Likely my Google Scholar page is more up to date.


PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. Sanju Sinha, …, Matthew G. Jones, …, Eytan Ruppin. Nature Cancer. 2024.

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. 2024.

Deciphering cell states and genealogies of human hematopoiesis. Chen Weng, Fulong Yu, Dian Yang, Michael Poeschla, L Alexander Liggett, Matthew G Jones, …, Vijay G Sankaran. Nature. 2024.


Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. John C Rose, Ivy Tsz-Lo Wong, Bence Daniel, Matthew G Jones, …, Howard Y Chang. BioRxiv. 2023

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

Best practices for single-cell analysis across modalities. Lukas Heumos*, Anna C. Schaar*, …, Single-cell Best Practices Consortium, Fabian J. Theis. Nature Reviews Genetics. 2023.

New Tools for Lineage Tracing in Cancer In Vivo. Matthew G Jones*, Dian Yang*, Jonathan Weissman. Annual Reviews in Cancer. 2023.

Lineage Tracing. Matthew G. Jones*, Zoe Piran*. Single-cell best practices. 2023.


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

PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and Phylogenetic Data. Matthew G Jones*, Yanay Rosen*, Nir Yosef. Cell Reports Methods. 2022


Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data. Khalil Ouardini, Romain Lopez, Matthew G Jones, Sebastian Prillo, Richard Zhang, Michael I. Jordan, Nir Yosef. ICML Workshop in Computational Biology. 2021.

Benchmarked approaches for cell lineage reconstructions of in vitro dividing cells and in silico models of Caenorhabditis elegans and Mus musculus developmental trees. Wuming Gong*, Alejandro Granados*, Jingyuan Hu*, Matthew G. Jones*, Ofir Raz*, Irepan Salvador-Martinez*, Hanrui Zhang*, …, Pablo Meyer. Cell Systems. 2021.

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.


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.

Robset Sequence Determinants of \(\alpha\)-Synuclein Toxicity in Yeast Implicate Membrane Binding. Robert W. Newberry, …, Matthew G Jones, …, Willaim F. Degrado, Martin Kampmann. ACS Chem Biol. 2020.


Functional interpretation of single cell similarity maps. David DeTomaso*, Matthew G Jones*, Meena Subramaniam, Tal Ashuach, Chun J. Ye, Nir Yosef. Nat. Comm. 2019.

Molecular recording of mammalian embryogenesis. Michelle M Chan, Zachary D Smith, Sefanie Grosswendt, Helene Kretzmer, Thomas M Norman, Britt Adamson, Marco Jost, Jeffrey J Quinn, Dian Yang, Matthew G Jones, Alex Khodaverdian, Nir Yosef, Alexander Messiner, Jonathan S Weissman. Nature. 2019.

Before 2019

SELAM: simulation of epistasis and local adapation during admixture with mate choice. Russell Corbett-Detig, Matt Jones. Bioinformatics. 2016.

PhD Thesis

Following Tumor Progression Step-By-Step with CRISPR/Cas9-Based Single-Cell Lineage Tracing Technologies and Improved Computational Methods. Matthew G. Jones. 2022.