Tomasz Jan Nowakowski

This study investigates rubella virus tropism in human brain slices and organoids, showing microglia as the primary target and revealing an interferon response in non-microglial cells.

The paper investigates whether transcriptomic cell type can be inferred from neuronal activity timing across multiple time scales using deep learning.

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

DynaMorph uses self-supervised learning to analyze morphodynamic states of live human microglia, identifying distinct states and transitions in response to disease-relevant stimuli.

This study develops hPSC-derived enteric ganglioids to model human ENS development and function, identifying drug candidates and PDGFR inhibition as key factors in NO neuron specification.

The paper introduces Piphys, an open-source platform for neural recording that enables remote control and scalability through cloud-based software and low-cost hardware.

The paper uses single-cell RNA-sequencing to identify dynamic molecular signatures during cortical arealization in the human brain, revealing gene expression patterns that define distinct cortical areas.

The paper analyzes de novo mutations in autism and developmental disorder trios to identify candidate genes and functional networks associated with neurodevelopmental disorders.

The UCSC Cell Browser allows visualization of gene expression and metadata in single-cell datasets through a web interface and Python package.

The paper examines how rare and common genomic variants affect brain functional connectivity, revealing how polygenicity and pleiotropy influence psychiatric conditions and brain networks.

The paper identifies molecular subtypes of human interneuron progenitors and immature interneurons using single-cell RNA sequencing and compares them to mouse data, revealing species-specific gene programs.

Single-cell RNA sequencing of 289,000 first-trimester human brain cells identifies nine telencephalic progenitor subpopulations, a transient mesenchymal-like population, human-enriched C1orf61+ and ID4+ progenitors, and low early organoid fidelity.

The paper creates a chromatin accessibility atlas of the developing human telencephalon to identify regulatory elements and their role in gene expression and neurodevelopmental disorders.

This study maps human microglia development and identifies cytokine-associated subtypes and functional roles in neural network maturation.

The paper maps chromatin accessibility in developing human brain and organoids using scATAC-seq, revealing cell type-specific regulatory elements and their role in neurodevelopment.

The paper uses chimpanzee cerebral organoids to identify human-specific genes in cortical development and finds increased PI3K/AKT/mTOR activation in human outer radial glia.

This study examines the role of noncoding variation in autism spectrum disorder using whole genome sequencing of 2,076 genomes, finding no significant association after correction for multiple testing.

The paper investigates how miRNA-mRNA networks regulate cell-type-specific transcriptomes during human brain development using AGO2-HITS-CLIP, single-cell profiling, and bipartite network analysis.

The paper identifies human-specific NOTCH2NL genes linked to neurodevelopmental disorders and shows they affect cortical neurogenesis through Notch signaling.