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Tomasz J. Nowakowski, Ph.D.

Assistant Professor, UCSF

Investigator, Chan Zuckerberg Biohub

Allen Institute for Brain Science, Next Generation Leader


Department of Anatomy

Department of Psychiatry

Chan Zuckerberg Biohub

The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF

Psychiatric Cell Map Initiative

Weill Institute for Neurosciences

Dr. Nowakowski received his B.Sc. in Biological Sciences with Honors in Physiology with Distinction in 2007, and Ph.D. in 2012 from the University of Edinburgh, where he worked with Drs. David Price and Thomas Pratt. He subsequently completed his postdoctoral work in the laboratory of Arnold Kriegstein at UCSF in 2017 where he pioneered the use of single cell RNA sequencing to study the heterogeneity of cellular populations, and later used that technique to characterize molecular heretogeneity of cell types across developmental stages and cortical areas. 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. More recently, Dr. Nowakowski and his colleagues described the emergence of cortical area specific neurons prior to sensory experience. This updated model has important implication for neuronal migration, area patterning, and cortical folding.

Honors and Awards


Allen Institute for Brain Science, Next Generation Leaders Council, 2018

Eppendorf & Science Prize for Neurobiology 2018

Chan-Zuckerberg Investigator, 2018

NARSAD Young Investigator Award, 2018

Cajal Club Krieg Cortical Explorer Award, 2017

Broad Foundation Innovation Award, 2017

Simons Foundation Autism Research Initiative (SFARI), Bridge to Independence Award, 2017

Wellcome Trust 4-Year PhD Studentship, 2007

Significant Publications

For full list of publications please follow: Pubmed

Nowakowski, TJ* (2018). Building blocks of the human brain. Science 362, 169.

Nowakowski TJ#, Bhaduri A*, Pollen AA*, et al. (2017) Spatiotemporal Gene Expression Trajectories Reveal Developmental Hierarchies of the Human Cortex, * co-first author; **co-corresponding author Science 358(6368):1318-1323 #- co-corresponding author PMID:2921757

Nowakowski TJ#, et al. (2016) Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development. Neuron 2016; PMID: 27657449; #-co-corresponding author

Research and Support Staff

Maureen Galvez - Administrative Assistant 

Julia Schroeder - Junior Assistant Specialist

Postdoctoral Scholars

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Ryan N. Delgado, M.D., Ph.D. 

I grew up in Phoenix, Arizona and attended the University of Arizona where I studied Molecular and Cellular Biology. As a student in the MD/PhD program at UCSF, I developed an interest in developmental biology and studied the role of the chromatin modifying protein Mll1 in maintaining the regional identity of stem cells in the postnatal subventricular zone. As a post-doc in the Nowakowski lab, I am interested in studying developmental lineage relationships between radial glia subtypes and postmitotic neurons and astrocytes in the cerebral cortex. Using single cell RNA sequencing, my goal is to discover new genetic programs regulating cell fate decisions during neurogenesis and gliogenesis.


California Institute of Regenerative Medicine Graduate Fellowship, 2013

Significant Publications

Delgado RN and Lim DA. Embryonic Nkx2.1-expressing neural precursor cells contribute to the regional heterogeneity of adult V–SVZ neural stem cells. Developmental Biology 2015; PMID: 26387477


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Galina Schmunk, Ph.D. 

I received my PhD from UC Irvine, where I discovered a previously unknown calcium signaling deficit across different forms of autism spectrum disorders. Working on autism made me interested in early human neurodevelopment and how prenatal environmental factors, including maternal inflammation, impact brain development and increase autism risks. For my postdoctoral training, I am interested in identifying gene expression profile governing glial maturation and intercellular interactions during neuro-glial interactions in developing brain, and to understand how genetic and environmental perturbations during early neurodevelopment translate into increased autism risk.


Ruth L. Kirschstein National Research Service Award (NRSA) Individual Postdoctoral Fellowship F32 – 2018

Significant Publications

Schmunk, G., Nguyen, R. L., Ferguson, D. L., Kumar, K., Parker, I. & Gargus, J. J. High-throughput screen detects calcium signaling dysfunction in typical sporadic autism spectrum disorder. Scientific Reports, 7, 40740 (2017).

Schmunk, G., Boubion, B. J., Smith, I. F., Parker, I. & Gargus, J. J. Shared functional defect in IP3R-mediated calcium signaling in diverse monogenic autism syndromes. Transl. Psychiatry 5, e643 (2015).

Graduate Students

David Shin - BMS 

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After spending the first 18 years of my life in the arid suburbs of Moreno Valley, CA, I moved to the opposite coast to study Molecular and Cellular Biology at Harvard College. Upon graduating, I worked as a research technician in Dr. Cristopher Bragg’s Lab at the Massachusetts General Hospital, where I generated iPSC-derived neuronal cell models to study the genetic basis of a rare neurodegenerative movement disorder known as X-linked Dystonia Parkinsonism (XDP).  For my graduate work, I am interested in studying the emergence of neocortical excitatory neurons before the onset of sensory experience and determining novel molecular programs that underlie areal fate specification.


National Science Foundation (NSF) Graduate Research Fellowship – 2018

Significant Publications

Aneichyk, T.*, Hendriks, W.T.*, Yadav, Y.*, Shin, D.*, Gao, D.*, Vaine, C.A., Collins, R.L., Domingo, A., Currall, B., Stortchevoi, A., et al. (2018). Dissecting the Causal Mechanism of X-Linked Dystonia Parkinsonism by Integrating Genome and Transcriptome Assembly. Cell 172, 897-909.   


Denise Allen - BMS

I grew up just south of San Francisco and returned home after obtaining my bachelor's degree in Molecular, Cell, and Developmental Biology from UCLA. During my time at UCLA I worked in Dr. Ellen Carpenter's lab studying the role of Reelin signaling in mammary gland and brain development, as well as in Dr. Bill Lowry's lab where I used an iPSC model to demonstrate that the loss of MECP2 induces cell stress and senescence in developing interneurons. I have now shifted my developmental interests the most abundant and multi-talented cell type in the brain: astrocytes. I am particularly interested in determining the genetic programs that direct the gliogenic switch, the lineage restriction of astrocytes and their precursors, and how these programs enable the emergence of astrocyte heterogeneity within the human brain.


National Science Foundation (NSF) Graduate Research Fellowship – 2018

Significant publications

Minori Ohashi*, Elena Korsakova*, Denise Allen, Peiyee Lee, Kai Fu, Benni Vargas, Jessica Cinkornpumin, Carlos Salas, Jenny Park, Igal Germanguz, Justin Langerman, Contantinos Chronis, Edward Kuoy, Stephen Tran, Xinshu Xiao, Matteo Pellegrini, Kathrin Plath, William Lowry. (2018). Loss of MECP2 Leads to Activation of p53 and Neuronal Senescence. Stem Cell Reports 10, 1453-1463.

*Co-first authors

Ryan Ziffra - BMS (joint with Nadav Ahituv lab)


I grew up in the north suburbs of Chicago, where I studied business administration at DePaul University. After a brief stint in Corporate America, I went back to school and obtained a second bachelor’s in biomedical science from Dominican University. I then worked as a research technician in the labs of Drs. Carole Ober and Marcelo Nobrega at The University of Chicago, where I investigated the epigenetic and regulatory genomic basis of human labor and preterm birth. I am now focused on elucidating the epigenetic and gene regulatory programs underlying human neurodevelopment and how dysfunction in these programs may lead to neurodevelopmental disorders such as Autism Spectrum Disorder.

Undergraduate Students


Shaun Cho - undergraduate volunteer, UC Berkeley


Lab Alumni

2018 Tamara Sharf - Undergraduate Student, UC Berkeley

2017 Johain Ounadjela - Undergraduate Student, Columbia University