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Tomasz Nowakowski, PhD

Title(s)Assistant Professor, Anatomy
SchoolSchool of Medicine
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 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.
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    1. Eirene Markenscoff-Papadimitriou, Sean Whalen, Pawel Przytycki, Reuben Thomas, Fadya Binyameen, Tomasz J. Nowakowski, Stephan J. Sanders, Matthew W. State, Katherine S. Pollard, John L. Rubenstein. A Chromatin Accessibility Atlas of the Developing Human Telencephalon. 2019 Oct 21; 811620.
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    2. 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. Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders. Nat Commun. 2019 Oct 15; 10(1):4679. PMID: 31616000.
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    3. Cadwell CR, Bhaduri A, Mostajo-Radji MA, Keefe MG, Nowakowski TJ. Development and Arealization of the Cerebral Cortex. Neuron. 2019 Sep 25; 103(6):980-1004. PMID: 31557462.
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    4. Andrews MG, Nowakowski TJ. "Human Brain Development through the Lens of Cerebral Organoid Models". Brain Res. 2019 Sep 19; 146470. PMID: 31542572.
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    5. Keefe MG, Nowakowski TJ. A recipe book for cell types in the human brain. Nature. 2019 Sep; 573(7772):36-37. PMID: 31481767.
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    6. 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; 2:155. PMID: 31069265.
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    7. 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. Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex. Neuron. 2019 Apr 03; 102(1):143-158.e7. PMID: 30770253.
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    8. 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. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell. 2019 Feb 07; 176(4):743-756.e17. PMID: 30735633.
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    9. 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. Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function. Cell Rep. 2019 Jan 29; 26(5):1157-1173.e5. PMID: 30699346.
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    10. 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. Neuroserpin expression during human brain development and in adult brain revealed by immunohistochemistry and single cell RNA sequencing. J Anat. 2019 Sep; 235(3):543-554. PMID: 30644551.
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    11. Alex A Pollen, Aparna Bhaduri, Madeline G Andrews, Tomasz J Nowakowski, Olivia S Meyerson, Mohammed A Mostajo-Radji, Elizabeth Di Lullo, Beatriz Alvarado, Melanie Bedolli, Max L Dougherty, Ian T Fiddes, Zev N Kronenberg, Joe Shuga, Anne A Leyrat, Jay A West, Marina Bershteyn, Craig B Lowe, Bryan J Pavolvic, Sofie R Salama, David Haussler, Evan Eichler, Arnold A Kriegstein. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. 2018 Dec 19; 500934.
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    12. Nowakowski TJ, Rani N, Golkaram M, Zhou HR, Alvarado B, Huch K, West JA, Leyrat A, Pollen AA, Kriegstein AR, Petzold LR, Kosik KS. Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development. Nat Neurosci. 2018 12; 21(12):1784-1792. PMID: 30455455.
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    13. Bhaduri A, Nowakowski TJ. Single-cell sequencing paints diverse pictures of the brain. Nature. 2018 11; 563(7729):38-39. PMID: 30382219.
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    14. Nowakowski TJ. Building blocks of the human brain. Science. 2018 Oct 12; 362(6411):169. PMID: 30309940.
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    15. Bhaduri A, Nowakowski TJ, Pollen AA, Kriegstein AR. Identification of cell types in a mouse brain single-cell atlas using low sampling coverage. BMC Biol. 2018 10 11; 16(1):113. PMID: 30309354.
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    16. Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE. Transcriptional fates of human-specific segmental duplications in brain. Genome Res. 2018 10; 28(10):1566-1576. PMID: 30228200.
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    17. Tomasz J Nowakowski, Neha Rani, Golkaram, Hongjun R Zhou, Beatriz Alvarado, Kylie Huch, Jay West, Anne Leyrat, Alex A Pollen, Arnold R Kriegstein, Linda R Petzold, Kenneth S Kosik. Regulation of Cell-Type-Specific Transcriptomes by miRNA Networks During Human Brain Development. 2018 Sep 9; 412510.
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    18. 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. 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. PMID: 30053424.
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    19. 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. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell. 2018 05 31; 173(6):1356-1369.e22. PMID: 29856954.
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    20. 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. 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. PMID: 29700473.
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    21. Kosik KS, Nowakowski T. Evolution of New miRNAs and Cerebro-Cortical Development. Annu Rev Neurosci. 2018 07 08; 41:119-137. PMID: 29618285.
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    22. 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. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science. 2017 12 08; 358(6368):1318-1323. PMID: 29217575.
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    23. Ian T Fiddes, Gerrald A Lodewijk, Meghan M Mooring, Colleen M Bosworth, Adam D Ewing, Gary L Mantalas, Adam M Novak, Anouk van den Bout, Alex Bishara, Jimi L Rosenkrantz, Ryan Lorig-Roach, Andrew R Field, Maximillian Haeussler, Lotte Russo, Aparna Bhaduri, Tomasz J Nowakowski, Alex A Pollen, Max L Dougherty, Xander Nuttle, Marie-Claude Addor, Simon Zwolinski, Sol Katzman, Arnold Kreigstein, Evan E Eichler, Sofie R Salama, Frank MJ Jacobs, David Haussler. Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis. 2017 Nov 17; 221226.
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    24. Aparna Bhaduri, Tomasz J. Nowakowski, Alex A. Pollen, Arnold R. Kriegstein. Saturating Single-Cell Datasets. 2017 Nov 12; 218370.
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    25. Donna M Werling, Harrison Brand, Joon-Yong An, Matthew R Stone, Joseph T Glessner, Lingxue Zhu, Ryan L Collins, Shan Dong, Ryan M Layer, Eiriene-Chloe Markenscoff-Papadimitriou, Andrew Farrell, Grace B Schwartz, Benjamin B Currall, Jeanselle Dea, Clif Duhn, Carolyn Erdman, Michael Gilson, Robert E Handsaker, Seva Kashin, Lambertus Klei, Jeffrey D Mandell, Tomasz J Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F Walker, Harold Z Wang, Mathew J Waterman, Xin He, Arnold R Kriegstein, John L Rubenstein, Nenad Sestan, Steven A McCarroll, Ben M Neale, Hilary Coon, A. Jeremy Willsey, Joseph D Buxbaum, Mark J Daly, Matthew W State, Aaron Quinlan, Gabor T Marth, Kathryn Roeder, Bernie Devlin, Michael E Talkowski, Stephan J Sanders. Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families. 2017 Apr 13; 127043.
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    26. Bershteyn M, Nowakowski TJ, Pollen AA, Di Lullo E, Nene A, Wynshaw-Boris A, Kriegstein AR. 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. PMID: 28111201.
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    27. Gambardella G, Carissimo A, Chen A, Cutillo L, Nowakowski TJ, di Bernardo D, Blelloch R. The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells. Nat Commun. 2017 01 19; 8:14126. PMID: 28102192.
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    28. Thomas Pratt, Tomasz Jan Nowakowski, David Jonathan Price. Chapter 16 microRNA and Neocortical Evolution. 2017 Jan 1; 283-299.
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    29. 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. 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. PMID: 27911847.
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    30. Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol. 2016 Nov 25; 12(11):889. PMID: 27888226.
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    31. Nowakowski TJ, Pollen AA, Sandoval-Espinosa C, Kriegstein AR. Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development. Neuron. 2016 Sep 21; 91(6):1219-1227. PMID: 27657449.
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    32. Hanna Retallack, Elizabeth Di Lullo, Carolina Arias, Kristeene A. Knopp, Carmen Sandoval-Espinosa, Matthew T. Laurie, Yan Zhou, Matthew Gormley, Walter R. Mancia Leon, Robert Krencik, Erik M. Ullian, Julien Spatazza, Alex A. Pollen, Katherine Ona, Tomasz J. Nowakowski, Joseph L. DeRisi, Susan J. Fisher, Arnold R. Kriegstein. Zika Virus in the Human Placenta and Developing Brain: Cell Tropism and Drug Inhibition. 2016 Jun 15; 058883.
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    33. Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS. A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. Neuron. 2016 06 15; 90(6):1174-1188. PMID: 27263970.
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    34. Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim DA, Kriegstein A. SCell: integrated analysis of single-cell RNA-seq data. Bioinformatics. 2016 07 15; 32(14):2219-20. PMID: 27153637.
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    35. Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 2016 Apr 14; 17:67. PMID: 27081004.
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    36. Nowakowski TJ, Pollen AA, Di Lullo E, Sandoval-Espinosa C, Bershteyn M, Kriegstein AR. 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. PMID: 27038591.
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    37. 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. Molecular identity of human outer radial glia during cortical development. Cell. 2015 Sep 24; 163(1):55-67. PMID: 26406371.
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    38. Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA. 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. PMID: 25800779.
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    39. Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC. Radial glia require PDGFD-PDGFRß signalling in human but not mouse neocortex. Nature. 2014 Nov 13; 515(7526):264-8. PMID: 25391964.
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    40. 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. 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. PMID: 25086649.
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    41. Nowakowski TJ, Mysiak KS, O'Leary T, Fotaki V, Pratt T, Price DJ. Loss of functional Dicer in mouse radial glia cell-autonomously prolongs cortical neurogenesis. Dev Biol. 2013 Oct 15; 382(2):530-7. PMID: 24012747.
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    42. Nowakowski TJ, Fotaki V, Pollock A, Sun T, Pratt T, Price DJ. 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. PMID: 23569256.
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    43. Pratt T, Davey JW, Nowakowski TJ, Raasumaa C, Rawlik K, McBride D, Clinton M, Mason JO, Price DJ. 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. PMID: 22360971.
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    44. Nowakowski TJ, Mysiak KS, Pratt T, Price DJ. Functional dicer is necessary for appropriate specification of radial glia during early development of mouse telencephalon. PLoS One. 2011; 6(8):e23013. PMID: 21826226.
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    45. Quinn JC, Molinek M, Nowakowski TJ, Mason JO, Price DJ. Novel lines of Pax6-/- embryonic stem cells exhibit reduced neurogenic capacity without loss of viability. BMC Neurosci. 2010 Feb 24; 11:26. PMID: 20178645.
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    46. Tomasz Jan Nowakowski, Tom Pratt, David J. Price. 01-P027 Investigating the roles of dicer1 endoribonuclease in embryonic organogenesis of mouse retina. 2009 Aug 1; 126:s58-s59.
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    47. A. Lafong, W. J. Hossack, J. Arlt, T. J. Nowakowski, N. D. Read. Multiple trap Laguerre-Gaussian holographic optical tweezers using a multiplexed ferroelectric SLM. 2006 Aug 31; 6326:63262s-63262s-8.
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    48. Lafong A, Hossack WJ, Arlt J, Nowakowski TJ, Read ND. Time-Multiplexed Laguerre-Gaussian holographic optical tweezers for biological applications. Opt Express. 2006 Apr 03; 14(7):3065-72. PMID: 19516447.
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