Yongsoo Kim

Department of Pathology, Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, the Netherlands.

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I am an assistant professor in oncogenomics at the Amsterdam Universtiy Medical Center (Amsterdam UMC). I am interested in how informatics technologies (especially machine learning) can make our life better, especially in the treatment of cancer patients. To this end, I exposed myself to both biology and computer science during my PhD training and postdoc period.

Together with other PIs in the group, I am leading the Tumor Genome Analysis Core (TGAC) of Cancer Center Amsterdam. You can find more about me in CV tab.

news

Jul 15, 2025 Statescope software is out
Jul 15, 2025 Cell2Sample project will start (ADORE funded project)
Nov 27, 2019 CCA grant accepted (150,000 Euros for 2 years)
Nov 06, 2019 Our work on a novel integration method (WON-PARAFAC) is published in Nature Communication
Jul 26, 2019 Hollis Brownstein Research Grant awarded by Leukemia research foundation (100,000 USD for 1 year)

latest posts

Jan 09, 2020 Switching to neovim
Dec 31, 2019 Vim environment creation

selected publications

  1. Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer
    Tesa M Severson, Yongsoo Kim, Stacey EP Joosten, Karianne Schuurman, Petra Van Der Groep, Cathy B Moelans, Natalie D Ter Hoeve, Quirine F Manson, John W Martens, Carolien HM Van Deurzen, and others
    Nature communications, 2018
  2. Integrative epigenetic taxonomy of primary prostate cancer
    Suzan Stelloo, Ekaterina Nevedomskaya, Yongsoo Kim, Karianne Schuurman, Eider Valle-Encinas, João Lobo, Oscar Krijgsman, Daniel Simon Peeper, Seiwon Laura Chang, Felix Yi-Chung Feng, and others
    Nature communications, 2018
  3. Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo
    Yongsoo Kim, Tycho Bismeijer, Wilbert Zwart, Lodewyk FA Wessels, and Daniel J Vis
    Nature communications, 2019
  4. Bayesian log-normal deconvolution for enhanced in silico microdissection of bulk gene expression data
    Bárbara Andrade Barbosa, Saskia D Asten, Ji Won Oh, Arantza Farina-Sarasqueta, Joanne Verheij, Frederike Dijk, Hanneke WM Laarhoven, Bauke Ylstra, Juan J Garcia Vallejo, Mark A Wiel, and Yongsoo Kim
    Nature communications, 2021
  5. Multi-scale spatial modeling of immune cell distributions enables survival prediction in primary central nervous system lymphoma
    Margaretha GM Roemer, Tim Brug, Erik Bosch, Daniella Berry, Nathalie Hijmering, Phylicia Stathi, Karin Weijers, Jeannette Doorduijn, Jacoline Bromberg, Mark Wiel, and Yongsoo Kim
    Iscience, 2023
  6. A comprehensive overview of RNA deconvolution methods and their application
    Yebin Im and Yongsoo Kim
    Molecules and cells, 2023
  7. Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution
    Yongsoo Kim, Jurriaan Janssen, Teodora Radonic, Mischa Steketee, Saskia Asten, Paul Eijk, Febe Maldegem, David Noske, Idris Bahce, Juan Garcia Vallejo, and others
    2024