2024 2024 Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data Adam C Weiner, Marc J Williams, Hongyu Shi, and 6 more authors Nature Communications 2024 HTML PDF Code CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution Khanh N Dinh, Ignacio Vázquez-Garcı́a, Andrew Chan, and 4 more authors bioRxiv 2024 HTML PDF Code Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes Minsoo Kim, Alexander N Gorelick, Ignacio Vázquez-Garcı́a, and 18 more authors Nature Genetics 2024 HTML PDF Code Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer Andrew W. McPherson, Ignacio Vazquez-Garcia, Matthew A. Myers, and 54 more authors bioRxiv 2024 HTML PDF Code Website Tracking clonal evolution of drug resistance in ovarian cancer patients by exploiting structural variants in cfDNA Marc J. Williams, Ignacio Vazquez-Garcia, Grittney Tam, and 24 more authors bioRxiv 2024 HTML PDF Insights on Future Directions in Cancer Research from the AACR NextGen Stars Israel Cañadas, Gabriele Casirati, Kathleen E. Houlahan, and 7 more authors Cancer Discovery Sep 2024 HTML PDF 2023 2023 The imaging and molecular annotation of xenografts and tumours (IMAXT) high throughput data and analysis infrastructure Eduardo A González-Solares, Ali Dariush, Carlos González-Fernández, and 8 more authors Biological Imaging Sep 2023 HTML PDF Transient chromosomal instability as a driver of ovarian cancer genome evolution Ignacio Vazquez-Garcia, Florian Uhlitz, Marc J Williams, and 8 more authors Cancer Research Sep 2023 HTML 2022 2022 Ovarian cancer mutational processes drive site-specific immune evasion Ignacio Vázquez-Garcı́a, Florian Uhlitz, Nicholas Ceglia, and 8 more authors Nature Sep 2022 HTML PDF Code Website Single-cell genomic variation induced by mutational processes in cancer Tyler Funnell, Ciara H O’Flanagan, Marc J Williams, and 8 more authors Nature Sep 2022 HTML PDF Website Fundamental immune–oncogenicity trade-offs define driver mutation fitness David Hoyos, Roberta Zappasodi, Isabell Schulze, and 8 more authors Nature Sep 2022 HTML PDF Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment Laura Kuett, Raúl Catena, Alaz Özcan, and 5 more authors Nature Cancer Sep 2022 HTML PDF Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies Sophia A Wild, Ian G Cannell, Ashley Nicholls, and 6 more authors Elife Sep 2022 HTML PDF Luna Pathology: An integrated open source platform for computational pathology research Doori Rose, Andrew Aukerman, Druv Patel, and 8 more authors Cancer Research Sep 2022 HTML Code Website Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer Kevin M Boehm, Emily A Aherne, Lora Ellenson, and 8 more authors Nature Cancer Sep 2022 HTML PDF Code Website 2021 2021 Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes Stefan C Dentro, Ignaty Leshchiner, Kerstin Haase, and 8 more authors Cell Sep 2021 HTML PDF Website Clonal fitness inferred from time-series modelling of single-cell cancer genomes Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, and 8 more authors Nature Sep 2021 HTML PDF Code Website 2020 2020 A community effort to create standards for evaluating tumor subclonal reconstruction Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, and 8 more authors Nature biotechnology Sep 2020 HTML PDF The evolutionary history of 2,658 cancers Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, and 8 more authors Nature Sep 2020 HTML PDF Code Website The repertoire of mutational signatures in human cancer Ludmil B Alexandrov, Jaegil Kim, Nicholas J Haradhvala, and 8 more authors Nature Sep 2020 HTML PDF Pan-cancer analysis of whole genomes ICGC/TCGA Pan-Cancer Analysis Whole Genomes Consortium Nature Sep 2020 HTML PDF BRCA mutations, homologous DNA repair deficiency, tumor mutational burden, and response to immune checkpoint inhibition in recurrent ovarian cancer Ying L Liu, Pier Selenica, Qin Zhou, and 8 more authors JCO Precision Oncology Sep 2020 HTML PDF Sex differences in oncogenic mutational processes Stephenie D Prokopec, Ren X Sun, Fouad Yousif, and 8 more authors Sep 2020 HTML PDF 2019 2019 Shared molecular targets confer resistance over short and long evolutionary timescales Jing Li, Ignacio Vázquez-Garcı́a, Karl Persson, and 8 more authors Molecular biology and evolution Sep 2019 HTML PDF Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing Emma Laks, Andrew McPherson, Hans Zahn, and 8 more authors Cell Sep 2019 HTML PDF Contrasting the impact of cytotoxic and cytostatic drug therapies on tumour progression Jani V Anttila, Mikhail Shubin, Johannes Cairns, and 6 more authors PLoS Computational Biology Sep 2019 HTML PDF 2017 2017 Clonal heterogeneity influences the fate of new adaptive mutations Ignacio Vázquez-Garcı́a, Francisco Salinas, Jing Li, and 8 more authors Cell Reports Sep 2017 HTML PDF Code 2015 2015 The value of monitoring to control evolving populations Andrej Fischer, Ignacio Vázquez-Garcı́a, and Ville Mustonen Proceedings of the National Academy of Sciences Sep 2015 HTML PDF 2014 2014 High-definition reconstruction of clonal composition in cancer Andrej Fischer, Ignacio Vázquez-Garcı́a, Christopher JR Illingworth, and 1 more author Cell Reports Sep 2014 HTML PDF Code Website
