Publications
Selected publications
Hung KL*, Jones MG*, Wong ITL*, Curtis EJ*, et al. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. Nature. 2024
Jones MG*, Sun D*, et al. Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis. BioRxiv. 2024.
Yang D*, Jones MG*, et al. Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution. Cell. 2022
Quinn JJ*, Jones MG*, et al. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science. 2021
Full Publication List
2025
Koblan LW*, Yost KE*, Zheng P*, Colgan WN*, Jones MG, et al. High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer. BioRxiv. 2025.
Huang YH*, Belk JA*, Zhang R, Weiser NE, Chiang Z, Jones MG, et al. Unified molecular approach for spatial epigenome, transcriptome, and cell lineages. PNAS. 2025
Yi H, Zhang S, …, Jones MG, et al. EcDNA-borne PVT1 fusion stabilizes oncogenic mRNAs. BioRxiv. 2025
Zhang J, Ubas AA, de Borja R, Svensson V, Thomas N, Thakar N, Lai I, Winters A, Khan U, Jones MG, et al. Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling. BioRxiv. 2025
Rose JC, Belk JA, Wong ITL, Luebeck J, Horn HT, Daniel B, Jones MG, et al. Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. Cancer Discovery. 2025
Prillo S, An K, Wu W, Kristanto I, Jones MG, Song YS, Yosef N. Tree reconstruction guarantees from CRISPR-Cas9 lineage tracing data using Neighbor-Joining. BioRxiv. 2025
2024
Hung KL, Jones MG*, Wong ITL, Curtis EJ, et al. Coordinated inheritance of extrachromosomal DNAs in cancer cells. Nature. 2024
Jones MG*, Sun D* et al. Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis. BioRxiv. 2024
Kraft K, Sedona SE*, Jones MG*, et al. Enhancer activation from transposable elements in extrachromosomal DNA. BioRxiv 2024
Zhu K*, Jones MG*, et al. CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. Genome Research. 2024
Sinha S, Vegesna R, Mukherjee S, Kammula AV, Dhruba SR, Wu W, Kerr DL, Niar NU, Jones MG, et al. PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors. Nature Cancer. 2024
Weng C, Yu F, Yang D, Poeschla M, Liggett LA, Jones MG, et al. Deciphering cell states and genealogies of human haematopoiesis. Nature. 2024
Noorani I*, Haughey M*, Luebeck J, Rowan A, Grönroos E, Terenzi F, Wong ITL, Kittel J, Bailey C, Weeden C, Bell D, Joo E, Barbe V, Jones MG, et al. Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma. BioRxiv. 2024
2023
Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F, Schiller HB, Single-Cell Best Practices Consortium (including Jones MG), Theis FJ. Best practices for single-cell analysis across modalities. Nature Reviews Genetics. 2023
Jones MG*, Yang D*, Weissman JS. New tools for lineage tracing in cancer in vivo. Annual Reviews of Cancer Biology. 2023
2022
Yang D*, Jones MG*, et al. Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution. Cell. 2022
Jones MG*, Rosen Y*, Yosef N. Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision. Cell Reports Methods. 2022
2021
Gong W*, Granados AA*, Hu J*, Jones MG*, Raz O*, Salvador-Martinez I*, Zhang H*, et al. Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees. Cell Systems. 2021
Ouardini K, Lopez R, Jones MG, et al. Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data. ICML Workshop in Computational Biology. 2021
Quinn JJ*, Jones MG*, et al. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science. 2021
2020
Jones MG*, Khodaverdian A*, Quinn JJ*, et al. Inference of single-cell phylogenies from lineage tracing data using Cassiopeia. Genome Biology. 2020
Newberry RW, …, Jones MG, et al. Robust sequence determinants of α-synuclein toxicity in yeast implicate membrane binding. ACS Chemical Biology. 2020
2019
DeTomaso D*, Jones MG*, et al. Functional interpretation of single cell similarity maps. Nature Communications. 2019
Chan MM*, Smith ZD*, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, et al. Molecular recording of mammalian embryogenesis. Nature. 2019
Prior to 2019
Corbett-Detig R and Jones M. SELAM: simulation of epistasis and local adaptation during admixture with mate choice. Bioinformatics. 2016