Dr. Boyan Bonev

Dr. Boyan Bonev leads the Brain Epigenomics Research Unit (BEG) at the Stem Cell Center of Helmholtz Munich, with the mission of improving the diagnosis and treatment of brain disorders using genomics and AI.

His research addresses a fundamental question: how does the epigenome - the layers of chemical modifications, 3D architecture, and regulatory elements that sit on top of our DNA - control which genes are active in each brain cell? Neurological disorders - from neurodegenerative diseases to autism and schizophrenia - affect one in six people worldwide, yet the vast majority of disease-associated genetic variants lie in the non-coding genome, where their functional impact remains unknown. Boyan’s group develops novel single-cell technologies to read the epigenome at multiple layers simultaneously, and combines these with human brain organoids, CRISPR-based perturbations, and machine learning to move from correlation to causation.

Since starting his lab in 2018 at the Helmholtz Munich, Boyan has built an internationally recognised program organized around two pillars. The first pursues a fundamental understanding of brain development and evolution: how is neuronal identity encoded in the cortex, and how has the epigenome been rewired as the human brain expanded during primate evolution? The second translates these insights into applications - collaborating with industry partners to identify early epigenomic biomarkers of neurological disorders and develop cell-type-specific enhancers for AAV-based gene therapies. This combination of basic discovery and translational application, enabled by the technologies his lab has pioneered, is what makes BEG unique within the Munich research landscape.

Among the group’s key contributions are the discovery that the transcription factor Neurog2 coordinates epigenetic remodeling across multiple molecular layers during cortical development (Nature Neuroscience, 2022); the development of 3DRAM-seq, a method for jointly profiling 3D genome architecture, RNA, chromatin accessibility, and DNA methylation in the same cells (Nature Cell Biology, 2023); the adaaptation of novel massively parallel reporter assays (MPRA) that can functionally validate thousands of enhancers in vivo and in human brain organoids; and the identification of Yy1 as an essential factor in epigenome remodeling during direct neuronal reprogramming (Nature Neuroscience, 2024).

Boyan is an EMBO Young Investigator and ERC Consolidator Grant awardee. He is embedded within the Munich scientific community through collaborations spanning the LMU, TUM, and Max Planck Institutes, and is affiliated with the LMU Graduate School for Neuroscience.