Tomasz Nowakowski, PhD

Associate Professor
Neurological Surgery

Dr. Nowakowski received his Ph.D. from the University of Edinburgh (UK) in 2012, where he developed his passion for understanding molecular mechanisms of brain development. Subsequently, he pursued postdoctoral training at the Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research at UCSF. In 2017, where he used single cell RNA sequencing to study the heterogeneity of cellular populations in the developing brain and discovered the biomarkers of outer radial glia.

He synthesized the current understanding of brain development and cortical expansion in the Supragranular Cortex Expansion Hypothesis, which extends the classic view of cortical development embodied in the Radial Unit Hypothesis to account for the massive expansion of the cortical OSVZ progenitor population, the protracted neurogenesis period in humans and primates, the loss of pial surface-contacting radial glia fibers mid-way through cortical neurogenesis, and the disproportionate expansion of supragranular cortical layers within primates. This updated model has important implication for neuronal migration, area patterning, and cortical folding.

Dr. Nowakowski established his own research group in 2017. His group seeks to understand how the human genome, a fundamental unit in biology, reproducibly generates the neuronal cell types of the brain that support its complex cognitive functions. In particular, Dr. Nowakowski is fascinated by inherited developmental mechanisms that recapitulate key morphological features of the body plan, while allowing sufficient flexibility to achieve the phenotypic variation we observe in nature. 

Recently developed technologies of single-cell sequencing, genome engineering, and in vitro modeling of tissue development have transformed our ability study the complex universe of cellular processes with unprecedented precision. Dr. Nowakowski’s independent research group seeks to utilize these technologies to uncover genetic control mechanisms underlying neurodevelopmental events and tissue organization in the cerebral cortex. These approaches may highlight cellular patterns of selective vulnerability in neurodevelopmental and neuropsychiatric disorders, including Autism Spectrum Disorders and Schizophrenia.

Research Summary: 
Developmental origins of cellular diversity in the nervous system. Molecular and cellular mechanisms of cortical development.

Websites

Publications: 

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

Type-I-interferon-responsive microglia shape cortical development and behavior.

Cell

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

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

A foundational atlas of autism protein interactions reveals molecular convergence.

bioRxiv : the preprint server for biology

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

Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy.

Science advances

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

Improving cellular diversity in human cerebellar organoids.

Cell stem cell

Steyert M, Nowakowski T

Single-cell analysis of prenatal and postnatal human cortical development.

Science (New York, N.Y.)

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

Spatiotemporal molecular dynamics of the developing human thalamus.

Science (New York, N.Y.)

Kim CN, Shin D, Wang A, Nowakowski TJ

Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids.

eLife

Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T

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, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntan? G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Sch?ffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundstr?m E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X

385 A Cell Resolution Atlas of the Human Cerebrovasculature Reveals Angiogenic and Inflammatory Cell Programs in Arteriovenous Malformations.

Neurosurgery

Ethan A. Winkler, Chang Kim, Jayden Ross, Joseph Garcia, Eugene Gil, Irene Oh, Lindsay Chen, David Wu, Joshua Catapano, Kunal P. Raygor, Kazim Narsinh, Helen Kim, Shantel Weinsheimer, Daniel Cooke, Brian Patrick Walcott, Michael T. Lawton, Nalin Gupta, Berislav Zlokovic, Edward F. Chang, Adib Adnan Abla, Daniel A. Lim, Tomasz Nowakowski

Transcriptomic cell type structures in vivo neuronal activity across multiple timescales.

Cell reports

Schneider A, Azabou M, McDougall-Vigier L, Parks DF, Ensley S, Bhaskaran-Nair K, Nowakowski T, Dyer EL, Hengen KB

A type I interferon response defines a conserved microglial state required for effective neuronal phagocytosis.

bioRxiv : the preprint server for biology

Dorman LC, Nguyen PT, Escoubas CC, Vainchtein ID, Xiao Y, Lidsky PV, Nakajo H, Silva NJ, Lagares-Linares C, Wang EY, Taloma SE, Cuevas B, Nakao-Inoue H, Rivera BM, Schwer B, Condello C, Andino R, Nowakowski TJ, Molofsky AV

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

Abstract 52: Prevalence Of Somatic Activating Kras Mutations In Pediatric And Adult Sporadic Brain Arteriovenous Malformations.

Stroke

Ethan A Winkler, Joseph Garcia, Cynthia Tsang, Jeffrey Nelson, Charles McCulloch, Shantel Weinsheimer, Christine K Fox, Heather Fullerton, Nerissa Ko, Hua Su, Tomasz Nowakowski, Daniel L Cooke, Steven Hetts, Ekin Guney, MELIKE PEKMEZCI, Tarik Tihan, Michael Lawton, Adib Abla, Nalin Gupta, Helen Kim

New York Stem Cell Foundation Robertson Investigators.

Cell stem cell

McKinley KL, van Boxtel R, Finley LWS, Pe?a CJ, Nowakowski TJ

In preprints: new insights into truncated radial glia.

Development (Cambridge, England)

Steyert M, Nowakowski TJ

Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders.

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

Wang T, Kim CN, Bakken TE, Gillentine MA, Henning B, Mao Y, Gilissen C, SPARK Consortium, Nowakowski TJ, Eichler EE

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

Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes.

Science (New York, N.Y.)

Allen DE, Donohue KC, Cadwell CR, Shin D, Keefe MG, Sohal VS, Nowakowski TJ

Dissecting cellular diversity of cortical GABAergic cells across multiple modalities: A turning point in neuronal taxonomy.

Faculty reviews

Arlotta P, Chen F, Lodato S, Margrie TW, Nowakowski TJ, Pederson T, Rico B

Microglial GPR56 is the molecular target of maternal immune activation-induced parvalbumin-positive interneuron deficits.

Science advances

Yu D, Li T, Delpech JC, Zhu B, Kishore P, Koshi T, Luo R, Pratt KJB, Popova G, Nowakowski TJ, Villeda SA, Piao X

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

A single-cell atlas of the normal and malformed human brain vasculature.

Science (New York, N.Y.)

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

Endoluminal Biopsy for Molecular Profiling of Human Brain Vascular Malformations.

Neurology

Winkler EA, 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

DynaMorph: self-supervised learning of morphodynamic states of live cells.

Molecular biology of the cell

Wu Z, Chhun BB, Popova G, Guo SM, Kim CN, Yeh LH, Nowakowski T, Zou J, Mehta SB

Nests of dividing neuroblasts sustain interneuron production for the developing human brain.

Science (New York, N.Y.)

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

Individual human cortical progenitors can produce excitatory and inhibitory neurons.

Nature

Delgado RN, Allen DE, Keefe MG, Mancia Leon WR, Ziffra RS, Crouch EE, Alvarez-Buylla A, Nowakowski TJ

Single-cell delineation of lineage and genetic identity in the mouse brain.

Nature

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

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

Endovascular Biopsy of Vertebrobasilar Aneurysm in Patient With Polyarteritis Nodosa.

Frontiers in neurology

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

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

An atlas of cortical arealization identifies dynamic molecular signatures.

Nature

Bhaduri A, Sandoval-Espinosa C, Otero-Garcia M, Oh I, Yin R, Eze UC, Nowakowski TJ, Kriegstein AR

Single-cell epigenomics reveals mechanisms of human cortical development.

Nature

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

Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids.

Cell stem cell

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

Low cost cloud based remote microscopy for biological sciences.

Internet of Things

Pierre V. Baudin, Victoria T. Ly, Pattawong Pansodtee, Erik A. Jung, Robert Currie, Ryan Hoffman, Helen Rankin Willsey, Alex A. Pollen, Tomasz J. Nowakowski, David Haussler, Mohammed A. Mostajo-Radji, Sofie Salama, Mircea Teodorescu

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

The CHD8/CHD7/Kismet family links blood-brain barrier glia and serotonin to ASD-associated sleep defects.

Science advances

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

Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience.

Neuron

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

The Expanding Cell Diversity of the Brain Vasculature.

Frontiers in physiology

Ross JM, Kim C, Allen D, Crouch EE, Narsinh K, Cooke DL, Abla AA, Nowakowski TJ, Winkler EA

Are Organoids Ready for Prime Time?

Cell stem cell

Bhaduri A, Andrews MG, Kriegstein AR, Nowakowski TJ

Revealing architectural order with quantitative label-free imaging and deep learning.

eLife

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 T, Mehta SB

A Chromatin Accessibility Atlas of the Developing Human Telencephalon.

Cell

Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL

Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2+ Granule Neuron Precursor.

Cell reports

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

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

Evolutionary Expansion of Human Cerebellar Germinal Zones.

Trends in neurosciences

Keefe MG, Nowakowski TJ

Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma.

Cell stem cell

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

Disruptive mutations in TANC2 define a neurodevelopmental syndrome associated with psychiatric disorders.

Nature communications

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

Development and Arealization of the Cerebral Cortex.

Neuron

Cadwell CR, Bhaduri A, Mostajo-Radji MA, Keefe MG, Nowakowski TJ

A recipe book for cell types in the human brain.

Nature

Keefe MG, Nowakowski TJ

Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration.

Communications biology

Linsley JW, Tripathi A, Epstein I, Schmunk G, Mount E, Campioni M, Oza V, Barch M, Javaherian A, Nowakowski TJ, Samsi S, Finkbeiner S

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

Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function.

Cell reports

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

Neuroserpin expression during human brain development and in adult brain revealed by immunohistochemistry and single cell RNA sequencing.

Journal of anatomy

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

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

Building blocks of the human brain.

Science (New York, N.Y.)

Nowakowski TJ

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

The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.

Cell

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

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

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

Nature genetics

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

Evolution of New miRNAs and Cerebro-Cortical Development.

Annual review of neuroscience

Kosik KS, Nowakowski T

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

The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells.

Nature communications

Gambardella G, Carissimo A, Chen A, Cutillo L, Nowakowski TJ, di Bernardo D, Blelloch R

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

Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A

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

Neuron

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

A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA.

Neuron

Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS

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

The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells.

Cell stem cell

Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA

Radial glia require PDGFD-PDGFRß 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

Loss of functional Dicer in mouse radial glia cell-autonomously prolongs cortical neurogenesis.

Developmental biology

Nowakowski TJ, Mysiak KS, O'Leary T, Fotaki V, Pratt T, Price DJ

MicroRNA-92b regulates the development of intermediate cortical progenitors in embryonic mouse brain.

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

Nowakowski TJ, Fotaki V, Pollock A, Sun T, Pratt T, Price DJ

The expression and activity of ß-catenin in the thalamus and its projections to the cerebral cortex in the mouse embryo.

BMC neuroscience

Pratt T, Davey JW, Nowakowski TJ, Raasumaa C, Rawlik K, McBride D, Clinton M, Mason JO, Price DJ

Novel lines of Pax6-/- embryonic stem cells exhibit reduced neurogenic capacity without loss of viability.

BMC neuroscience

Quinn JC, Molinek M, Nowakowski TJ, Mason JO, Price DJ

Time-Multiplexed Laguerre-Gaussian holographic optical tweezers for biological applications.

Optics express

Lafong A, Hossack WJ, Arlt J, Nowakowski TJ, Read ND