Tomasz Nowakowski, PhD

Asst Professor in Residence
+1 415 476-0878

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.



A Chromatin Accessibility Atlas of the Developing Human Telencephalon.


Eirene Markenscoff-Papadimitriou,Sean Whalen,Pawel Przytycki,Reuben Thomas,Fadya Binyameen,Tomasz J. Nowakowski,Stephan J. Sanders,Matthew W. State,Katherine S. Pollard,John L. Rubenstein

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


Alex A Pollen,Aparna Bhaduri,Madeline G Andrews,Tomasz J Nowakowski,Olivia S Meyerson,Mohammed A Mostajo-Radji,Elizabeth Di Lullo,Beatriz Alvarado,Melanie Bedolli,Max L Dougherty,Ian T Fiddes,Zev N Kronenberg,Joe Shuga,Anne A Leyrat,Jay A West,Marina Bershteyn,Craig B Lowe,Bryan J Pavolvic,Sofie R Salama,David Haussler,Evan Eichler,Arnold A Kriegstein

Regulation of Cell-Type-Specific Transcriptomes by miRNA Networks During Human Brain Development.


Tomasz J Nowakowski,Neha Rani, Golkaram,Hongjun R Zhou,Beatriz Alvarado,Kylie Huch,Jay West,Anne Leyrat,Alex A Pollen,Arnold R Kriegstein,Linda R Petzold,Kenneth S Kosik

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis.


Ian T Fiddes,Gerrald A Lodewijk,Meghan M Mooring,Colleen M Bosworth,Adam D Ewing,Gary L Mantalas,Adam M Novak,Anouk van den Bout,Alex Bishara,Jimi L Rosenkrantz,Ryan Lorig-Roach,Andrew R Field,Maximillian Haeussler,Lotte Russo,Aparna Bhaduri,Tomasz J Nowakowski,Alex A Pollen,Max L Dougherty,Xander Nuttle,Marie-Claude Addor,Simon Zwolinski,Sol Katzman,Arnold Kreigstein,Evan E Eichler,Sofie R Salama,Frank MJ Jacobs,David Haussler

Saturating Single-Cell Datasets.


Aparna Bhaduri,Tomasz J. Nowakowski,Alex A. Pollen,Arnold R. Kriegstein

Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families.


Donna M Werling,Harrison Brand,Joon-Yong An,Matthew R Stone,Joseph T Glessner,Lingxue Zhu,Ryan L Collins,Shan Dong,Ryan M Layer,Eiriene-Chloe Markenscoff-Papadimitriou,Andrew Farrell,Grace B Schwartz,Benjamin B Currall,Jeanselle Dea,Clif Duhn,Carolyn Erdman,Michael Gilson,Robert E Handsaker,Seva Kashin,Lambertus Klei,Jeffrey D Mandell,Tomasz J Nowakowski,Yuwen Liu,Sirisha Pochareddy,Louw Smith,Michael F Walker,Harold Z Wang,Mathew J Waterman,Xin He,Arnold R Kriegstein,John L Rubenstein,Nenad Sestan,Steven A McCarroll,Ben M Neale,Hilary Coon,A. Jeremy Willsey,Joseph D Buxbaum,Mark J Daly,Matthew W State,Aaron Quinlan,Gabor T Marth,Kathryn Roeder,Bernie Devlin,Michael E Talkowski,Stephan J Sanders

Chapter 16 microRNA and Neocortical Evolution.

Thomas Pratt,Tomasz Jan Nowakowski,David Jonathan Price

Zika Virus in the Human Placenta and Developing Brain: Cell Tropism and Drug Inhibition.


Hanna Retallack,Elizabeth Di Lullo,Carolina Arias,Kristeene A. Knopp,Carmen Sandoval-Espinosa,Matthew T. Laurie,Yan Zhou,Matthew Gormley,Walter R. Mancia Leon,Robert Krencik,Erik M. Ullian,Julien Spatazza,Alex A. Pollen,Katherine Ona,Tomasz J. Nowakowski,Joseph L. DeRisi,Susan J. Fisher,Arnold R. Kriegstein

01-P027 Investigating the roles of dicer1 endoribonuclease in embryonic organogenesis of mouse retina.

Mechanisms of development

Tomasz Jan Nowakowski,Tom Pratt,David J. Price

Multiple trap Laguerre-Gaussian holographic optical tweezers using a multiplexed ferroelectric SLM.

Proceedings of SPIE

A. Lafong,W. J. Hossack,J. Arlt,T. J. Nowakowski,N. D. Read