Induced pluripotent stem cell (iPSC)–derived organoids have emerged as powerful model systems for studying human development, disease mechanisms, and therapeutic responses. In this project, we aim to generate, characterize, and analyze iPSC-derived organoids to uncover molecular and cellular mechanisms underlying human brain development and neurodegenerative disorders. Organoids provide a unique opportunity to model patient-specific phenotypes in vitro, enabling us to bridge the gap between traditional cell culture systems and in vivo models. We will employ high-throughput sequencing (single-cell and bulk RNA-seq), epigenomic profiling, and advanced imaging techniques to characterize the cellular heterogeneity and dynamic changes occurring during organoid maturation. Computational analyses will be central to this work: large-scale multi-omics datasets will be processed, integrated, and modeled using state-of-the-art pipelines on high-performance computing (HPC) resources. This includes read alignment, variant calling, clustering, trajectory inference, and network analyses. The outcomes of this project will enhance our understanding of organoid biology and its application to disease modeling. Furthermore, the computational strategies and workflows developed will be broadly applicable to other iPSC-derived systems. By combining stem cell biology, genomics, and advanced computational approaches, we expect to generate insights that will facilitate translational applications, such as drug screening and personalized medicine. The requested NAISS/UPPMAX resources are critical for managing and analyzing the large and complex datasets generated in this project. HPC capacity will allow efficient processing of terabyte-scale sequencing and imaging data, while secure storage ensures compliance with data protection regulations. This project will contribute to both fundamental biological knowledge and the development of computational resources for the Swedish research community.