Publications

Likely my Google Scholar page is more up to date.

2025

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling. Jesse Zhang, Airol A Ubas, …, Matthew G. Jones, …, Daniele Merico, Nima Alidoust, Hani Goodarzi, Johnny Yu. BioRxiv. 2025

EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs. Hyerim Yi*, Shu Zhang*, …, Matthew G. Jones, …, Paul S. Mischel, Howard Y. Chang. BioRxiv. 2025

2024

Enhancer activation from transposable elements in extrachromosomal DNA. Katerina Kraft*, Sedona E. Murphy*, Matthew G. Jones*, …, Howard Y. Chang. BioRxiv. 2024

Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining. Sebastian Prillo, Kevin An, Wilson Wu, Ivan Kristanto, Matthew G Jones, Yun S Song, Nir Yosef. BioRxiv. 2024

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. John C Rose, Julia A. Belk, Ivy Tsz-Lo Wong, Jens Luebeck, Hudson T. Horn, Bence Daniel, Matthew G Jones, …, Howard Y Chang. Cancer Discovery. 2024

Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis. Matthew G. Jones*, Dawei Sun*, …, Fei Chen, Jonathan S. Weissman, Nir Yosef, Dian Yang. BioRxiv. 2024.

<<<<<<< HEAD CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. Kaiyuan Zhu*, Matthew G. Jones*, Jens Luebeck, …, Paul S. Mischel, Howard Y. Chang, Vineet Bafna. BioRxiv (Accepted to Genome Research). 2024.