Bogdan Bintu

The paper uses 3D MERFISH to show that mRNA partitioning during cell division generates transcriptomically distinct cell types in Crepidula atrasolea embryos.

This paper develops a multimodal spatial transcriptomics approach to study CAG repeat expansion, huntingtin aggregation, and neuron loss in Huntington's Disease using human brain tissue.

MERFISHEYES provides a web-based platform for visualizing and sharing spatial transcriptomics data, enabling interactive exploration and cross-dataset comparisons.

The paper shows that olfactory receptor expression in the nose follows a spatial code controlled by a retinoic acid gradient, aligning epithelial and brain maps.

The paper introduces a whole-embryo spatial transcriptomics method and generates a comprehensive gene expression and chromatin accessibility atlas in zebrafish embryos.

This study uses single-molecule spatial genomics to show how extrachromosomal DNA is organized and regulated in glioblastoma, linking it to tumor heterogeneity and microenvironmental influences.

PantheonOS introduces a multi-agent framework for automated genomics analysis, achieving super-human performance in batch correction and gene panel selection across diverse biological tasks.

This study creates a 3D multi-omic atlas of developing human basal ganglia and inhibitory neurons, revealing lineage-specific 3D genomic dynamics and regulatory programs associated with neuropsychiatric disease risk.

This paper creates a high-resolution spatial transcriptomic atlas of the human basal ganglia, identifying 60 cell types and their spatial organization across multiple nuclei.

MERFISH+ enables high-resolution spatial multi-omics mapping of gene expression and chromatin organization in developing human hearts with subcellular resolution.

The paper maps molecular and spatial organization of the mouse primary olfactory system in response to social odors using MERFISH and identifies spatial domains of sensory responses.

The paper introduces hamFISH, a method for multiplexed in situ hybridization to profile gene expression, connectivity, and activity in the medial amygdala of mice, identifying 16 inhibitory and 10 excitatory neuron types.

This study identifies ChmC, a phage protein that binds RNA and facilitates mRNA transport through the phage nucleus-like compartment, essential for infection.

This paper demonstrates that transient suppression of PTBP1 in aged glial cells can re-activate neurogenesis in murine and human brains, generating new neurons through canonical pathways.

This study investigates how CTCF binding sites mediate transcriptional insulation in mouse embryonic stem cells, showing that insulation depends on CTCF site number, sequence context, and TAD boundary location.