Samuel G. Regalado

Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.

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.

Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers

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

Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers

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

Lineage recording in monoclonal gastruloids reveals heritable modes of early development

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

Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens

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.

Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements

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.

Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types

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.

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

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.

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

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

A temporally resolved, multiplex molecular recorder based on sequential genome editing

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.

Telomere length set point regulation in human pluripotent stem cells critically depends on the shelterin protein TPP1

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.