Tomasz Nowakowski, PhD

Title(s)Associate Professor, Neurological Surgery
SchoolSchool of Medicine
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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
    University of California, San Francisco, CA09/2021Diversity, Equity, and Inclusion Champion Training
    Collapse Awards and Honors
    Vilcek Foundation2024Vilcek Prize for Creative Promise in Biomedical Science
    The Japan Neuroscience Society2023Joseph Altman Award in Developmental Neuroscience
    New York Stem Cell Foundation2022Robertson Neuroscience Investigator
    Sontag Foundation2021  - 2024Distinguished Scientist Award
    Chan-Zuckerberg Biohub2018  - 2021Investigator
    Klingenstein-Simons Fund2021Fellowship Award in Neuroscience
    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 Overview 
    Collapse In The News

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    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. Massively parallel characterization of regulatory elements in the developing human cortex. Science. 2024 May 24; 384(6698):eadh0559. 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. PMID: 38781390.
      View in: PubMed   Mentions:
    2. Type-I-interferon-responsive microglia shape cortical development and behavior. Cell. 2024 Apr 11; 187(8):1936-1954.e24. 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. PMID: 38490196; PMCID: PMC11015974.
      View in: PubMed   Mentions:    Fields:    
    3. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell. 2024 03 07; 31(3):421-432.e8. 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. PMID: 38382530; PMCID: PMC10939828.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    4. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv. 2024 Feb 08. 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, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. PMID: 38076945; PMCID: PMC10705567.
      View in: PubMed   Mentions:
    5. 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. 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. PMID: 38266077; PMCID: PMC10807795.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    6. Improving cellular diversity in human cerebellar organoids. Cell Stem Cell. 2024 01 04; 31(1):3-4. Steyert M, Nowakowski T. PMID: 38181748.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    7. Spatiotemporal molecular dynamics of the developing human thalamus. Science. 2023 10 13; 382(6667):eadf9941. Kim CN, Shin D, Wang A, Nowakowski TJ. PMID: 37824646; PMCID: PMC10758299.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    8. Single-cell analysis of prenatal and postnatal human cortical development. Science. 2023 10 13; 382(6667):eadf0834. 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. PMID: 37824647; PMCID: PMC11005279.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    9. Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids. Elife. 2023 07 20; 12. Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T. PMID: 37470786; PMCID: PMC10370260.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    10. Three-dimensional genome rewiring in loci with human accelerated regions. Science. 2023 04 28; 380(6643):eabm1696. 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. PMID: 37104607; PMCID: PMC10999243.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    11. 385 A Cell Resolution Atlas of the Human Cerebrovasculature Reveals Angiogenic and Inflammatory Cell Programs in Arteriovenous Malformations. Neurosurgery. 2023 Apr 1; 69(Supplement_1):69-69. Winkler WE, Kim KC, Ross RJ, Garcia GJ, Gil GE, Oh OI, Chen CL, Wu WD, Catapano CJ, Raygor RK, Narsinh NK, Kim KH, Weinsheimer WS, Cooke CD, Walcott WB, Lawton LM, Gupta GN, Zlokovic ZB, Chang CE, Abla AA, Lim LD, Nowakowski NT. .
      View in: Publisher Site   Mentions:
    12. Transcriptomic cell type structures in vivo neuronal activity across multiple timescales. Cell Rep. 2023 04 25; 42(4):112318. Schneider A, Azabou M, McDougall-Vigier L, Parks DF, Ensley S, Bhaskaran-Nair K, Nowakowski T, Dyer EL, Hengen KB. PMID: 36995938; PMCID: PMC10539488.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    13. Type I interferon responsive microglia shape cortical development and behavior. bioRxiv. 2023 Mar 20. 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, Molofsky AV. PMID: 35233577; PMCID: PMC8887080.
      View in: PubMed   Mentions:
    14. Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex. bioRxiv. 2023 Feb 16. 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. PMID: 36824845; PMCID: PMC9949039.
      View in: PubMed   Mentions:
    15. Abstract 52: Prevalence Of Somatic Activating Kras Mutations In Pediatric And Adult Sporadic Brain Arteriovenous Malformations. Stroke. 2023 Feb 1; 54(Suppl_1):a52-a52. Winkler WE, Garcia GJ, Tsang TC, Nelson NJ, McCulloch MC, Weinsheimer WS, Fox FC, Fullerton FH, Ko KN, Su SH, Nowakowski NT, Cooke CD, Hetts HS, Guney GE, PEKMEZCI PM, Tihan TT, Lawton LM, Abla AA, Gupta GN, Kim KH. .
      View in: Publisher Site   Mentions:
    16. New York Stem Cell Foundation Robertson Investigators. Cell Stem Cell. 2022 Dec 01; 29(12):1621-1623. McKinley KL, van Boxtel R, Finley LWS, Peña CJ, Nowakowski TJ. PMID: 36459965.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    17. In preprints: new insights into truncated radial glia. Development. 2022 Nov 15; 149(22). Steyert M, Nowakowski TJ. PMID: 36382646.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    18. Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders. Proc Natl Acad Sci U S A. 2022 11 15; 119(46):e2203491119. Wang T, Kim CN, Bakken TE, Gillentine MA, Henning B, Mao Y, Gilissen C, SPARK Consortium, Nowakowski TJ, Eichler EE. PMID: 36350923; PMCID: PMC9674258.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    19. IoT cloud laboratory: Internet of Things architecture for cellular biology. Internet Things (Amst). 2022 Nov; 20. 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, Mostajo-Radji MA, Salama SR, Teodorescu M, Haussler D. PMID: 37383277; PMCID: PMC10305744.
      View in: PubMed   Mentions: 3  
    20. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells. 2022 09 08; 11(18). Nowakowski TJ, Salama SR. PMID: 36139380; PMCID: PMC9496777.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    21. Tropism of SARS-CoV-2 for human cortical astrocytes. Proc Natl Acad Sci U S A. 2022 07 26; 119(30):e2122236119. 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 D, Salma J, Pollen AA, Nowakowski TJ, Ullian E, Kumar GR, Winkler EA, Crouch EE, Ott M, Kriegstein AR. PMID: 35858406; PMCID: PMC9335272.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    22. Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes. Science. 2022 06 24; 376(6600):1441-1446. Allen DE, Donohue KC, Cadwell CR, Shin D, Keefe MG, Sohal VS, Nowakowski TJ. PMID: 35587512; PMCID: PMC9233096.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    23. Dissecting cellular diversity of cortical GABAergic cells across multiple modalities: A turning point in neuronal taxonomy. Fac Rev. 2022; 11:13. Arlotta P, Chen F, Lodato S, Margrie TW, Nowakowski TJ, Pederson T, Rico B. PMID: 35719130; PMCID: PMC9190211.
      View in: PubMed   Mentions:
    24. Microglial GPR56 is the molecular target of maternal immune activation-induced parvalbumin-positive interneuron deficits. Sci Adv. 2022 05 06; 8(18):eabm2545. Yu D, Li T, Delpech JC, Zhu B, Kishore P, Koshi T, Luo R, Pratt KJB, Popova G, Nowakowski TJ, Villeda SA, Piao X. PMID: 35544642; PMCID: PMC9075805.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    25. The development and evolution of inhibitory neurons in primate cerebrum. Nature. 2022 03; 603(7903):871-877. Schmitz MT, Sandoval K, Chen CP, Mostajo-Radji MA, Seeley WW, Nowakowski TJ, Ye CJ, Paredes MF, Pollen AA. PMID: 35322231; PMCID: PMC8967711.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    26. A single-cell atlas of the normal and malformed human brain vasculature. Science. 2022 03 04; 375(6584):eabi7377. 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, Lim DA, Nowakowski TJ. PMID: 35084939; PMCID: PMC8995178.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansCells
    27. Endoluminal Biopsy for Molecular Profiling of Human Brain Vascular Malformations. Neurology. 2022 04 19; 98(16):e1637-e1647. 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. PMID: 35145012; PMCID: PMC9052570.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    28. DynaMorph: self-supervised learning of morphodynamic states of live cells. Mol Biol Cell. 2022 05 15; 33(6):ar59. Wu Z, Chhun BB, Popova G, Guo SM, Kim CN, Yeh LH, Nowakowski T, Zou J, Mehta SB. PMID: 35138913; PMCID: PMC9265147.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    29. Nests of dividing neuroblasts sustain interneuron production for the developing human brain. Science. 2022 01 28; 375(6579):eabk2346. 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 J, Vento M, Scott J, Studholme C, Nowakowski TJ, Kriegstein AR, Oldham MC, Hasenstaub A, Garcia-Verdugo JM, Alvarez-Buylla A, Huang EJ. PMID: 35084970; PMCID: PMC8887556.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    30. Single-cell delineation of lineage and genetic identity in the mouse brain. Nature. 2022 01; 601(7893):404-409. 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. PMID: 34912118; PMCID: PMC8770128.
      View in: PubMed   Mentions: 46     Fields:    Translation:AnimalsCells
    31. Individual human cortical progenitors can produce excitatory and inhibitory neurons. Nature. 2022 01; 601(7893):397-403. Delgado RN, Allen DE, Keefe MG, Mancia Leon WR, Ziffra RS, Crouch EE, Alvarez-Buylla A, Nowakowski TJ. PMID: 34912114; PMCID: PMC8994470.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    32. UCSC Cell Browser: visualize your single-cell data. Bioinformatics. 2021 12 07; 37(23):4578-4580. Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M. PMID: 34244710; PMCID: PMC8652023.
      View in: PubMed   Mentions: 63     Fields:    
    33. Endovascular Biopsy of Vertebrobasilar Aneurysm in Patient With Polyarteritis Nodosa. Front Neurol. 2021; 12:697105. 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. PMID: 34887823; PMCID: PMC8650719.
      View in: PubMed   Mentions: 2  
    34. Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments. J Neural Eng. 2021 11 12; 18(6). 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. PMID: 34666315; PMCID: PMC8667733.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    35. Picroscope: low-cost system for simultaneous longitudinal biological imaging. Commun Biol. 2021 11 04; 4(1):1261. 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. PMID: 34737378; PMCID: PMC8569150.
      View in: PubMed   Mentions: 8  Translation:Animals
    36. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021 10; 598(7879):205-213. 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. PMID: 34616060; PMCID: PMC8494642.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansCells
    37. An atlas of cortical arealization identifies dynamic molecular signatures. Nature. 2021 10; 598(7879):200-204. Bhaduri A, Sandoval-Espinosa C, Otero-Garcia M, Oh I, Yin R, Eze UC, Nowakowski TJ, Kriegstein AR. PMID: 34616070; PMCID: PMC8494648.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansCells
    38. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids. Cell Stem Cell. 2021 12 02; 28(12):2153-2166.e6. 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. PMID: 34536354; PMCID: PMC8642295.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    39. Low cost cloud based remote microscopy for biological sciences. Internet of Things. 2021 Sep 1; 100454. Baudin BP, Ly LV, Pansodtee PP, Jung JE, Currie CR, Hoffman HR, Willsey WH, Pollen PA, Nowakowski NT, Haussler HD, Mostajo-Radji MM, Salama SS, Teodorescu TM. .
      View in: Publisher Site   Mentions:
    40. Distinct nuclear compartment-associated genome architecture in the developing mammalian brain. Nat Neurosci. 2021 09; 24(9):1235-1242. Ahanger SH, Delgado RN, Gil E, Cole MA, Zhao J, Hong SJ, Kriegstein AR, Nowakowski TJ, Pollen AA, Lim DA. PMID: 34239128; PMCID: PMC8410652.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    41. The CHD8/CHD7/Kismet family links blood-brain barrier glia and serotonin to ASD-associated sleep defects. Sci Adv. 2021 06; 7(23). 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. PMID: 34088660; PMCID: PMC8177706.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    42. 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. 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. PMID: 33887193; PMCID: PMC8145999.
      View in: PubMed   Mentions: 10     Fields:    
    43. Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders. Genome Med. 2021 04 19; 13(1):63. 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, Zanni G, Bertini E, Zweier C, Schuhmann S, Wiesener A, Pepper M, Panjwani H, Torti E, Abid F, Anselm I, Srivastava S, Atwal P, Bacino CA, Bhat G, Cobian K, Bird LM, Friedman J, Wright MS, Callewaert B, Petit F, Mathieu S, Afenjar A, Christensen CK, White KM, Elpeleg O, Berger I, Espineli EJ, Fagerberg C, Brasch-Andersen C, Hansen LK, Feyma T, Hughes S, Thiffault I, Sullivan B, Yan S, Keller K, Keren B, Mignot C, Kooy F, Meuwissen M, Basinger A, Kukolich M, Philips M, Ortega L, Drummond-Borg M, Lauridsen M, Sorensen K, Lehman A, CAUSES Study, Lopez-Rangel E, Levy P, Lessel D, Lotze T, Madan-Khetarpal S, Sebastian J, Vento J, Vats D, Benman LM, Mckee S, Mirzaa GM, Muss C, Pappas J, Peeters H, Romano C, Elia M, Galesi O, Simon MEH, van Gassen KLI, Simpson K, Stratton R, Syed S, Thevenon J, Palafoll IV, Vitobello A, Bournez M, Faivre L, Xia K, SPARK Consortium, Earl RK, Nowakowski T, Bernier RA, Eichler EE. PMID: 33874999; PMCID: PMC8056596.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    44. Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. Nat Neurosci. 2021 04; 24(4):584-594. Eze UC, Bhaduri A, Haeussler M, Nowakowski TJ, Kriegstein AR. PMID: 33723434; PMCID: PMC8012207.
      View in: PubMed   Mentions: 130     Fields:    Translation:HumansAnimalsCells
    45. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron. 2021 03 03; 109(5):788-804.e8. 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. PMID: 33497602; PMCID: PMC8132462.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    46. The Expanding Cell Diversity of the Brain Vasculature. Front Physiol. 2020; 11:600767. Ross JM, Kim C, Allen D, Crouch EE, Narsinh K, Cooke DL, Abla AA, Nowakowski TJ, Winkler EA. PMID: 33343397; PMCID: PMC7744630.
      View in: PubMed   Mentions: 22  
    47. Are Organoids Ready for Prime Time? Cell Stem Cell. 2020 09 03; 27(3):361-365. Bhaduri A, Andrews MG, Kriegstein AR, Nowakowski TJ. PMID: 32888425; PMCID: PMC7559415.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    48. Revealing architectural order with quantitative label-free imaging and deep learning. Elife. 2020 07 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 TJ, Mehta SB. PMID: 32716843; PMCID: PMC7431134.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    49. A Chromatin Accessibility Atlas of the Developing Human Telencephalon. Cell. 2020 08 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; PMCID: PMC7415678.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansAnimalsCells
    50. Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2+ Granule Neuron Precursor. Cell Rep. 2020 04 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: 22     Fields:    Translation:HumansAnimalsCells
    51. 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; PMCID: PMC7433012.
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    52. Evolutionary Expansion of Human Cerebellar Germinal Zones. Trends Neurosci. 2020 02; 43(2):75-77. Keefe MG, Nowakowski TJ. PMID: 31954525.
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    53. 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; PMCID: PMC7029801.
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    54. 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, University of Washington Center for Mendelian Genomics, 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; PMCID: PMC6794285.
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    55. 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; PMCID: PMC9245854.
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    56. Human brain development through the lens of cerebral organoid models. Brain Res. 2019 12 15; 1725:146470. Andrews MG, Nowakowski TJ. PMID: 31542572; PMCID: PMC6887101.
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    57. A recipe book for cell types in the human brain. Nature. 2019 09; 573(7772):36-37. Keefe MG, Nowakowski TJ. PMID: 31481767.
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    58. 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; PMCID: PMC6494885.
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    59. 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; PMCID: PMC7648658.
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    60. 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; PMCID: PMC6544371.
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    61. 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; PMCID: PMC6602795.
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    62. 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; PMCID: PMC6704272.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    63. 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; PMCID: PMC6312854.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    64. Single-cell sequencing paints diverse pictures of the brain. Nature. 2018 11; 563(7729):38-39. Bhaduri A, Nowakowski TJ. PMID: 30382219.
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    65. Building blocks of the human brain. Science. 2018 Oct 12; 362(6411):169. Nowakowski TJ. PMID: 30309940.
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    66. 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; PMCID: PMC6180488.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    67. 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; PMCID: PMC6169893.
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    68. 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; PMCID: PMC6247911.
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    69. 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; PMCID: PMC5986104.
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    70. 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; PMCID: PMC5961723.
      View in: PubMed   Mentions: 133     Fields:    Translation:Humans
    71. 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: 15     Fields:    Translation:HumansAnimals
    72. 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; PMCID: PMC5991609.
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    73. 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; PMCID: PMC5667944.
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    74. 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; PMCID: PMC5253645.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    75. 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; PMCID: PMC5167169.
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    76. 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; PMCID: PMC5147052.
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    77. 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; PMCID: PMC5087333.
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    78. 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; PMCID: PMC4911262.
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    79. 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; PMCID: PMC4937196.
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    80. 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; PMCID: PMC4831157.
      View in: PubMed   Mentions: 165     Fields:    Translation:HumansCells
    81. 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; PMCID: PMC4860115.
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    82. 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; PMCID: PMC4583716.
      View in: PubMed   Mentions: 372     Fields:    Translation:HumansAnimalsCells
    83. 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; PMCID: PMC4388801.
      View in: PubMed   Mentions: 181     Fields:    Translation:HumansAnimalsCells
    84. Radial glia require PDGFD-PDGFRβ 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; PMCID: PMC4231536.
      View in: PubMed   Mentions: 87     Fields:    Translation:HumansAnimalsCells
    85. 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; PMCID: PMC4191988.
      View in: PubMed   Mentions: 405     Fields:    Translation:HumansAnimalsCells
    86. 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; PMCID: PMC3793872.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    87. 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; PMCID: PMC3637761.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    88. The expression and activity of β-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; PMCID: PMC3347985.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    89. 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; PMCID: PMC3149632.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    90. 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; PMCID: PMC2837049.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    91. 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.
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