Tom Nowakowski, Ph.D

Profile

Awards

Vilcek Prize for Creative Promise in Biomedical Science (2024)

Joseph Altman Award in Developmental Neuroscience (2023)

NYSCF Robertson Neuroscience Investigator (2022)

CZI Investigator (2021)

Sontag Foundation Award (2021)

Klingenstein Simons Fellowship in Neuroscience (2021)

CZ Biohub Intercampuss Investigator (2018)

Eppendorf & Science Prize in Neurobiology, Finalist (2018)

Wellcome Trust PhD Fellowship (2008), The University of Edinburgh

Clif Duhn - Lab Manager

Adam Kazerounian - Junior Specialist

I'm from Danville, California and went to Diablo Valley College for two years before transferring to UC Berkeley for Molecular & Cellular Biology with an emphasis in genetics. I spent a year in an algal biology lab at Berkeley helping construct a transcriptomic library for Chlamydomonas reinhardtii before making the switch to the Nowakowski lab in my senior year. I’m currently interested in refining our approaches for fate tracing of neural progenitors.

Sih-Rong Wu, Ph.D.

I received my master’s degree from National Yang-Ming University, Taiwan where I first met the beauty and the complexity of the brains by studying neurodegenerative disorders. During my PhD training at Baylor College of Medicine, I was intrigued by the molecular mechanisms giving rise to neuronal diversity. I elucidated the heterogeneity of pontine nuclei neurons and their molecular driver during development in mice. As a postdoc in NOW lab, I am interested in studying the human brain development and its implications in psychiatric disorders.

Significant Publications

Wu SR, Butts JC, Caudill MS, Revelli JP, Dhindsa RS, Durham MA, Zoghbi HY. Atoh1 drives the heterogeneity of the pontine nuclei neurons and promotes their differentiation. Sci Adv. 2023 Jun 30;9(26):eadg1671. doi: 10.1126/sciadv.adg1671.

Anthony Lee, M.D. Ph.D.

I was an MD/PhD student at UCSF and received my PhD in Vikaas Sohal’s lab where I studied how interneuron-subtypes in the prefrontal cortex contribute to information flow and avoidance behaviors. I stayed at UCSF for neurosurgery residency. For my post-doctoral training, I am interested in applying single-cell sequencing techniques to study circuitry of the human brain.

Awards

NINDS R25 Fellowship 2023

NIMH F30 Fellowship 2015

Significant Publications

AT Lee, M Cunniff, J Sz, SA Wilke, FJ Luongo, IT Ellwood, S Ponnavolu, VS Sohal. VIP interneurons contribute to avoidance behavior by regulating information flow across hippocampal-prefrontal networks. Neuron, 2019. 

AT Lee, D Vogt, JL Rubenstein, VS Sohal. A class of GABAergic neurons in the prefrontal cortex sends long-range projections to the nucleus accumbens and elicits acute avoidance behavior. J Neuroscience, 2014. 

AT Lee, SM Gee, D Vogt, T Patel, JL Rubenstein, VS Sohal. Pyramidal Neurons in Prefrontal Cortex Receive Subtype- Specific Forms of Excitation and Inhibition. Neuron, 2014. 

John Andrews, M.D.

Before coming to UCSF, I received my MD from Yale University School of Medicine where I worked in Hal Blumenfeld’s Lab as an HHMI-CURE fellow, study brainstem arousal pathways using in vivo patch clamping of single neurons in a rodent model of epilepsy. I came to UCSF for neurosurgical residency, where my clinical focuses are epilepsy, brain tumors and pediatric neurosurgery. My postdoctoral work in the NOW Lab focuses on developing new therapeutic applications using ex vivo human brain tissue.

 Awards:

NINDS R25 Fellowship (2022)

Howard Hughes Medical Institute (HHMI-CURE) medical research fellow (2016)

Significant publications:

1.     Andrews, J. P., Yue, Z., Ryu, J. H., Neske, G., McCormick, D. A., & Blumenfeld, H. (2019). Mechanisms of decreased cholinergic arousal in focal seizures: In vivo whole-cell recordings from the pedunculopontine tegmental nucleus. Experimental neurology, 314, 74-81.

2.     Andrews, J. P., Gummadavelli, A., Farooque, P., Bonito, J., Arencibia, C., Blumenfeld, H., & Spencer, D. D. (2019). Association of seizure spread with surgical failure in epilepsy. JAMA neurology, 76(4), 462-469.

3.     Andrews, J. P., Cahn, N., Speidel, B. A., Chung, J. E., Levy, D. F., Wilson, S. M., Berger, M. S., & Chang, E. F. (2022). Dissociation of Broca’s area from Broca’s aphasia in patients undergoing neurosurgical resections. J Neurosurg, 138(3), 847-857.

4.     Motelow, J.E., Li, W., Zhan, Q., Mishra, A. M., Sachdev, R. S., Liu, G., Gummadavelli, A., Zayyad, Z., Lee, Hyun S., Chu, V., Andrews, J.P., Englot, D. J., Herman, P., Sanganahalli, B. G., Hyder, F., & Blumenfeld, H. (2015). Decreased Subcortical Cholinergic Arousal in Focal Seizures. Neuron, 85(3), 561-572.

Guohua Yuan, Ph.D.

Significant publications

Guohua Yuan, Shimin Le, Mingxi Yao, Hui Qian, Xin Zhou, Jie Yan, Hu Chen. Elasticity of the Transition State Leading to an Unexpected Mechanical Stabilization of Titin Immunoglobulin Domains. Angewandte Chemie, 2017, 129(20): 5582-5585. (Cited by 72)

Hu Chen†, Guohua Yuan† (co-first author), Ricksen S. Winardhi, Mingxi Yao, Ionel Popa, Julio M. Fernandez, and Jie Yan. Dynamics of Equilibrium Folding and Unfolding Transitions of Titin Immunoglobulin Domain under Constant Forces. Journal of the American Chemical Society, 2015, 137, 3540-3546. (Cited by 144)

Zilong Guo, Haiyan Hong, Guohua Yuan, Hui Qian, Bing Li, Yi Cao, Wei Wang, Chen-Xu Wu, and Hu Chen. "Hidden Intermediate State and Second Pathway Determining Folding and Unfolding Dynamics of GB1 Protein at Low Forces." Physical Review Letters, 2020, 125, no. 19: 198101.

Zhoujie Yang, Guohua Yuan, Weili Zhai, Jie Yan, Hu Chen. The kinetics of force-dependent hybridization and strand-peeling of short DNA fragments[J]. Science China Physics, Mechanics & Astronomy, 2016, 59(8): 680013.

Weili Zhai, Guohua Yuan, Chao Liu, Hu Chen. Improved data analysis method of single-molecule experiments based on probability optimization[J]. Chinese Physics B, 2018, 27(1): 018703.

Varun Suresh, Ph.D.

I graduated with a master's in biotechnology from SIES College, University of Mumbai, where I first encountered how rewarding research can be. Subsequently, in Dr.Deepak Modi's lab at NIRRCH, I fell in love with mammalian development. For my PhD, I worked in the lab of Prof Shubha Tole, TIFR Mumbai, to decipher molecular pathways in the developing forebrain. In my post-doctoral training at the NOW lab, I am excited to understand the genomic basis of neurodevelopment and disease across brain regions.

Awards

1. VATAT Fellowship Weizmann Institute of Science, Israel. 2020

2. Sarojini Damodaran Fellowship, TIFR. 2022.

Significant Publications

1. Parichha, A., Suresh, V., Chatterjee, M., Kshirsagar, A., Ben-Reuven, L., Olender, T., Taketo, M.M., Radosevic, V., Bobic-Rasonja, M., Trnski, S., et al. (2022). Constitutive activation of canonical Wnt signaling disrupts choroid plexus epithelial fate. Nat. Commun. 13, 633. 10.1038/s41467-021-27602-z.

2. Suresh, V., Muralidharan, B., Pradhan, S.J., Bose, M., D’Souza, L., Parichha, A., Reddy, P.C., Galande, S., and Tole, S. (2023). Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2. PLoS Genet. 19, e1010874. 10.1371/journal.pgen.1010874.

3. Suresh, V., Bhattacharya, B., Tshuva, R.Y., Danan Gotthold, M., Olender, T., Bose, M., Pradhan, S.J., Ben Zeev, B., Smith, R.S., Tole, S., et al. (2023). PRDM16 co-operates with LHX2 to shape the human brain. BioRxiv. 10.1101/2023.08.12.553065.

Kelsey Hennick

Awards

Ruth L. Kirschstein Predoctoral Individual National Research Service Award F31 - 2023

Significant Publications

Kim WT, Hennick K, Johnson J, Finnerty B, Choo S, Short SB, Drubin C, Forster R, McMaster ML, Hockemeyer D. (2021) Cancer-associated POT1 mutations lead to telomere elongation without induction of a DNA damage response. EMBO J Jun 15;40(12):e107346

Boyle JM, Hennick KM, Regalado SG, Vogan JM, Zhang X, Collins K, Hockemeyer D. (2020) Telomere length set point regulation in human pluripotent stem cells critically depends on the shelterin protein TPP1. Mol Biol Cell Nov 1;31(23):2583-2596.

Marilyn Steyert

I fell in love with research during my time at St. Mary’s College of Maryland where I received undergraduate degree in Biology with minors in Neuroscience and Music. After college, I became deeply interested in cortical wiring and genome engineering in the Poulopoulos lab at University of Maryland Baltimore. As a graduate student in the Nowakowski lab, my interests have shifted to the stem cells of the developing brain. I hope to uncover what makes neural stem cell subtypes of the developing cortex unique.

Awards

National Science Foundation (NSF) Graduate Research Fellowship – 2021

Significant Publications

Deng, Chengyu, Sean Whalen, Marilyn Steyert, Ryan Ziffra, Pawel F. Przytycki, Fumitaka Inoue, Daniela Alves Pereira, et al. 2023. “Massively Parallel Characterization of Psychiatric Disorder-Associated and Cell-Type-Specific Regulatory Elements in the Developing Human Cortex.” bioRxiv. https://doi.org/10.1101/2023.02.15.528663.

David Shin

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.

Awards

National Science Foundation (NSF) Graduate Research Fellowship – 2018

Significant Publications

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. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell 2024 Feb 13:S1934-5909(24)00040-7. doi: 10.1016/j.stem.2024.01.010. PMID: 38382530

Kim CN*, Shin D* (co-first), Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. Science 2023 Oct 13;382(6667):eadf9941. doi: 10.1126/science.adf9941.

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.   

Matt Keefe

I’m originally from Pennsylvania, where I attended the Pennsylvania State University as an undergraduate studying Molecular and Cell Biology. During my time there I worked in a lab focused on using transcription factors to convert astrocytes to neurons in neurodegenerative conditions ranging from Alzheimer’s disease to spinal cord injury. I became very interested in cell fate plasticity and neurogenesis, and in the Nowakowski lab I hope to employ novel technologies to further understand the intrinsic and extrinsic factors that influence the development of specific neuronal subtypes.

Awards

National Defense Science and Engineering Graduate (NDSEG) Fellowship - 2020

Significant publications: 

Keefe MG, Nowakowski TJ. (2019) A recipe book for cell types in the human brain. Nature 573(7772):36-37; PMID: 31481767

Keefe MG, Nowakowski TJ. Evolutionary Expansion of Human Cerebellar Germinal Zones. Trends Neurosci. 2020; PMID: 31954525

Derek Bogdanoff

Awards

Significant publications: 

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. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021 Oct;598(7879):205-213.

Lee Y, Bogdanoff D, Wang Y, Hartoularos GC, Woo JM, Mowery CT, Nisonoff HM, Lee DS, Sun Y, Lee J, Mehdizadeh S, Cantlon J, Shifrut E, Ngyuen DN, Roth TL, Song YS, Marson A, Chow ED, Ye CJ. XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment. Sci Adv. 2021 Apr 21;7(17):eabg4755

Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA. (2018) Mapping the Genetic Landscape of Human Cells. Cell. 174(4):953-967

Bogdanoff D, Jou T, Lee B (2015) Characterization of Action and Efficiency of Tn5 Transposase Through Comparative qPCR Journal of Experimental Microbiology and Immunology

Chang Kim

Awards

2023 - UCSF Discovery Fellowship

Significant publications: 

Kim CN, Shin D, Wang A, Nowakowski TJ. Spatiotemporal molecular dynamics of the developing human thalamus. Science 2023 Oct 13;382(6667):eadf9941. doi: 10.1126/science.adf9941.

Winkler EA*, Kim CN* (co-first), Ross JM, Garcia JH, Gil E, Oh I, Chen LQ, Wu D, Catapano JS, Raygor K, Narsinh K, Kim H, Weinsheimer S, Coole DL, Walcott BP, Lawton MT, Gupta N, Zlokovic BV, Chang EF, Abla AA, Lim DA, Nowakowski TJ Single cell atlas of the normal and malformed human brain vasculature. Science 2022. eabi7377. doi: 10.1126/science.abi7377.

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. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021 Oct;598(7879):205-213. PMID: 34616060

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. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids Cell Stem Cell. 2021 Sep 16;S1934-5909(21)00376-3. PMID: 34536354

Julio Rivera-de Jesus

(joint with David Schaffer, UC Berkeley)

Born and raised in Puerto Rico, I attended the University of Puerto Rico-Mayagüez and earned a B.S. in Chemical Engineering. During this time, my research efforts focused on tuning and analyzing structural and chemical properties of Zn-based Quantum dots and their potential imaging and phototherapeutic applications. Often, I found myself very excited about the therapeutic potential of the project, which sparked my interest to pursue graduate studies and areas of research focused on the development of gene therapy, drug delivery technologies.

In my free time I enjoy cooking and exploring local breweries and cuisine in the bay area.

Publications:

1.     Rivera-de Jesus, J., Bailon, S.J., and Perales, O.J., “One-step Aqueous Synthesis of Zn-based Quantum Dots as Potential Generators of Reactive Oxygen Species”. Submitted to: MRS Advances, 2018. Published: January 15th2019.

2.     Luciano-Velázquez, J., Xin, Y., Su, Y.F., Quiles-Vélez, C., Cruz-Romero, S.A., Torres-Mejías, G.E., Rivera-de Jesús, J., and Bailón-Ruiz, S.J., “Synthesis, characterization, and photocatalytic activity of ZnS and Mn-doped ZnS nanostructures”. Submitted to: MRS Advances. Published: May 5th, 2021

Nishant Chadha

I am an undergraduate student at UC Berkeley studying BioMedical Engineering, Human Rights, and Molecular & Cellular Biology with an emphasis in Neurobiology. Since my sophomore year, I've been actively engaged in research at the NOW Lab, dedicating my efforts to exploring the genetic basis of Autism Spectrum Disorder (ASD). I am particularly interested in understanding the establishment of sexually dimorphic features during development, with the future goal of identifying potential therapeutic targets for disorders exhibiting sex-biased penetrance.