| Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics 24 (8), 550-572, 2023 | 557 | 2023 |
| Molecular recording of mammalian embryogenesis MM Chan, ZD Smith, S Grosswendt, H Kretzmer, TM Norman, B Adamson, ... Nature 570 (7759), 77-82, 2019 | 354 | 2019 |
| Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts JJ Quinn, MG Jones, RA Okimoto, S Nanjo, MM Chan, N Yosef, ... Science 371 (6532), eabc1944, 2021 | 253 | 2021 |
| Functional interpretation of single cell similarity maps D DeTomaso, MG Jones, M Subramaniam, T Ashuach, CJ Ye, N Yosef Nature Communications 10, 2019 | 217 | 2019 |
| Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution D Yang, MG Jones, S Naranjo, WM Rideout, KHJ Min, R Ho, W Wu, ... Cell 185 (11), 1905-1923. e25, 2022 | 216 | 2022 |
| Inference of single-cell phylogenies from lineage tracing data using Cassiopeia MG Jones, A Khodaverdian, JJ Quinn, MM Chan, JA Hussmann, R Wang, ... Genome biology 21, 1-27, 2020 | 104 | 2020 |
| Deciphering cell states and genealogies of human haematopoiesis C Weng, F Yu, D Yang, M Poeschla, LA Liggett, MG Jones, X Qiu, ... Nature 627 (8003), 389-398, 2024 | 53 | 2024 |
| Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees W Gong, AA Granados, J Hu, MG Jones, O Raz, I Salvador-Martínez, ... Cell systems 12 (8), 810-826. e4, 2021 | 48 | 2021 |
| SELAM: simulation of epistasis and local adaptation during admixture with mate choice R Corbett-Detig, M Jones Bioinformatics 32 (19), 3035-3037, 2016 | 27 | 2016 |
| PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors S Sinha, R Vegesna, S Mukherjee, AV Kammula, SR Dhruba, W Wu, ... Nature Cancer, 1-15, 2024 | 19 | 2024 |
| New tools for lineage tracing in cancer in vivo MG Jones, D Yang, JS Weissman Annual Review of Cancer Biology 7 (1), 111-129, 2023 | 12 | 2023 |
| Robust sequence determinants of α-synuclein toxicity in yeast implicate membrane binding RW Newberry, T Arhar, J Costello, GC Hartoularos, AM Maxwell, ... ACS chemical biology 15 (8), 2137-2153, 2020 | 12 | 2020 |
| Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data K Ouardini, R Lopez, MG Jones, S Prillo, R Zhang, MI Jordan, N Yosef bioRxiv, 2021.05. 28.446021, 2021 | 11 | 2021 |
| Coordinated inheritance of extrachromosomal DNAs in cancer cells KL Hung, MG Jones, ITL Wong, EJ Curtis, JT Lange, BJ He, J Luebeck, ... Nature 635 (8037), 201-209, 2024 | 8* | 2024 |
| Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision MG Jones, Y Rosen, N Yosef Cell reports methods 2 (4), 2022 | 8* | 2022 |
| CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing K Zhu, MG Jones, J Luebeck, X Bu, H Yi, KL Hung, ITL Wong, S Zhang, ... International Conference on Research in Computational Molecular Biology, 454-457, 2024 | 5 | 2024 |
| Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair JC Rose, JA Belk, ITL Wong, J Luebeck, HT Horn, B Daniel, MG Jones, ... Cancer Discovery 15 (1), 69-82, 2025 | 2 | 2025 |
| Spatiotemporal lineage tracing reveals the dynamic spatial architecture of tumor growth and metastasis MG Jones, D Sun, KHJ Min, WN Colgan, L Tian, JA Weir, VZ Chen, ... bioRxiv, 2024 | 1 | 2024 |
| Abstract PR014: PVT1 fusion on extrachromosomal DNA (ecDNA) increases oncogene RNA stability and cancer cell growth H Yi, S Zhang, MG Jones, JA Belk, J Swinderman, Q Shi, EJ Curtis, ... Molecular Cancer Therapeutics 23 (11_Supplement), PR014-PR014, 2024 | | 2024 |
| Enhancer activation from transposable elements in extrachromosomal DNA K Kraft, SE Murphy, MG Jones, Q Shi, A Bhargava-Shah, C Luong, ... bioRxiv, 2024 | | 2024 |
