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Tomasz Nowakowski, PhD

Title(s)Assistant Professor, Anatomy
SchoolSchool of Medicine
Address1550 Fourth Street
Phone415-476-0878
ORCID ORCID Icon0000-0003-2345-4964 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of Edinburgh , Edinburgh, UKBSc07/2007Biological Sciences
    University of Edinburgh , Edinburgh, UKPhD06/2012Biomedical Sciences
    University of California, San Francisco, San Francisco, CApostdoc06/2017Developmental Neurobiology
    Collapse Awards and Honors
    Chan-Zuckerberg Biohub2018Investigator
    Allen Institute for Brain Science2018  - 2021Next Generation Leaders Council, Member
    Eppendorf & Science Prize for Neurobiology2018Finalist
    Cajal Club2017Krieg Cortical Explorer
    Simons Foundation for Autism Research2018  - 2021Simons Foundation Bridge to Independence Award
    Brain & Behavior Research Foundation2019  - 2021NARSAD Young Investigator Award
    Broad Center Regenerative Med & Stem Cell Research 2017  - 2018Broad Innovation Award
    Wellcome Trust2007  - 2011Wellcome Trust 4-Year Studentship

    Collapse Research 
    Collapse Research Activities and Funding
    Mapping Developmental Lineage Relationships in the Cerebral Cortex
    NIH/NIMH RF1MH121268Sep 17, 2019 - Aug 31, 2022
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Featured Videos

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Are Organoids Ready for Prime Time? Cell Stem Cell. 2020 Sep 03; 27(3):361-365. Bhaduri A, Andrews MG, Kriegstein AR, Nowakowski TJ. PMID: 32888425.
      View in: PubMed   Mentions:    Fields:    
    2. Revealing architectural order with quantitative label-free imaging and deep learning. Elife. 2020 Jul 27; 9. 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 T, Mehta SB. PMID: 32716843.
      View in: PubMed   Mentions: 1     Fields:    
    3. A Chromatin Accessibility Atlas of the Developing Human Telencephalon. Cell. 2020 Aug 06; 182(3):754-769.e18. Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL. PMID: 32610082.
      View in: PubMed   Mentions:    Fields:    
    4. Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2+ Granule Neuron Precursor. Cell Rep. 2020 Apr 14; 31(2):107511. 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. PMID: 32294450.
      View in: PubMed   Mentions: 1     Fields:    
    5. Cell stress in cortical organoids impairs molecular subtype specification. Nature. 2020 02; 578(7793):142-148. 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. PMID: 31996853.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    6. Evolutionary Expansion of Human Cerebellar Germinal Zones. Trends Neurosci. 2020 Feb; 43(2):75-77. Keefe MG, Nowakowski TJ. PMID: 31954525.
      View in: PubMed   Mentions:    Fields:    
    7. Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma. Cell Stem Cell. 2020 01 02; 26(1):48-63.e6. 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, Nowakowski TJ, Lim DA, Diaz A, Raleigh DR, Kriegstein AR. PMID: 31901251.
      View in: PubMed   Mentions: 5     Fields:    
    8. Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders. Nat Commun. 2019 10 15; 10(1):4679. 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, Brunner HG, Yntema HG, Long M, Zhao W, Hu Z, Colson C, Richard N, Schwartz CE, Romano C, Castiglia L, Bottitta M, Dhar SU, Erwin DJ, Emrick L, Keren B, Afenjar A, Zhu B, Bai B, Stankiewicz P, Herman K, Mercimek-Andrews S, Juusola J, Wilfert AB, Abou Jamra R, Büttner B, Mefford HC, Muir AM, Scheffer IE, Regan BM, Malone S, Gecz J, Cobben J, Weiss MM, Waisfisz Q, Bijlsma EK, Hoffer MJV, Ruivenkamp CAL, Sartori S, Xia F, Rosenfeld JA, Bernier RA, Wangler MF, Yamamoto S, Xia K, Stegmann APA, Bellen HJ, Murgia A, Eichler EE. PMID: 31616000.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    9. Development and Arealization of the Cerebral Cortex. Neuron. 2019 09 25; 103(6):980-1004. Cadwell CR, Bhaduri A, Mostajo-Radji MA, Keefe MG, Nowakowski TJ. PMID: 31557462.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    10. Human brain development through the lens of cerebral organoid models. Brain Res. 2019 12 15; 1725:146470. Andrews MG, Nowakowski TJ. PMID: 31542572.
      View in: PubMed   Mentions: 1     Fields:    
    11. A recipe book for cell types in the human brain. Nature. 2019 09; 573(7772):36-37. Keefe MG, Nowakowski TJ. PMID: 31481767.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    12. Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration. Commun Biol. 2019; 2:155. Linsley JW, Tripathi A, Epstein I, Schmunk G, Mount E, Campioni M, Oza V, Barch M, Javaherian A, Nowakowski TJ, Samsi S, Finkbeiner S. PMID: 31069265.
      View in: PubMed   Mentions:
    13. Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex. Neuron. 2019 04 03; 102(1):143-158.e7. 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-Buylla A, Paredes MF, Nowakowski TJ, Pollen AA, Kriegstein AR. PMID: 30770253.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    14. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell. 2019 02 07; 176(4):743-756.e17. 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, Lowe CB, Pavlovic BJ, Salama SR, Haussler D, Eichler EE, Kriegstein AR. PMID: 30735633.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    15. Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function. Cell Rep. 2019 01 29; 26(5):1157-1173.e5. 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. PMID: 30699346.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    16. Neuroserpin expression during human brain development and in adult brain revealed by immunohistochemistry and single cell RNA sequencing. J Anat. 2019 09; 235(3):543-554. 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. PMID: 30644551.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    17. Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development. Nat Neurosci. 2018 12; 21(12):1784-1792. Nowakowski TJ, Rani N, Golkaram M, Zhou HR, Alvarado B, Huch K, West JA, Leyrat A, Pollen AA, Kriegstein AR, Petzold LR, Kosik KS. PMID: 30455455.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    18. Single-cell sequencing paints diverse pictures of the brain. Nature. 2018 11; 563(7729):38-39. Bhaduri A, Nowakowski TJ. PMID: 30382219.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    19. Building blocks of the human brain. Science. 2018 Oct 12; 362(6411):169. Nowakowski TJ. PMID: 30309940.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    20. Identification of cell types in a mouse brain single-cell atlas using low sampling coverage. BMC Biol. 2018 10 11; 16(1):113. Bhaduri A, Nowakowski TJ, Pollen AA, Kriegstein AR. PMID: 30309354.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    21. Transcriptional fates of human-specific segmental duplications in brain. Genome Res. 2018 10; 28(10):1566-1576. Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE. PMID: 30228200.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    22. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 07 26; 174(3):505-520. 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, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. PMID: 30053424.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    23. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell. 2018 05 31; 173(6):1356-1369.e22. 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, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, Kriegstein A, Eichler EE, Salama SR, Jacobs FMJ, Haussler D. PMID: 29856954.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    24. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat Genet. 2018 04 26; 50(5):727-736. 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, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ. PMID: 29700473.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    25. Evolution of New miRNAs and Cerebro-Cortical Development. Annu Rev Neurosci. 2018 07 08; 41:119-137. Kosik KS, Nowakowski T. PMID: 29618285.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimals
    26. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science. 2017 12 08; 358(6368):1318-1323. 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, Kriegstein AR. PMID: 29217575.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansCells
    27. The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells. Nat Commun. 2017 01 19; 8:14126. Gambardella G, Carissimo A, Chen A, Cutillo L, Nowakowski TJ, di Bernardo D, Blelloch R. PMID: 28102192.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    28. Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia. Cell Stem Cell. 2017 04 06; 20(4):435-449.e4. Bershteyn M, Nowakowski TJ, Pollen AA, Di Lullo E, Nene A, Wynshaw-Boris A, Kriegstein AR. PMID: 28111201.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansCells
    29. Chapter 16 microRNA and Neocortical Evolution. Essentials of Noncoding RNA in Neuroscience. 2017 Jan 1; 283-299. Thomas Pratt, Tomasz Jan Nowakowski, David Jonathan Price. .
      View in: Publisher Site   Mentions:
    30. Zika virus cell tropism in the developing human brain and inhibition by azithromycin. Proc Natl Acad Sci U S A. 2016 12 13; 113(50):14408-14413. 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. PMID: 27911847.
      View in: PubMed   Mentions: 117     Fields:    Translation:HumansCells
    31. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol. 2016 Nov 25; 12(11):889. Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A. PMID: 27888226.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    32. Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development. Neuron. 2016 Sep 21; 91(6):1219-1227. Nowakowski TJ, Pollen AA, Sandoval-Espinosa C, Kriegstein AR. PMID: 27657449.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    33. A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. Neuron. 2016 06 15; 90(6):1174-1188. Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS. PMID: 27263970.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    34. SCell: integrated analysis of single-cell RNA-seq data. Bioinformatics. 2016 07 15; 32(14):2219-20. Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim DA, Kriegstein A. PMID: 27153637.
      View in: PubMed   Mentions: 14     Fields:    
    35. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 2016 Apr 14; 17:67. Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA. PMID: 27081004.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    36. Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells. Cell Stem Cell. 2016 05 05; 18(5):591-6. Nowakowski TJ, Pollen AA, Di Lullo E, Sandoval-Espinosa C, Bershteyn M, Kriegstein AR. PMID: 27038591.
      View in: PubMed   Mentions: 151     Fields:    Translation:AnimalsCells
    37. Molecular identity of human outer radial glia during cortical development. Cell. 2015 Sep 24; 163(1):55-67. 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. PMID: 26406371.
      View in: PubMed   Mentions: 134     Fields:    Translation:HumansAnimalsCells
    38. The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell. 2015 Apr 02; 16(4):439-447. Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA. PMID: 25800779.
      View in: PubMed   Mentions: 82     Fields:    Translation:HumansAnimalsCells
    39. Radial glia require PDGFD-PDGFRß signalling in human but not mouse neocortex. Nature. 2014 Nov 13; 515(7526):264-8. Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC. PMID: 25391964.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    40. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol. 2014 Oct; 32(10):1053-8. 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, Wu S, Knutsson L, Alvarado B, Wang J, Weaver LS, May AP, Jones RC, Unger MA, Kriegstein AR, West JA. PMID: 25086649.
      View in: PubMed   Mentions: 212     Fields:    Translation:HumansAnimalsCells
    41. Loss of functional Dicer in mouse radial glia cell-autonomously prolongs cortical neurogenesis. Dev Biol. 2013 Oct 15; 382(2):530-7. Nowakowski TJ, Mysiak KS, O'Leary T, Fotaki V, Pratt T, Price DJ. PMID: 24012747.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    42. MicroRNA-92b regulates the development of intermediate cortical progenitors in embryonic mouse brain. Proc Natl Acad Sci U S A. 2013 Apr 23; 110(17):7056-61. Nowakowski TJ, Fotaki V, Pollock A, Sun T, Pratt T, Price DJ. PMID: 23569256.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    43. The expression and activity of ß-catenin in the thalamus and its projections to the cerebral cortex in the mouse embryo. BMC Neurosci. 2012 Feb 23; 13:20. Pratt T, Davey JW, Nowakowski TJ, Raasumaa C, Rawlik K, McBride D, Clinton M, Mason JO, Price DJ. PMID: 22360971.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    44. Functional dicer is necessary for appropriate specification of radial glia during early development of mouse telencephalon. PLoS One. 2011; 6(8):e23013. Nowakowski TJ, Mysiak KS, Pratt T, Price DJ. PMID: 21826226.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    45. Novel lines of Pax6-/- embryonic stem cells exhibit reduced neurogenic capacity without loss of viability. BMC Neurosci. 2010 Feb 24; 11:26. Quinn JC, Molinek M, Nowakowski TJ, Mason JO, Price DJ. PMID: 20178645.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    46. 01-P027 Investigating the roles of dicer1 endoribonuclease in embryonic organogenesis of mouse retina. Mechanisms of Development. 2009 Aug 1; 126:s58-s59. Tomasz Jan Nowakowski, Tom Pratt, David J. Price. .
      View in: Publisher Site   Mentions:
    47. Time-Multiplexed Laguerre-Gaussian holographic optical tweezers for biological applications. Opt Express. 2006 Apr 03; 14(7):3065-72. Lafong A, Hossack WJ, Arlt J, Nowakowski TJ, Read ND. PMID: 19516447.
      View in: PubMed   Mentions: 3     Fields:    
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