Alex Pollen, PhD

Associate Professor
Neurology
[email protected]

Alex Pollen, PhD studies the genomic basis for evolutionary specializations of the human brain with a focus on cortical development.

Publications: 

Implementation and validation of single-cell genomics experiments in neuroscience.

Nature neuroscience

Colonna M, Konopka G, Liddelow SA, Nowakowski T, Awatramani R, Bateup HS, Cadwell CR, Caglayan E, Chen JL, Gillis J, Kampmann M, Krienen F, Marsh SE, Monje M, O'Dea MR, Patani R, Pollen AA, Quintana FJ, Scavuzzo M, Schmitz M, Sloan SA, Tesar PJ, Tollkuhn J, Tosches MA, Urbanek ME, Werner JM, Bayraktar OA, Gokce O, Habib N

Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability.

bioRxiv : the preprint server for biology

Nolbrant S, Wallace JL, Ding J, Zhu T, Sevetson JL, Kajtez J, Baldacci IA, Corrigan EK, Hoglin K, McMullen R, Schmitz MT, Breevoort A, Swope D, Wu F, Pavlovic BJ, Salama SR, Kirkeby A, Huang H, Schaefer NK, Pollen AA

Conservation, alteration, and redistribution of mammalian striatal interneurons.

bioRxiv : the preprint server for biology

Corrigan EK, DeBerardine M, Poddar A, Turrero García M, Schmitz MT, Harwell CC, Paredes MF, Krienen FM, Pollen AA

Massively parallel characterization of regulatory elements in the developing human cortex.

Science (New York, N.Y.)

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

Structurally divergent and recurrently mutated regions of primate genomes.

Cell

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, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE

Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders.

Cell stem cell

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

Mapping cis- and trans-regulatory target genes of human-specific deletions.

bioRxiv : the preprint server for biology

Fair T, Pavlovic BJ, Schaefer NK, Pollen AA

A cross-species proteomic map reveals neoteny of human synapse development.

Nature

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, García-Verdugo JM, Alvarez-Buylla A, Liu Z, Kriegstein AR

Comparative landscape of genetic dependencies in human and chimpanzee stem cells.

Cell

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.)

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

Fair T, Pollen AA

Comparative landscape of genetic dependencies in human and chimpanzee stem cells.

bioRxiv : the preprint server for biology

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

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

Machine learning dissection of human accelerated regions in primate neurodevelopment.

Neuron

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, Kriegstein A, Rubenstein JL, Shendure J, Pollen AA, Ahituv N, Pollard KS

IoT cloud laboratory: Internet of Things architecture for cellular biology.

Internet of things (Amsterdam, Netherlands)

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

Tropism of SARS-CoV-2 for human cortical astrocytes.

Proceedings of the National Academy of Sciences of the United States of America

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

The development and evolution of inhibitory neurons in primate cerebrum.

Nature

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

Pavlovic BJ, Fox D, Schaefer NK, Pollen AA

UCSC Cell Browser: visualize your single-cell data.

Bioinformatics (Oxford, England)

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

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

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

Distinct nuclear compartment-associated genome architecture in the developing mammalian brain.

Nature neuroscience

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

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

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

Direct analysis of brain phenotypes via neural blastocyst complementation.

Nature protocols

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

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

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

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

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

Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex.

Neuron

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

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.

Cell

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

Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development.

Nature neuroscience

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

Bhaduri A, Nowakowski TJ, Pollen AA, Kriegstein AR

Transcriptional fates of human-specific segmental duplications in brain.

Genome research

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

Mostajo-Radji MA, Pollen AA

High-resolution comparative analysis of great ape genomes.

Science (New York, N.Y.)

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

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.

Cell

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

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.

Science (New York, N.Y.)

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

Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia.

Cell stem cell

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

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

M?ller 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

Pollen AA, Kriegstein AR

Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development.

Neuron

Nowakowski TJ, Pollen AA, Sandoval-Espinosa C, Kriegstein AR

SCell: integrated analysis of single-cell RNA-seq data.

Bioinformatics (Oxford, England)

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

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

Nowakowski TJ, Pollen AA, Di Lullo E, Sandoval-Espinosa C, Bershteyn M, Kriegstein AR

Molecular identity of human outer radial glia during cortical development.

Cell

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

Radial glia require PDGFD-PDGFR� signalling in human but not mouse neocortex.

Nature

Lui JH, Nowakowski TJ, Pollen AA, Javaherian A, Kriegstein AR, Oldham MC

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.

Nature biotechnology

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

How unique is the human neocortex?

Development (Cambridge, England)

Molnár Z, Pollen A

The genomic basis of adaptive evolution in threespine sticklebacks.

Nature

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

Human-specific loss of regulatory DNA and the evolution of human-specific traits.

Nature

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

Beyond neuroanatomy: novel approaches to studying brain evolution.

Brain, behavior and evolution

Pollen AA, Hofmann HA

cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans.

Cell

Miller CT, Beleza S, Pollen AA, Schluter D, Kittles RA, Shriver MD, Kingsley DM

Comparative aspects of cortical neurogenesis in vertebrates.

Journal of anatomy

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

Pollen AA, Dobberfuhl AP, Scace J, Igulu MM, Renn SC, Shumway CA, Hofmann HA