Michael Kosicki

ProPer-seq is a cost-effective, barcode-free single-cell perturbation profiling method that enables scalable analysis of synthetic biology perturbations and reveals transcriptional control principles.

The paper identifies active human neural enhancers and CRISPRa gRNAs that upregulate NDD risk genes, providing a resource for cis-regulatory therapy development.

The paper identifies hidden enhancers in mouse embryos that are not detected by conventional chromatin profiling methods, highlighting a significant gap in enhancer discovery.

The paper maps the mutagenic sensitivity of human enhancers in vivo by systematically mutating enhancer sequences and using predictive modeling to identify critical nucleotides.

The paper presents a single-cell multi-omics atlas of human development and uses deep learning to analyze regulatory DNA motifs and their impact on chromatin accessibility and gene expression.

Learning and removing Tn5/DNase-I sequence bias lets a small base-resolution CNN (ChromBPNet) recover TF motifs and footprints from accessibility data and rival Enformer at predicting chromatin QTL effects.

The paper investigates how DNA repair genes influence Cas9-induced mutations by analyzing mutational outcomes across 2,838 synthetic targets in mouse cells, revealing gene-specific roles and improving predictive models.

This study creates a gene regulation map of the human fetal heart to interpret genetic variants associated with congenital heart disease and cardiac traits, identifying valvular interstitial cells as key regulators.

The paper develops a cell type-aware framework to identify non-coding variants in Mendelian disorders by integrating single-cell multi-omic data and applying it to congenital cranial dysinnervation disorders.

The paper maps chondrogenic enhancers in limb and axial skeleton development and shows their role in explaining human height heritability.

The paper combines massively parallel reporter assays and mouse transgenic assays to study the functional impact of non-coding variants on neuronal enhancer activity, finding strong correlations and additional pleiotropic effects.

The paper identifies 14,000 human craniofacial enhancers across developmental stages and shows 56% are conserved in mice, providing cell type- and stage-specific activity profiles.

The paper identifies widespread epigenomic changes in idiopathic dilated cardiomyopathy, showing a shift toward fetal-like enhancer states and providing a data resource for further study.

The paper investigates how Cas9-induced large deletions and small indels are regulated, showing their connection through repair mechanisms and locus-specific factors.

The paper predicts Cas9-induced mutation outcomes based on surrounding DNA sequence using data from over 1 billion mutational outcomes.