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For: Leighton J, Hu M, Sei E, Meric-Bernstam F, Navin NE. Reconstructing mutational lineages in breast cancer by multi-patient-targeted single-cell DNA sequencing. Cell Genom 2023;3:100215. [PMID: 36777188 PMCID: PMC9903705 DOI: 10.1016/j.xgen.2022.100215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
1
Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X, Xia Q, Xu Z, Fu Y, Zhang G, Wu H, Guo G, Guo H, Ruan Y, Wang Y, Xing D, Xu X, Zhang Z. Advances and applications in single-cell and spatial genomics. SCIENCE CHINA. LIFE SCIENCES 2025;68:1226-1282. [PMID: 39792333 DOI: 10.1007/s11427-024-2770-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 10/10/2024] [Indexed: 01/12/2025]
2
Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M, Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nat Biotechnol 2025;43:581-592. [PMID: 38862616 PMCID: PMC11994449 DOI: 10.1038/s41587-024-02250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
3
Maulding ND, Zou J, Zhou W, Metcalfe C, Stuart JM, Ye X, Hafner M. Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer. NPJ Syst Biol Appl 2025;11:5. [PMID: 39794360 PMCID: PMC11723929 DOI: 10.1038/s41540-024-00485-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 12/25/2024] [Indexed: 01/13/2025]  Open
4
Lin Y, Wang J, Wang K, Bai S, Thennavan A, Wei R, Yan Y, Li J, Elgamal H, Sei E, Casasent A, Rao M, Tang C, Multani AS, Ma J, Montalvan J, Nagi C, Winocour S, Lim B, Thompson A, Navin N. Normal breast tissues harbour rare populations of aneuploid epithelial cells. Nature 2024;636:663-670. [PMID: 39567687 DOI: 10.1038/s41586-024-08129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/27/2024] [Indexed: 11/22/2024]
5
Yuan DJ, Zinno J, Botella T, Dhingra D, Wang S, Hawkins A, Swett A, Sotelo J, Raviram R, Hughes C, Potenski C, Yokoyama A, Kakiuchi N, Ogawa S, Landau DA. Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595241. [PMID: 38826366 PMCID: PMC11142212 DOI: 10.1101/2024.05.22.595241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
6
Liu Y, Edrisi M, Yan Z, A Ogilvie H, Nakhleh L. NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model. Algorithms Mol Biol 2024;19:18. [PMID: 38685065 PMCID: PMC11059640 DOI: 10.1186/s13015-024-00264-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/27/2024] [Indexed: 05/02/2024]  Open
7
Goyal Y, Busch GT, Pillai M, Li J, Boe RH, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, Mellis IA, Kiani K, Alicea GM, Fane ME, Ahmed SS, Li H, Chen Y, Chai C, Kaster J, Witt RG, Lazcano R, Ingram DR, Johnson SB, Wani K, Dunagin MC, Lazar AJ, Weeraratna AT, Wargo JA, Herlyn M, Raj A. Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells. Nature 2023;620:651-659. [PMID: 37468627 PMCID: PMC10628994 DOI: 10.1038/s41586-023-06342-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
8
Pillai M, Hojel E, Jolly MK, Goyal Y. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools. NATURE COMPUTATIONAL SCIENCE 2023;3:301-313. [PMID: 38177938 DOI: 10.1038/s43588-023-00427-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/03/2023] [Indexed: 01/06/2024]
9
Zhang H, Karnoub ER, Umeda S, Chaligné R, Masilionis I, McIntyre CA, Sashittal P, Hayashi A, Zucker A, Mullen K, Hong J, Makohon-Moore A, Iacobuzio-Donahue CA. Application of high-throughput single-nucleus DNA sequencing in pancreatic cancer. Nat Commun 2023;14:749. [PMID: 36765116 PMCID: PMC9918733 DOI: 10.1038/s41467-023-36344-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023]  Open
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