Matthew G. Jones

Pycea provides a toolkit for analyzing single-cell lineage tracing data, integrating with Scanpy and offering visualization and statistical methods for lineage trees.

This study uses spatial transcriptomics and lineage tracing to show how tumor subclones drive microenvironmental changes that promote metastasis in a mouse model.

This study shows that a genetically engineered mouse model of osteosarcoma recapitulates the genomic complexity and driver mutations observed in human osteosarcoma.

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.

A genome-wide plasmid screen, Retain-seq, identifies thousands of CpG-rich promoter-like human elements that tether episomes to mitotic chromosomes, shape ecDNA structure, and lose function when methylated.

The paper introduces Tahoe-x1, a large-scale perturbation-trained single-cell foundation model with 3 billion parameters, achieving state-of-the-art performance in cancer-related tasks.

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

This study investigates the spatial-temporal evolution of extrachromosomal DNA (ecDNA) in glioblastoma, showing that EGFR ecDNA drives tumor evolution and identifies a potential therapeutic window for early intervention.

PEtracer maps cell state and lineage dynamics in vivo with high spatial resolution using prime editing and multimodal imaging.

The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.

A 100-million-cell atlas: 50 cancer lines pooled as spheroid villages, treated with 379 drugs at several doses, profiled by combinatorial-barcoding scRNA-seq and embedded with a 10-dimensional scVI model.

This paper develops a Neighbor-Joining algorithm with theoretical guarantees for reconstructing phylogenies from CRISPR-Cas9 lineage tracing data, showing improved performance on simulated and real data.

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

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

PhyloVision is an open-source software tool that integrates single-cell transcriptomic and phylogenetic data to identify heritable gene modules associated with lineage relationships.

The paper introduces Cassiopeia, a method for inferring single-cell phylogenies from lineage tracing data, and benchmarks it against traditional methods using a large experimental dataset.

VISION annotates variation sources in single-cell RNA-seq data without preconceived group stratification, linking findings to clinical phenotypes in lupus B cells.

The paper develops a molecular recorder to track lineage and define a mouse cell fate map using scRNA-seq, revealing transcriptional convergence of endodermal cells and estimating progenitor cell numbers.