M. G. Jones

CoRAL accurately resolves extrachromosomal DNA genomestructures with long-read sequencing

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair

This study uses a CRISPR-based method to investigate ecDNA formation, showing efficient circularization and distinct repair pathways for ecDNA and chromosomal scars.

Coordinated inheritance of extrachromosomal DNA species in human cancer cells

This study shows that multiple extrachromosomal DNA species are coordinately inherited in cancer cells through mitotic co-segregation, enabling oncogene cooperation and guiding therapeutic strategies.

Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution

The paper tracks tumor evolution in a mouse model using lineage tracing and single-cell RNA-seq, revealing plasticity, fitness-associated programs, and stereotypical evolutionary trajectories.

Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data

The paper introduces TreeVAE, a probabilistic framework to reconstruct unobserved ancestral cellular states from single-cell lineage tracing and transcriptomics data, showing improved performance over benchmarks.

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

The paper uses single-cell lineage tracing and RNA-seq to identify diverse metastatic behaviors and their drivers in lung cancer xenografts in mice.

Label-free and Multimodal Second Harmonic Generation Light Sheet Microscopy

This paper demonstrates a label-free SHG-LSM technique for 3D imaging of collagen and other harmonophores, combining SHG with light sheet microscopy for multimodal imaging.

Super-resolved polarisation-enhanced second harmonic generation for direct imaging of nanoscale changes in collagen architecture

This paper introduces a super-resolution SHG technique that achieves nanoscale imaging of collagen architecture without fluorescent labels, revealing previously unobservable structural changes.