Tomasz Jan Nowakowski

The paper provides a high-resolution molecular and cellular analysis of Broca's area and motor cortex across developmental stages, identifying distinct cellular signatures and vulnerabilities to neurodevelopmental disorders.

Reprocessing nine human brain datasets (2,157,582 cells, 156 donors, GW6 to adulthood) under one marker-based taxonomy yields 35 replicable cell types with cell type-specific timing of adult-like maturation.

The paper investigates how sex steroid hormones influence metabolic and neuronal programs during human cortical development using single-cell RNA-seq and hormone exposure experiments.

The paper isolates and characterizes two postnatal human neural stem cell subsets, showing their fate biases and decline in frequency over time.

The paper uses STARMAPS to analyze single-cell RNA sequencing data and identifies spatial and temporal patterns of ASD-associated gene enrichment in specific brain regions.

The paper identifies transcriptional and epigenomic differences in Brodmann Area 22 in autism, linking them to RFX3-dependent networks and verbal ability.

This study integrates single-cell and spatial transcriptomics with live-cell imaging to characterize tumor heterogeneity in supratentorial ependymomas, revealing distinct progenitor-like states and spatial organization patterns.

This paper introduces a tunable granular biomaterial, MAGIC matrix, that enables precise control of initial conditions for tissue growth, leading to improved organoid reproducibility and complexity.

The paper uses optogenetic WNT activation in human gastruloids to study germ layer self-organization and finds it drives mesendoderm differentiation and patterning.

The paper identifies transcription factors and effector genes involved in human cortical neurogenesis using CRISPRi screening in a primary culture system.

This paper introduces vascularized cortical assembloids (vCAs) that model neurovascular co-development and show improved cellular specialization and connectivity compared to standard cortical organoids.

This study maps ASD genetic liability across cortical cell types using a functional genetic burden analysis of 124,416 individuals, showing developmentally dynamic liabilities and variant-specific contributions to different cell types.

The paper presents a spatial transcriptomic atlas of autism-associated genes in the developing human brain, identifying convergence in the thalamus and germinal zones.

The paper identifies cell-type-specific molecular and regulatory changes in D1 striosome medium spiny neurons and astrocytes in ASD using single-nucleus multiomic profiling in human putamen.

ANTIPODE integrates single-cell data across species to identify homologous cell types and reveal gene regulatory divergence in developing mammalian brains.

This study shows that TS21 accelerates radial glia lineage progression, leading to premature production of inhibitory neurons and oligodendrocytes in Down syndrome.

The paper identifies sex-biased molecular vulnerabilities in the developing human cortex linked to neurodevelopmental disorders by integrating transcriptomic and epigenomic data with mutation analysis.

The paper shows microglia regulate GABAergic neurogenesis in the prenatal human brain via IGF1, using single-cell transcriptomics and organoid models.

The paper identifies CHD genes that disrupt NPC biology and are enriched for ciliary biology, linking cilia dysfunction to ASD and CHD comorbidity.

The paper identifies enhancer-AAV tools for specific neuronal subtypes and validates them across species.

The paper uses CRISPRi to screen ASD risk genes in microglia, identifying ADNP's role in synaptic pruning and endocytosis.

This study creates a 3D histological cell atlas of the developing human brain, providing detailed cell counts, proliferative dynamics, and cell type distribution at 13-14 and 20-21 gestational weeks.

This study shows that group 2 innate lymphoid cells (ILC2s) and their cytokine IL-13 promote inhibitory synapse development and adult social behavior.

This study shows that ADGRG1 in microglia helps protect against Alzheimer's disease by improving amyloid clearance and reducing pathology.

The paper introduces a method to map neuronal circuits using barcoded rabies virus and single-nucleus RNA sequencing, revealing cell-type-specific circuit motifs in developing human cerebral cortex.

The paper identifies 46,802 enhancers and 164 psychiatric disorder variants with regulatory effects in the developing cortex and organoids using massively parallel reporter assays and deep learning.

This study identifies a Type I interferon-responsive microglial subset that engulfs neurons during brain development and shows its role in shaping cortical structure and behavior.

The paper constructs a PPI network of 100 high-confidence ASD genes, identifies novel interactions, and uses AlphaFold-Multimer to prioritize variants for functional validation in organoids.

The paper constructs a single-cell transcriptomic atlas of human cortical development, identifying lineage and sex-specific gene expression programs linked to autism risk.

The paper uses single cell and spatial transcriptomics to study thalamic development in humans, identifying molecular mechanisms of nuclei formation and neuron subtypes.