 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
• UCSC Cell Browser: visualize your single-cell data.
  Bioinformatics (Oxford, England) 2021 Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M
• Endovascular Biopsy of Vertebrobasilar Aneurysm in Patient With Polyarteritis Nodosa.
  Frontiers in neurology 2021 Narsinh KH, Narsinh K, McCoy DB, Sun Z, Halabi C, Meisel K, Tihan T, Chaganti K, Amans MR, Halbach VV, Higashida RT, Hetts SW, Dowd CF, Winkler EA, Abla AA, Nowakowski TJ, Cooke DL
• Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments.
  Journal of neural engineering 2021 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
• Picroscope: low-cost system for simultaneous longitudinal biological imaging.
  Communications biology 2021 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, …
• An atlas of cortical arealization identifies dynamic molecular signatures.
  Nature 2021 Bhaduri A, Sandoval-Espinosa C, Otero-Garcia M, Oh I, Yin R, Eze UC, Nowakowski TJ, Kriegstein AR
• Single-cell epigenomics reveals mechanisms of human cortical development.
  Nature 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
• Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids.
  Cell stem cell 2021 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
• Low cost cloud based remote microscopy for biological sciences.
  Internet of Things 2021 Pierre V. Baudin, Victoria T. Ly, Pattawong Pansodtee, Erik A. Jung, Robert Currie, Ryan Hoffman, Helen Rankin Willsey, Alex A. Pollen, Tomasz J. Nowakowski, David Haussler, Mohammed A. Mostajo-Radji,…
• Distinct nuclear compartment-associated genome architecture in the developing mammalian brain.
  Nature neuroscience 2021 Ahanger SH, Delgado RN, Gil E, Cole MA, Zhao J, Hong SJ, Kriegstein AR, Nowakowski TJ, Pollen AA, Lim DA
• The CHD8/CHD7/Kismet family links blood-brain barrier glia and serotonin to ASD-associated sleep defects.
  Science advances 2021 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, …
• Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience.
  Neuron 2021 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
• Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders.
  Genome medicine 2021 Gillentine MA, Wang T, Hoekzema K, Rosenfeld J, Liu P, Guo H, Kim CN, De Vries BBA, Vissers LELM, Nordenskjold M, Kvarnung M, Lindstrand A, Nordgren A, Gecz J, Iascone M, Cereda A, Scatigno A, Maitz S…
• Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia.
  Nature neuroscience 2021 Eze UC, Bhaduri A, Haeussler M, Nowakowski TJ, Kriegstein AR
• Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience.
  Neuron 2021 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
• The Expanding Cell Diversity of the Brain Vasculature.
  Frontiers in physiology 2020 Ross JM, Kim C, Allen D, Crouch EE, Narsinh K, Cooke DL, Abla AA, Nowakowski TJ, Winkler EA
• Are Organoids Ready for Prime Time?
  Cell stem cell 2020 Bhaduri A, Andrews MG, Kriegstein AR, Nowakowski TJ
• Revealing architectural order with quantitative label-free imaging and deep learning.
  eLife 2020 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
• A Chromatin Accessibility Atlas of the Developing Human Telencephalon.
  Cell 2020 Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL
• Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2+ Granule Neuron Precursor.
  Cell reports 2020 Selvadurai HJ, Luis E, Desai K, Lan X, Vladoiu MC, Whitley O, Galvin C, Vanner RJ, Lee L, Whetstone H, Kushida M, Nowakowski T, Diamandis P, Hawkins C, Bader G, Kriegstein A, Taylor MD, Dirks PB
• Cell stress in cortical organoids impairs molecular subtype specification.
  Nature 2020 Bhaduri A, Andrews MG, Mancia Leon W, Jung D, Shin D, Allen D, Jung D, Schmunk G, Haeussler M, Salma J, Pollen AA, Nowakowski TJ, Kriegstein AR
• Evolutionary Expansion of Human Cerebellar Germinal Zones.
  Trends in neurosciences 2020 Keefe MG, Nowakowski TJ
• A prothrombotic state and denser clot formation in patients following acute limb ischemia of unknown cause.
  Thrombosis research 2020 Karpinska IA, Nowakowski T, Wypasek E, Plens K, Undas A
• Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma.
  Cell stem cell 2020 Bhaduri A, Di Lullo E, Jung D, Müller S, Crouch EE, Espinosa CS, Ozawa T, Alvarado B, Spatazza J, Cadwell CR, Wilkins G, Velmeshev D, Liu SJ, Malatesta M, Andrews MG, Mostajo-Radji MA, Huang EJ, …
• Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders.
  Nature communications 2019 Guo H, Bettella E, Marcogliese PC, Zhao R, Andrews JC, Nowakowski TJ, Gillentine MA, Hoekzema K, Wang T, Wu H, Jangam S, Liu C, Ni H, Willemsen MH, van Bon BW, Rinne T, Stevens SJC, Kleefstra T, …
• Development and Arealization of the Cerebral Cortex.
  Neuron 2019 Cadwell CR, Bhaduri A, Mostajo-Radji MA, Keefe MG, Nowakowski TJ
• Human brain development through the lens of cerebral organoid models.
  Brain research 2019 Andrews MG, Nowakowski TJ
• A recipe book for cell types in the human brain.
  Nature 2019 Keefe MG, Nowakowski TJ
• Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration.
  Communications biology 2019 Linsley JW, Tripathi A, Epstein I, Schmunk G, Mount E, Campioni M, Oza V, Barch M, Javaherian A, Nowakowski TJ, Samsi S, Finkbeiner S
• Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex.
  Neuron 2019 Mayer S, Chen J, Velmeshev D, Mayer A, Eze UC, Bhaduri A, Cunha CE, Jung D, Arjun A, Li E, Alvarado B, Wang S, Lovegren N, Gonzales ML, Szpankowski L, Leyrat A, West JAA, Panagiotakos G, Alvarez-…
• Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.
  Cell 2019 Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, …
• Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function.
  Cell reports 2019 Pai EL, Vogt D, Clemente-Perez A, McKinsey GL, Cho FS, Hu JS, Wimer M, Paul A, Fazel Darbandi S, Pla R, Nowakowski TJ, Goodrich LV, Paz JT, Rubenstein JLR
• Neuroserpin expression during human brain development and in adult brain revealed by immunohistochemistry and single cell RNA sequencing.
  Journal of anatomy 2019 Adorjan I, Tyler T, Bhaduri A, Demharter S, Finszter CK, Bako M, Sebok OM, Nowakowski TJ, Khodosevich K, Møllgård K, Kriegstein AR, Shi L, Hoerder-Suabedissen A, Ansorge O, Molnár Z
• Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development.
  Nature neuroscience 2018 Nowakowski TJ, Rani N, Golkaram M, Zhou HR, Alvarado B, Huch K, West JA, Leyrat A, Pollen AA, Kriegstein AR, Petzold LR, Kosik KS
• Single-cell sequencing paints diverse pictures of the brain.
  Nature 2018 Bhaduri A, Nowakowski TJ
• Building blocks of the human brain.
  Science (New York, N.Y.) 2018 Nowakowski TJ
• Identification of cell types in a mouse brain single-cell atlas using low sampling coverage.
  BMC biology 2018 Bhaduri A, Nowakowski TJ, Pollen AA, Kriegstein AR
• Transcriptional fates of human-specific segmental duplications in brain.
  Genome research 2018 Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE
• The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.
  Cell 2018 Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, …
• Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.
  Cell 2018 Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, …
• An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.
  Nature genetics 2018 Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, …
• Evolution of New miRNAs and Cerebro-Cortical Development.
  Annual review of neuroscience 2018 Kosik KS, Nowakowski T
• Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.
  Science (New York, N.Y.) 2017 Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M, Sandoval-Espinosa C, Liu SJ, Velmeshev D, Ounadjela JR, Shuga J, Wang X, Lim DA, West JA, Leyrat AA, Kent WJ…
• Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia.
  Cell stem cell 2017 Bershteyn M, Nowakowski TJ, Pollen AA, Di Lullo E, Nene A, Wynshaw-Boris A, Kriegstein AR
• The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells.
  Nature communications 2017 Gambardella G, Carissimo A, Chen A, Cutillo L, Nowakowski TJ, di Bernardo D, Blelloch R
• Zika virus cell tropism in the developing human brain and inhibition by azithromycin.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Retallack H, Di Lullo E, Arias C, Knopp KA, Laurie MT, Sandoval-Espinosa C, Mancia Leon WR, Krencik R, Ullian EM, Spatazza J, Pollen AA, Mandel-Brehm C, Nowakowski TJ, Kriegstein AR, DeRisi JL
• Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas.
  Molecular systems biology 2016 Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A
• Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development.
  Neuron 2016 Nowakowski TJ, Pollen AA, Sandoval-Espinosa C, Kriegstein AR
• A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA.
  Neuron 2016 Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS
• SCell: integrated analysis of single-cell RNA-seq data.
  Bioinformatics (Oxford, England) 2016 Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim DA, Kriegstein A
• Single-cell analysis of long non-coding RNAs in the developing human neocortex.
  Genome biology 2016 Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA
• Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells.
  Cell stem cell 2016 Nowakowski TJ, Pollen AA, Di Lullo E, Sandoval-Espinosa C, Bershteyn M, Kriegstein AR
• Molecular identity of human outer radial glia during cortical development.
  Cell 2015 Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR
• The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells.
  Cell stem cell 2015 Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA
• Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex.
  Nature 2014 Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC
• Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
  Nature biotechnology 2014 Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, Li N, Szpankowski L, Fowler B, Chen P, Ramalingam N, Sun G, Thu M, Norris M, Lebofsky R, Toppani D, Kemp DW, Wong M, Clerkson B, Jones BN,…
• Loss of functional Dicer in mouse radial glia cell-autonomously prolongs cortical neurogenesis.
  Developmental biology 2013 Nowakowski TJ, Mysiak KS, O'Leary T, Fotaki V, Pratt T, Price DJ
• MicroRNA-92b regulates the development of intermediate cortical progenitors in embryonic mouse brain.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Nowakowski TJ, Fotaki V, Pollock A, Sun T, Pratt T, Price DJ
• The expression and activity of β-catenin in the thalamus and its projections to the cerebral cortex in the mouse embryo.
  BMC neuroscience 2012 Pratt T, Davey JW, Nowakowski TJ, Raasumaa C, Rawlik K, McBride D, Clinton M, Mason JO, Price DJ
• Functional dicer is necessary for appropriate specification of radial glia during early development of mouse telencephalon.
  PloS one 2011 Nowakowski TJ, Mysiak KS, Pratt T, Price DJ
• Novel lines of Pax6-/- embryonic stem cells exhibit reduced neurogenic capacity without loss of viability.
  BMC neuroscience 2010 Quinn JC, Molinek M, Nowakowski TJ, Mason JO, Price DJ
• Time-Multiplexed Laguerre-Gaussian holographic optical tweezers for biological applications.
  Optics express 2006 Lafong A, Hossack WJ, Arlt J, Nowakowski TJ, Read ND