Matthew G. Jones, PhD


About Me

I am an NCI K99/R00 Postdoctoral Scholar at Stanford University in Howard Chang's lab. Generally, I am interested in studying how tumors evolve over time, especially under various pressures exerted by the immune system and therapies. My work typically takes advantage of high-throughput sequencing assays (e.g., scRNA-seq and spatial transcriptomics), lineage-tracing technologies, and new computational tools and inference techniques.

My current research focuses on building more predictive models of tumor evolution, with a focus on how circular, oncogenic extrachromosomal DNA (ecDNA) reshape traditional rules of inheritance to accelerate tumor evolution and overcome targeted therapies. A key outcome of my research thus far is contributing to the discovery that ecDNA amplifications are often co-inherited during mitosis, leading to non-coding oncogenic amplifications and new therapeutic opportunities. Previously, I developed single-cell evolving lineage tracing technologies and computational tools. In this, I developed Cassiopeia, a software suite for reconstructing single-cell phylogenies from continuous CRISPR/Cas9 barcoding data. We used these tools to study how aggressive cancers evolve from a single transformed cell and eventually metastasize throughout a body.

In 2020, I spent the summer as a research intern at Google Brain Genomics working on deep learning methods for Electronic Health Record (EHR) data.

Previously, I completed my PhD in Bioinformatics at UC San Francisco and UC Berkeley advised by Jonathan Weissman and Nir Yosef. Before my graduate work, I studied Computer Science at UC Berkeley and worked in the Nielsen Lab on developing simulators for large admixture events. And before that, I grew up in a small town outside of Pasadena, CA where I was a tri-sport athelete and musician.

Research Interests

  • Cancer evolution

  • Cancer immunology

  • Lineage tracing

  • Genomics technology

Selected Publications

  1. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. King L Hung*, Matthew G Jones*, Ivy Tzo-Lo Wong*, EJ Curtis*, …, Paul S Mischel, Howard Y Chang. BioRxiv. 2023

  2. Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution. Dian Yang*, Matthew G Jones*, …, Nir Yosef, Tyler Jacks, Jonathan S Weissman. Cell. 2022

  3. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Jeffrey J. Quinn*, Matthew G Jones*, Ross A Okimoto, Shigeki Nanjo, Michelle M Chan, Nir Yosef, Trever G Bivona, Jonathan S Weissman. Science. 2021.

  4. Inference of Single Cell Phylogenies from Lineage Tracing Data with Cassiopeia. Matthew G Jones*, Jeffrey J Quinn*, Alex Khodaverdian*, Michelle M Chan, Jeffrey A Hussmann, Robert Wang, Chenling Xu, Jonathan S Weissman, Nir Yosef. Genome Biology. 2020.

Find my full publication list here.

Beyond Science

In my downtime, you can find me engrossed in a book, playing guitar, or listening to my records. I often am looking for an excuse to get outside or to travel.