publications

Publications in reversed chronological order.

2026

  1. zhang2026convergent.jpg
    A convergent uPAR-positive tumor ecosystem creates broad vulnerability to CAR T cell therapy
    Zeda Zhang, Yu-Jui Ho, Xin Fang, Minseo Kim, Marguerite Li, Wei Luan, Clemens Hinterleitner, Sascha Haubner, Friederike Kogel, Edwin C. Pratt, Elif Ozcelik, José Reyes, Qingwen Jiang, Vincent W. Yang, Yu-Jung Chen, Tao Wang, Haijiao Liu, Haonan Hu, Xueqian Zhuang, Jin Park, Stella V. Paffenholz, Kevin Chen, Qing Chang, Amanda Kulick, Jing Zhang, Eric Chan, Eric Rosiek, Ning Fan, Riley A. Williams, Adam C. Wang, Samuel Freeman, Sha Tian, Gertrude Gunset, Andreina Garcia Angus, Nicolas Lecomte, Selma Yeni Yildirim, Emily Ali, Michelle Wu, Ileana C. Miranda, Cristina R. Antonescu, Olca Basturk, Zeynep Tarcan, Natasha Rekhtman, Christina Wilson, Merve Basar, Jennifer L. Sauter, Hikmat A. Al-Ahmadie, Samuel Singer, Christine Iacobuzio-Donahue, Charles Rudin, Elisa Stanchina, Karuna Ganesh, Paul B. Romesser, Britta Weigelt, Dan Dongeun Huh, Josef Leibold, Judith Feucht, Ignacio Vazquez-Garcia, Matthew J. Bott, Dmitriy Zamarin, Sohrab P. Shah, Jason S. Lewis, Corina Amor, Dana Pe’er, Jorge Mansilla-Soto, Aveline Filliol, Michel Sadelain, and Scott W. Lowe#
    Cell, 2026
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2025

  1. mcpherson2025ongoing.png
    Ongoing genome doubling shapes evolvability and immunity in ovarian cancer
    Andrew W. McPherson*, Ignacio Vazquez-Garcia*, Matthew A. Myers*, Duaa H. Al-Rawi*, Matthew Zatzman*, Adam C. Weiner, Samuel S. Freeman, Neeman Mohibullah, Gryte Satas, Marc J. Williams, Nicholas Ceglia, Danguolė Norkūnaitė, Allen W. Zhang, Jun Li, Jamie L.P. Lim, Michelle Wu, Seongmin Choi, Eliyahu Havasov, Diljot Grewal, Hongyu Shi, Minsoo Kim, Roland F. Schwarz, Tom L. Kaufmann, Khanh N. Dinh, Florian Uhlitz, Julie Tran, Yushi Wu, Ruchi Patel, Satish Ramakrishnan, DooA Kim, Justin Clarke, Hunter Green, Emily Ali, Melody DiBona, Nancy Varice, Ritika Kundra, Vance Broach, Ginger J. Gardner, Kara Long Roche, Yukio Sonoda, Oliver Zivanovic, Sarah H. Kim, Rachel N. Grisham, Ying L. Liu, Agnes Viale, Nicole Rusk, Yulia Lakhman, Lora H. Ellenson, Simon Tavaré, Samuel AJR Aparicio, Dennis S. Chi, Carol Aghajanian, Nadeem R. Abu-Rustum, Claire F. Friedman, Dmitriy Zamarin, Britta Weigelt, Samuel F. Bakhoum, and Sohrab P. Shah
    Nature, 2025
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  2. bressan2025cancer.png
    Cancer Research in the Age of Spatial Omics: Lessons from IMAXT
    Dario Bressan, IMAXT Cancer Grand Challenges Consortium, Nicholas Walton, and Gregory J Hannon
    Cancer Discovery, 2025
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  3. dinh2025cinner.png
    CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution
    Khanh N Dinh#, Ignacio Vazquez-Garcia#, Andrew Chan, Rhea Malhotra, Adam Weiner, Andrew McPherson, and Simon Tavaré#
    PLoS Computational Biology, 2025
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  4. stur2025dynamic.jpg
    The dynamic immune behavior of primary and metastatic ovarian carcinoma
    Elaine Stur, Fuduan Peng, Pang-ning Teng, Emine Bayraktar, Min Hu, Sara Corvigno, David J Brown, Sanghoon Lee, Kathleen N Moore, Nicholas W Bateman, Kathleen M Darcy, George L Maxwell, Thomas P. Conrads, Nidhi Sahni, Ignacio Vázquez-García, Sohrab P Shah, Joseph Celestino, Nicole D. Fleming, Nicholas E Navin, Linghua Wang, and Anil K Sood
    npj Precision Oncology, 2025
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  5. williams2025tracking.png
    Tracking clonal evolution during treatment in ovarian cancer using cell-free DNA
    Marc J. Williams#, Ignacio Vazquez-Garcia, Grittney Tam, Michelle Wu, Nancy Varice, Eliyahu Havasov, Hongyu Shi, Duaa H. Al-Rawi, Gryte Satas, Hannah J. Lees, Jake June-Koo Lee, Matthew A. Myers, Matthew Zatzman, Nicole Rusk, Emily Ali, Ronak H. Shah, Michael F. Berger, Neeman Mohibullah, Yulia Lakhman, Dennis S. Chi, Nadeem R. Abu-Rustum, Carol Aghajanian, Andrew McPherson, Dmitriy Zamarin, Brian Loomis, Britta Weigelt, Claire F. Friedman, and Sohrab P. Shah#
    Nature, 2025
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  6. zare2025uncertainty.png
    Uncertainty-aware generative oversampling using an entropy-guided conditional variational autoencoder
    Amirhossein Zare, Amirhessam Zare, Parmida Sadat Pezeshki, Herlock Rahimi, Ali Ebrahimi, Ignacio Vazquez-Garcia, and Leo Anthony Celi
    arXiv, 2025
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2024

  1. weiner2024inferring.png
    Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data
    Adam C Weiner, Marc J Williams, Hongyu Shi, Ignacio Vazquez-Garcia, Sohrab Salehi, Nicole Rusk, Samuel Aparicio, Sohrab P Shah, and Andrew McPherson
    Nature Communications, 2024
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  2. kim2024single.png
    Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes
    Minsoo Kim, Alexander N. Gorelick, Ignacio Vazquez-Garcia, Marc J. Williams, Sohrab Salehi, Hongyu Shi, Adam C. Weiner, Nick Ceglia, Tyler Funnell, Tricia Park, Sonia Boscenco, Ciara H. O’Flanagan, Hui Jiang, Diljot Grewal, Cerise Tang, Nicole Rusk, Payam A. Gammage, Andrew McPherson, Sam Aparicio, Sohrab P. Shah, and Ed Reznik
    Nature Genetics, 2024
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  3. canadas2024insights.png
    Insights on Future Directions in Cancer Research from the AACR NextGen Stars
    Israel Cañadas, Gabriele Casirati, Kathleen E. Houlahan, Kara N. Maxwell, Arnav Mehta, Abhijit Parolia, Olivier Saulnier, Alison M. Taylor, Claire E. Thomas, and Ignacio Vazquez-Garcia
    Cancer Discovery, Sep 2024
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2023

  1. gonzalez2023imaging.png
    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, Aybüke Küpcü Yoldaş, Alireza Molaeinezhad, Mohammad Al Sa’d, Leigh Smith, Tristan Whitmarsh, Neil Millar, Nicholas Chornay, and  others
    Biological Imaging, Sep 2023
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  2. Transient chromosomal instability as a driver of ovarian cancer genome evolution
    Ignacio Vazquez-Garcia, Florian Uhlitz, Marc J Williams, Jun Li, Hongyu Shi, Samuel Freeman, Matthew Myers, MSK SPECTRUM Consortium, Britta Weigelt, Dmitriy Zamarin, and  others
    Cancer Research, Sep 2023
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2022

  1. vazquez2022ovarian.png
    Ovarian cancer mutational processes drive site-specific immune evasion
    Ignacio Vazquez-Garcia*, Florian Uhlitz*, Nicholas Ceglia, Jamie LP Lim, Michelle Wu, Neeman Mohibullah, Juliana Niyazov, Arvin Eric B Ruiz, Kevin M Boehm, Viktoria Bojilova, and  others
    Nature, Sep 2022
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  2. funnell2022single.png
    Single-cell genomic variation induced by mutational processes in cancer
    Tyler Funnell*, Ciara H O’Flanagan*, Marc J Williams*, Andrew McPherson, Steven McKinney, Farhia Kabeer, Hakwoo Lee, Sohrab Salehi, Ignacio Vazquez-Garcia, Hongyu Shi, and  others
    Nature, Sep 2022
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  3. hoyos2022fundamental.png
    Fundamental immune–oncogenicity trade-offs define driver mutation fitness
    David Hoyos*, Roberta Zappasodi*, Isabell Schulze, Zachary Sethna, Kelvin César Andrade, Dean F Bajorin, Chaitanya Bandlamudi, Margaret K Callahan, Samuel A Funt, Sine R Hadrup, and  others
    Nature, Sep 2022
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  4. kuett2022three.png
    Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment
    Laura Kuett*, Raúl Catena*, Alaz Özcan, Alex Plüss, Peter Schraml, Holger Moch, Natalie Souza, and Bernd Bodenmiller
    Nature Cancer, Sep 2022
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  5. wild2022clonal.png
    Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies
    Sophia A Wild, Ian G Cannell, Ashley Nicholls, Katarzyna Kania, Dario Bressan, Gregory J Hannon, Kirsty Sawicka, CRUK IMAXT Grand Challenge Team, and  others
    Elife, Sep 2022
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  6. rose2022luna.png
    Luna Pathology: An integrated open source platform for computational pathology research
    Doori Rose, Andrew Aukerman, Druv Patel, Arfath Pasha, Armaan Kohli, Ignacio Vazquez-Garcia, Kevin Boehm, Rami Vanguri, Matthew Shabet, Vassiliki Mancoridis, and  others
    Cancer Research, Sep 2022
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  7. boehm2022multimodal.png
    Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer
    Kevin M Boehm, Emily A Aherne, Lora Ellenson, Ines Nikolovski, Mohammed Alghamdi, Ignacio Vazquez-Garcia, Dmitriy Zamarin, Kara Long Roche, Ying Liu, Druv Patel, and  others
    Nature Cancer, Sep 2022
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2021

  1. dentro2021characterizing.png
    Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
    Stefan C Dentro, Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G Deshwar, Kaixian Yu, Yulia Rubanova, Geoff Macintyre, Jonas Demeulemeester, and  others
    Cell, Sep 2021
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  2. salehi2021clonal.png
    Clonal fitness inferred from time-series modelling of single-cell cancer genomes
    Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J Williams, Kieran R Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, and  others
    Nature, Sep 2021
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2020

  1. salcedo2020community.png
    A community effort to create standards for evaluating tumor subclonal reconstruction
    Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G Espiritu, Amit G Deshwar, Matei David, Nathan M Wilson, Stefan Dentro, Jeff A Wintersinger, Lydia Y Liu, Minjeong Ko, and  others
    Nature biotechnology, Sep 2020
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  2. gerstung2020evolutionary.png
    The evolutionary history of 2,658 cancers
    Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, and  others
    Nature, Sep 2020
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  3. alexandrov2020repertoire.png
    The repertoire of mutational signatures in human cancer
    Ludmil B Alexandrov, Jaegil Kim, Nicholas J Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R Covington, Dmitry A Gordenin, Erik N Bergstrom, and  others
    Nature, Sep 2020
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  4. icgc2020pan.jpeg
    Pan-cancer analysis of whole genomes
    ICGC/TCGA Pan-Cancer Analysis Whole Genomes Consortium
    Nature, Sep 2020
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  5. liu2020brca.png
    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, Alexia Iasonos, Margaret Callahan, Noah Z Feit, Julia Boland, Ignacio Vazquez-Garcia, Diana Mandelker, Ahmet Zehir, and  others
    JCO Precision Oncology, Sep 2020
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  6. prokopec2020sex.png
    Sex differences in oncogenic mutational processes
    Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, Fatima Al-Shahrour, Gurnit Atwal, Peter J Bailey, Andrew V Biankin, Paul C Boutros, Peter J Campbell, and  others
    Sep 2020
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2019

  1. li2019shared.png
    Shared molecular targets confer resistance over short and long evolutionary timescales
    Jing Li, Ignacio Vazquez-Garcia, Karl Persson, Asier González, Jia-Xing Yue, Benjamin Barré, Michael N Hall, Anthony Long, Jonas Warringer, Ville Mustonen, and Gianni Liti#
    Molecular biology and evolution, Sep 2019
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  2. laks2019clonal.jpg
    Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing
    Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, Jazmine Brimhall, Justina Biele, Beixi Wang, Tehmina Masud, Jerome Ting, and  others
    Cell, Sep 2019
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  3. anttila2019contrasting.png
    Contrasting the impact of cytotoxic and cytostatic drug therapies on tumour progression
    Jani V Anttila, Mikhail Shubin, Johannes Cairns, Florian Borse, Qingli Guo, Tommi Mononen, Ignacio Vazquez-Garcia, Otto Pulkkinen, and Ville Mustonen
    PLoS Computational Biology, Sep 2019
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2017

  1. vazquez2017clonal.png
    Clonal heterogeneity influences the fate of new adaptive mutations
    Ignacio Vazquez-Garcia#, Francisco Salinas, Jing Li, Andrej Fischer, Benjamin Barré, Johan Hallin, Anders Bergström, Elisa Alonso-Perez, Jonas Warringer, Ville Mustonen#, and Gianni Liti#
    Cell Reports, Sep 2017
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2015

  1. fischer2015value.png
    The value of monitoring to control evolving populations
    Andrej Fischer, Ignacio Vazquez-Garcia, and Ville Mustonen
    Proceedings of the National Academy of Sciences, Sep 2015
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2014

  1. fischer2014high.jpg
    High-definition reconstruction of clonal composition in cancer
    Andrej Fischer, Ignacio Vazquez-Garcia, Christopher JR Illingworth, and Ville Mustonen
    Cell Reports, Sep 2014
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