Projects funded by the NCN

Information on the principal investigator and host institution

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TUMORMAP: Mapping tumor subclones and their immune microenvironment in ultra-high spatial and molecular resolution

2020/38/E/NZ2/00305

Keywords:

machine learning probabilistic modeling spatial modeling tumor microenvironment tumor evolution tumor imaging

Descriptors:

  • NZ2_007:
  • NZ2_008:

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

Host institution :

Uniwersytet Warszawski, Wydział Matematyki, Informatyki i Mechaniki

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Ewa Szczurek 

Number of co-investigators in the project: 5

Call: SONATA BIS 10 - announced on 2020-07-29

Amount awarded: 1 927 200 PLN

Project start date (Y-m-d): 2021-04-09

Project end date (Y-m-d): 2026-04-08

Project duration:: 60 months (the same as in the proposal)

Project status: Pending project

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (3)
  1. CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants.
    Authors:
    Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Shafighi, Szymon M. Kiełbasa, Hugo W. van Kessel, Ruben A. L. de Groen, Joost S. P. Vermaat, Julieta H. Sepúlveda Yáñez, Marcelo A. Navarrete, Hendrik Veelken, Cornelis A. M. van Bergen & Ewa Szczurek
    Academic press:
    Genome Biology (rok: 2024, tom: 25, strony: 286), Wydawca: Biomed Central
    Status:
    Published
    DOI:
    10.1186/s13059-024-03417-1 - link to the publication
  2. Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope
    Authors:
    Shadi Shafighi, Agnieszka Geras, Barbara Jurzysta, Alireza Sahaf Naeini, Igor Filipiuk, Alicja Ra̧czkowska, Hosein Toosi, Łukasz Koperski, Kim Thrane, Camilla Engblom, Jeff E. Mold, Xinsong Chen, Johan Hartman, Dominika Nowis, Alessandra Carbone, Jens Lagergren & Ewa Szczurek
    Academic press:
    Nature Communications (rok: 2024, tom: 15, strony: 9343), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41467-024-53374-3 - link to the publication
  3. SIEVE: joint inference of single nucleotide variants and cell phylogeny from single-cell DNA sequencing data
    Authors:
    S. Kang, N. Borgsmuller, M. Valecha, J. Kuipers, J.M. Alves, S. Prado-Lopez, D. Chantada, N. Beerenwinkel, D. Posada, E. Szczurek
    Academic press:
    Genome Biology (rok: 2022, tom: 23, strony: 248), Wydawca: Biomed Central
    Status:
    Published
    DOI:
    10.1186/s13059-022-02813-9 - link to the publication

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