Samuel G. Regalado

SciPhy estimates time-scaled phylogenies and cell population parameters from sequential genetic lineage tracing data using a Bayesian framework, showing improved accuracy over existing methods.

The paper systematically perturbs enhancer sequences to study their functional properties and robustness, revealing insights into regulatory sequence space and enhancer activity.

The paper studies the evolutionary changes of mammalian enhancers by analyzing orthologous sequences across multiple species and using deep learning to model functional changes.

The paper develops monoclonal gastruloids from single mouse embryonic stem cells and uses DNA Typewriter to reveal heritable lineage biases in early development.

The paper develops monoclonal embryoids with genetic barcoding to overcome clonal complexity bottlenecks in mosaic organoid screens, enabling more accurate quantification of genetic perturbation effects.

The paper describes a CRISPRa screening method combining multiplex perturbations with sc-RNA-seq to identify cell-type-specific regulatory elements and their target genes.

This study induces human gastruloids with embryo-like structures using retinoic acid and shows they match E9.5 mouse embryos in developmental stage through single-cell RNA-seq and computational staging.

The paper uses a combined single-cell genetic and chemical screening platform to analyze kinase dependencies in glioblastoma response to targeted therapy, identifying adaptive signaling and potential combination therapies.

This paper develops scQers, single-cell quantitative expression reporters, to measure enhancer activity across multicellular systems with high precision and range.

This paper introduces DNA Ticker Tape, a system for in vivo molecular recording that sequentially records events using CRISPR-Cas9 and prime editing, demonstrating its ability to record complex event histories and cell lineage.

This study shows that TPP1 isoforms and specific residues regulate telomere length set point in human pluripotent stem cells, with TPP1L compensating for TPP1S loss and affecting telomere stability and elongation.