2024 2024 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 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 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 2023 HTML Single-cell DNA replication dynamics in genomically unstable cancers Adam C Weiner, Marc J Williams, Hongyu Shi, and 6 more authors bioRxiv 2023 HTML PDF Code 2022 2022 Ovarian cancer mutational processes drive site-specific immune evasion Ignacio Vázquez-Garcı́a, Florian Uhlitz, Nicholas Ceglia, and 8 more authors Nature 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 2022 HTML PDF Website Fundamental immune–oncogenicity trade-offs define driver mutation fitness David Hoyos, Roberta Zappasodi, Isabell Schulze, and 8 more authors Nature 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 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 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 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 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 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 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 2020 HTML PDF The evolutionary history of 2,658 cancers Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, and 8 more authors Nature 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 2020 HTML PDF Pan-cancer analysis of whole genomes ICGC/TCGA Pan-Cancer Analysis Whole Genomes Consortium Nature 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 2020 HTML PDF Sex differences in oncogenic mutational processes Stephenie D Prokopec, Ren X Sun, Fouad Yousif, and 8 more authors 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 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 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 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 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 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 2014 HTML PDF Code Website
