Alex Pollen, PhD
Associate Professor
Neurology
School of Medicine

Websites

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• Pollen Lab website (pollenlab.org)

Publications (60)

Top publication keywords:
NeuronsHominidaeOlfactory BulbNeural Stem CellsNeurogliaNeurogenesisBiological EvolutionNeocortexCerebral CortexBrainPluripotent Stem CellsNervous SystemMacacaPan troglodytesOrganoids

• Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.
  Cell 2019 Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, …
• High-resolution comparative analysis of great ape genomes.
  Science (New York, N.Y.) 2018 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, …
• Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.
  Science (New York, N.Y.) 2017 Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M, Sandoval-Espinosa C, Liu SJ, Velmeshev D, Ounadjela JR, Shuga J, Wang X, Lim DA, West JA, Leyrat AA, Kent WJ…
• Molecular identity of human outer radial glia during cortical development.
  Cell 2015 Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR
• Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
  Nature biotechnology 2014 Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, Li N, Szpankowski L, Fowler B, Chen P, Ramalingam N, Sun G, Thu M, Norris M, Lebofsky R, Toppani D, Kemp DW, Wong M, Clerkson B, Jones BN,…
• Human-specific loss of regulatory DNA and the evolution of human-specific traits.
  Nature 2011 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

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• Structurally divergent and recurrently mutated regions of primate genomes.
  Cell 2024 Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, …
• Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders.
  Cell stem cell 2024 Shin D, Kim CN, Ross J, Hennick KM, Wu SR, Paranjape N, Leonard R, Wang JC, Keefe MG, Pavlovic BJ, Donohue KC, Moreau C, Wigdor EM, Larson HH, Allen DE, Cadwell CR, Bhaduri A, Popova G, Bearden CE, …
• Mapping cis- and trans-regulatory target genes of human-specific deletions.
  bioRxiv : the preprint server for biology 2023 Fair T, Pavlovic BJ, Schaefer NK, Pollen AA
• Human neuronal maturation comes of age: cellular mechanisms and species differences.
  Nature reviews. Neuroscience 2023 Wallace JL, Pollen AA
• A cross-species proteomic map reveals neoteny of human synapse development.
  Nature 2023 Wang L, Pang K, Zhou L, Cebrián-Silla A, González-Granero S, Wang S, Bi Q, White ML, Ho B, Li J, Li T, Perez Y, Huang EJ, Winkler EA, Paredes MF, Kovner R, Sestan N, Pollen AA, Liu P, Li J, Piao X, …
• Comparative landscape of genetic dependencies in human and chimpanzee stem cells.
  Cell 2023 She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA
• Three-dimensional genome rewiring in loci with human accelerated regions.
  Science (New York, N.Y.) 2023 Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Zoonomia Consortium§, Nowakowski T, Ahituv N, Pollen A, Pollard KS
• Genetic architecture of human brain evolution.
  Current opinion in neurobiology 2023 Fair T, Pollen AA
• Comparative landscape of genetic dependencies in human and chimpanzee stem cells.
  bioRxiv : the preprint server for biology 2023 She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA
• Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex.
  bioRxiv : the preprint server for biology 2023 Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen A, Nowakowski TJ, Ahituv N, Pollard KS
• Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution.
  Nature reviews. Genetics 2023 Pollen AA, Kilik U, Lowe CB, Camp JG
• Machine learning dissection of human accelerated regions in primate neurodevelopment.
  Neuron 2023 Whalen S, Inoue F, Ryu H, Fair T, Markenscoff-Papadimitriou E, Keough K, Kircher M, Martin B, Alvarado B, Elor O, Laboy Cintron D, Williams A, Hassan Samee MA, Thomas S, Krencik R, Ullian EM, …
• Filling an ARHGAP in our knowledge of human brain evolution.
  EMBO reports 2022 Ding J, Pollen AA
• IoT cloud laboratory: Internet of Things architecture for cellular biology.
  Internet of things (Amsterdam, Netherlands) 2022 Parks DF, Voitiuk K, Geng J, Elliott MAT, Keefe MG, Jung EA, Robbins A, Baudin PV, Ly VT, Hawthorne N, Yong D, Sanso SE, Rezaee N, Sevetson JL, Seiler ST, Currie R, Pollen AA, Hengen KB, Nowakowski TJ…
• Tropism of SARS-CoV-2 for human cortical astrocytes.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Andrews MG, Mukhtar T, Eze UC, Simoneau CR, Ross J, Parikshak N, Wang S, Zhou L, Koontz M, Velmeshev D, Siebert CV, Gemenes KM, Tabata T, Perez Y, Wang L, Mostajo-Radji MA, de Majo M, Donohue KC, Shin…
• The development and evolution of inhibitory neurons in primate cerebrum.
  Nature 2022 Schmitz MT, Sandoval K, Chen CP, Mostajo-Radji MA, Seeley WW, Nowakowski TJ, Ye CJ, Paredes MF, Pollen AA
• Rethinking nomenclature for interspecies cell fusions.
  Nature reviews. Genetics 2022 Pavlovic BJ, Fox D, Schaefer NK, Pollen AA
• UCSC Cell Browser: visualize your single-cell data.
  Bioinformatics (Oxford, England) 2021 Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M
• Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments.
  Journal of neural engineering 2021 Voitiuk K, Geng J, Keefe MG, Parks DF, Sanso SE, Hawthorne N, Freeman DB, Currie R, Mostajo-Radji MA, Pollen AA, Nowakowski TJ, Salama SR, Teodorescu M, Haussler D
• Picroscope: low-cost system for simultaneous longitudinal biological imaging.
  Communications biology 2021 Ly VT, Baudin PV, Pansodtee P, Jung EA, Voitiuk K, Rosen YM, Willsey HR, Mantalas GL, Seiler ST, Selberg JA, Cordero SA, Ross JM, Rolandi M, Pollen AA, Nowakowski TJ, Haussler D, Mostajo-Radji MA, …
• The genetic symphony underlying evolution of the brain's prefrontal cortex.
  Nature 2021 Wallace JL, Pollen AA
• Distinct nuclear compartment-associated genome architecture in the developing mammalian brain.
  Nature neuroscience 2021 Ahanger SH, Delgado RN, Gil E, Cole MA, Zhao J, Hong SJ, Kriegstein AR, Nowakowski TJ, Pollen AA, Lim DA
• Tropism of SARS-CoV-2 for Developing Human Cortical Astrocytes.
  bioRxiv : the preprint server for biology 2021 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
• Cell-type-specific 3D epigenomes in the developing human cortex.
  Nature 2020 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, …
• Direct analysis of brain phenotypes via neural blastocyst complementation.
  Nature protocols 2020 Dai HQ, Liang Z, Chang AN, Chapdelaine-Williams AM, Alvarado B, Pollen AA, Alt FW, Schwer B
• Recurrent inversion toggling and great ape genome evolution.
  Nature genetics 2020 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
• Cell stress in cortical organoids impairs molecular subtype specification.
  Nature 2020 Bhaduri A, Andrews MG, Mancia Leon W, Jung D, Shin D, Allen D, Jung D, Schmunk G, Haeussler M, Salma J, Pollen AA, Nowakowski TJ, Kriegstein AR
• Reverse engineering human brain evolution using organoid models.
  Brain research 2019 Mostajo-Radji MA, Schmitz MT, Montoya ST, Pollen AA
• Human-specific tandem repeat expansion and differential gene expression during primate evolution.
  Proceedings of the National Academy of Sciences of the United States of America 2019 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
• Getting to the heart of cardiovascular evolution in humans.
  eLife 2019 Pollen A, Pavlovic BJ
• Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution.
  Human genetics 2019 Fiddes IT, Pollen AA, Davis JM, Sikela JM
• Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex.
  Neuron 2019 Mayer S, Chen J, Velmeshev D, Mayer A, Eze UC, Bhaduri A, Cunha CE, Jung D, Arjun A, Li E, Alvarado B, Wang S, Lovegren N, Gonzales ML, Szpankowski L, Leyrat A, West JAA, Panagiotakos G, Alvarez-…
• Physiological Models of Human Neuronal Development and Disease.
  Neuron 2018 Mostajo-Radji MA, Pollen AA
• Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development.
  Nature neuroscience 2018 Nowakowski TJ, Rani N, Golkaram M, Zhou HR, Alvarado B, Huch K, West JA, Leyrat A, Pollen AA, Kriegstein AR, Petzold LR, Kosik KS
• Identification of cell types in a mouse brain single-cell atlas using low sampling coverage.
  BMC biology 2018 Bhaduri A, Nowakowski TJ, Pollen AA, Kriegstein AR
• Transcriptional fates of human-specific segmental duplications in brain.
  Genome research 2018 Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE
• Postmitotic Fate Refinement in the Subplate.
  Cell stem cell 2018 Mostajo-Radji MA, Pollen AA
• Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.
  Cell 2018 Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, …
• Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia.
  Cell stem cell 2017 Bershteyn M, Nowakowski TJ, Pollen AA, Di Lullo E, Nene A, Wynshaw-Boris A, Kriegstein AR
• Zika virus cell tropism in the developing human brain and inhibition by azithromycin.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Retallack H, Di Lullo E, Arias C, Knopp KA, Laurie MT, Sandoval-Espinosa C, Mancia Leon WR, Krencik R, Ullian EM, Spatazza J, Pollen AA, Mandel-Brehm C, Nowakowski TJ, Kriegstein AR, DeRisi JL
• Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas.
  Molecular systems biology 2016 Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A
• Primate Neurons Flex Their Musclin.
  Neuron 2016 Pollen AA, Kriegstein AR
• Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development.
  Neuron 2016 Nowakowski TJ, Pollen AA, Sandoval-Espinosa C, Kriegstein AR
• SCell: integrated analysis of single-cell RNA-seq data.
  Bioinformatics (Oxford, England) 2016 Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim DA, Kriegstein A
• Single-cell analysis of long non-coding RNAs in the developing human neocortex.
  Genome biology 2016 Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA
• Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells.
  Cell stem cell 2016 Nowakowski TJ, Pollen AA, Di Lullo E, Sandoval-Espinosa C, Bershteyn M, Kriegstein AR
• Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex.
  Nature 2014 Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC
• How unique is the human neocortex?
  Development (Cambridge, England) 2014 Molnár Z, Pollen A
• The genomic basis of adaptive evolution in threespine sticklebacks.
  Nature 2012 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 …
• Interspecific profiling of gene expression informed by comparative genomic hybridization: A review and a novel approach in African cichlid fishes.
  Integrative and comparative biology 2009 Machado HE, Pollen AA, Hofmann HA, Renn SC
• Beyond neuroanatomy: novel approaches to studying brain evolution.
  Brain, behavior and evolution 2008 Pollen AA, Hofmann HA
• cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans.
  Cell 2007 Miller CT, Beleza S, Pollen AA, Schluter D, Kittles RA, Shriver MD, Kingsley DM
• Comparative aspects of cortical neurogenesis in vertebrates.
  Journal of anatomy 2007 Cheung AF, Pollen AA, Tavare A, DeProto J, Molnár Z
• Environmental complexity and social organization sculpt the brain in Lake Tanganyikan cichlid fish.
  Brain, behavior and evolution 2007 Pollen AA, Dobberfuhl AP, Scace J, Igulu MM, Renn SC, Shumway CA, Hofmann HA