Beth Martin

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Locus-Scale Massively Parallel Reporter Assays

The paper introduces LAMPRAs to measure how cis-regulatory element composition affects gene expression using synthetic loci.

Large-scale discovery of neural enhancers for cis-regulation therapies

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

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.

Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types

The paper identifies functional cis-regulatory elements in three human cell types using lentiMPRAs and develops predictive models for CRE function.

Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording

The paper designs and characterizes diverse genomic parts for precise genome editing and molecular recording in mammalian cells.

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.

Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

The paper uses single-nucleus ATAC-Seq and RNA-Seq to analyze age and sex differences in human heart cells, identifying gene expression and chromatin changes linked to these factors.

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

This paper identifies epigenetic features affecting prime editing efficiency and shows how chromatin state can be manipulated to enhance or reduce editing efficiency at specific genomic loci.

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

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.

A multiplex, prime editing framework for identifying drug resistance variants at scale

This paper introduces prime-SGE, a prime editing framework for assessing drug resistance variants across multiple oncogenes in a single experiment.

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.

Multiplex genomic recording of enhancer and signal transduction activity in mammalian cells

This paper introduces ENGRAM, a method to genomically record enhancer and signal transduction activity in mammalian cells, demonstrating its ability to track multiple transcriptional reporters with high fidelity.

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.

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress is a simplified COVID-19 testing protocol that eliminates the need for transport media and nucleic acid extraction, achieving high sensitivity and specificity.

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

The paper shows that MPRA data exhibit strand asymmetry favoring naturally transcribed strands, suggesting biological functions driving this effect across gene bodies and Alu elements.

A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assays

This study evaluates how experimental design, orientation, and sequence context affect MPRA results, finding significant differences in regulatory activity measurements.

TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

TransMPRA combines CRISPR perturbation and MPRAs to identify trans-acting factors influencing enhancer activity.

Saturation mutagenesis of disease-associated regulatory elements

The paper performs saturation mutagenesis on disease-associated regulatory elements to assess the functional effects of mutations, revealing variability in transcription factor binding site density and predictive power of conservation scores.

Accurate functional classification of thousands of BRCA1 variants with saturation genome editing

The paper functionally classifies thousands of BRCA1 variants using saturation genome editing to determine their impact on cancer risk.

Multiplex Assessment of Protein Variant Abundance by Massively Parallel Sequencing

This paper introduces VAMP-seq, a method to assess the abundance of protein variants, and identifies pathogenic variants in PTEN and TPMT.

crisprQTL mapping as a genome-wide association framework for cellular genetic screens

This paper introduces crisprQTL mapping to identify gene regulation by using CRISPR perturbations and single-cell RNA-seq in human cells, finding 128 cis-regulatory elements affecting nearby genes.

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

The paper compares chromosomal and episomal enhancer activity using a novel assay, finding significant differences in activity and predictability.