Colin Kern

The paper identifies a widespread transcript leakage issue in spatial transcriptomics and introduces DeLeakage, a Bayesian method that improves data cleaning and cell-type annotation.

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.

The paper creates a single-cell atlas of transcription and chromatin states in the human brain, identifying regulatory programs and linking them to neuropsychiatric disorders.

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.

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

The paper creates a high-resolution multimodal lung atlas using single-nucleus RNA and chromatin data from 11 healthy adults, identifying 70 cell populations and 332,846 chromatin regions.

Bento enables subcellular analysis of spatial transcriptomics data by defining domains, annotating localization patterns, and quantifying gene colocalization, demonstrating its use on multiple datasets.

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.

The paper constructs a single-cell chromatin accessibility atlas of the human brain, identifies cell-type-specific regulatory elements, and develops models to predict regulatory function of disease risk variants.

This paper introduces a spatial genome aligner that reconstructs chromosome architectures from DNA-FISH data and identifies chromosome ploidies, revealing new insights into chromatin organization.

The paper identifies and compares chromatin accessibility in cattle, pig, and mouse tissues using ATAC-seq, finding species-specific regulatory elements and conservation patterns.

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.