Alex Pollen, PhD

Title(s)Associate Professor, Neurology
SchoolSchool of Medicine
Address1651 4th Street
San Francisco CA 94158
Phone--
ORCID ORCID Icon0000-0003-3263-8634 Additional info
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    Other Positions
    Title(s)UCSF Weill Institute for Neurosciences


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    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. 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:    Fields:    Translation:HumansCells
    2. 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: 2     Fields:    Translation:AnimalsCells
    3. Rethinking nomenclature for interspecies cell fusions. Nat Rev Genet. 2022 05; 23(5):315-320. Pavlovic BJ, Fox D, Schaefer NK, Pollen AA. PMID: 35082442.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. 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: 1     Fields:    Translation:Humans
    5. 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: 2  Translation:Animals
    6. The genetic symphony underlying evolution of the brain's prefrontal cortex. Nature. 2021 10; 598(7881):417-418. Wallace JL, Pollen AA. PMID: 34588642.
      View in: PubMed   Mentions:    Fields:    
    7. UCSC Cell Browser: Visualize Your Single-Cell Data. Bioinformatics. 2021 Jul 09. 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: 12     Fields:    
    8. 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: 5     Fields:    Translation:HumansAnimalsCells
    9. Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes. bioRxiv. 2021 Jan 18. Andrews MG, Mukhtar T, Eze UC, Simoneau CR, Perez Y, Mostajo-Radji MA, Wang S, Velmeshev D, Salma J, Kumar GR, Pollen AA, Crouch EE, Ott M, Kriegstein AR. PMID: 33469577; PMCID: PMC7814814.
      View in: PubMed   Mentions:
    10. Cell-type-specific 3D epigenomes in the developing human cortex. Nature. 2020 11; 587(7835):644-649. Song M, Pebworth MP, Yang X, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Li B, Maliskova L, Lee J, Liu W, Pollen AA, Li Y, Wang T, Hu M, Kriegstein AR, Shen Y. PMID: 33057195; PMCID: PMC7704572.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    11. Direct analysis of brain phenotypes via neural blastocyst complementation. Nat Protoc. 2020 10; 15(10):3154-3181. Dai HQ, Liang Z, Chang AN, Chapdelaine-Williams AM, Alvarado B, Pollen AA, Alt FW, Schwer B. PMID: 32778838; PMCID: PMC7685531.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    12. Recurrent inversion toggling and great ape genome evolution. Nat Genet. 2020 08; 52(8):849-858. Porubsky D, Sanders AD, Höps W, Hsieh P, Sulovari A, Li R, Mercuri L, Sorensen M, Murali SC, Gordon D, Cantsilieris S, Pollen AA, Ventura M, Antonacci F, Marschall T, Korbel JO, Eichler EE. PMID: 32541924; PMCID: PMC7415573.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    13. 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.
      View in: PubMed   Mentions: 123     Fields:    Translation:HumansCells
    14. Reverse engineering human brain evolution using organoid models. Brain Res. 2020 02 15; 1729:146582. Mostajo-Radji MA, Schmitz MT, Montoya ST, Pollen AA. PMID: 31809699; PMCID: PMC7058376.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    15. Human-specific tandem repeat expansion and differential gene expression during primate evolution. Proc Natl Acad Sci U S A. 2019 11 12; 116(46):23243-23253. Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA, Human Genome Structural Variation Consortium, Warren WC, Pollen AA, Chaisson MJP, Eichler EE. PMID: 31659027; PMCID: PMC6859368.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    16. Getting to the heart of cardiovascular evolution in humans. Elife. 2019 05 28; 8. Pollen A, Pavlovic BJ. PMID: 31135336; PMCID: PMC6538371.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    17. Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution. Hum Genet. 2019 Jul; 138(7):715-721. Fiddes IT, Pollen AA, Davis JM, Sikela JM. PMID: 31087184; PMCID: PMC6611739.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    18. 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.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    19. 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.
      View in: PubMed   Mentions: 142     Fields:    Translation:HumansAnimalsCells
    20. Physiological Models of Human Neuronal Development and Disease. Neuron. 2018 12 05; 100(5):1025-1027. Mostajo-Radji MA, Pollen AA. PMID: 30521777.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    21. 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: 46     Fields:    Translation:HumansCells
    22. 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: 7     Fields:    Translation:Animals
    23. 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.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    24. Postmitotic Fate Refinement in the Subplate. Cell Stem Cell. 2018 07 05; 23(1):7-9. Mostajo-Radji MA, Pollen AA. PMID: 29979992.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    25. High-resolution comparative analysis of great ape genomes. Science. 2018 06 08; 360(6393). Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. PMID: 29880660; PMCID: PMC6178954.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansAnimals
    26. 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.
      View in: PubMed   Mentions: 125     Fields:    Translation:HumansAnimalsCells
    27. 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.
      View in: PubMed   Mentions: 248     Fields:    Translation:HumansCells
    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; PMCID: PMC5667944.
      View in: PubMed   Mentions: 186     Fields:    Translation:HumansCells
    29. 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.
      View in: PubMed   Mentions: 232     Fields:    Translation:HumansCells
    30. 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.
      View in: PubMed   Mentions: 47     Fields:    Translation:Humans
    31. Primate Neurons Flex Their Musclin. Neuron. 2016 Nov 23; 92(4):681-683. Pollen AA, Kriegstein AR. PMID: 27883900.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    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; PMCID: PMC5087333.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansCells
    33. 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.
      View in: PubMed   Mentions: 24     Fields:    
    34. 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: 144     Fields:    Translation:HumansCells
    35. 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.
      View in: PubMed   Mentions: 251     Fields:    Translation:AnimalsCells
    36. 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: 294     Fields:    Translation:HumansAnimalsCells
    37. 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: 72     Fields:    Translation:HumansAnimalsCells
    38. 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: 367     Fields:    Translation:HumansAnimalsCells
    39. How unique is the human neocortex? Development. 2014 Jan; 141(1):11-6. Molnár Z, Pollen A. PMID: 24346696.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimals
    40. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 2012 Apr 04; 484(7392):55-61. Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C, Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM. PMID: 22481358; PMCID: PMC3322419.
      View in: PubMed   Mentions: 597     Fields:    Translation:AnimalsCells
    41. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 2011 Mar 10; 471(7337):216-9. McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM. PMID: 21390129; PMCID: PMC3071156.
      View in: PubMed   Mentions: 188     Fields:    Translation:HumansAnimalsCells
    42. Interspecific profiling of gene expression informed by comparative genomic hybridization: A review and a novel approach in African cichlid fishes. Integr Comp Biol. 2009 Dec; 49(6):644-59. Machado HE, Pollen AA, Hofmann HA, Renn SC. PMID: 21665847.
      View in: PubMed   Mentions: 7     Fields:    
    43. Beyond neuroanatomy: novel approaches to studying brain evolution. Brain Behav Evol. 2008; 72(2):145-58. Pollen AA, Hofmann HA. PMID: 18836260.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    44. cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell. 2007 Dec 14; 131(6):1179-89. Miller CT, Beleza S, Pollen AA, Schluter D, Kittles RA, Shriver MD, Kingsley DM. PMID: 18083106; PMCID: PMC2900316.
      View in: PubMed   Mentions: 158     Fields:    Translation:HumansAnimalsCells
    45. Comparative aspects of cortical neurogenesis in vertebrates. J Anat. 2007 Aug; 211(2):164-76. Cheung AF, Pollen AA, Tavare A, DeProto J, Molnár Z. PMID: 17634059; PMCID: PMC2375772.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansAnimalsCells
    46. Environmental complexity and social organization sculpt the brain in Lake Tanganyikan cichlid fish. Brain Behav Evol. 2007; 70(1):21-39. Pollen AA, Dobberfuhl AP, Scace J, Igulu MM, Renn SC, Shumway CA, Hofmann HA. PMID: 17389793.
      View in: PubMed   Mentions: 54     Fields:    Translation:Animals
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