Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Combined genomic, phenotypic and spatial analysis of intra-tumor heterogeneity

2019/33/B/NZ2/00956

Keywords:

cancer heterogeneity statistical data analysis machine learning

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 Ewa Szczurek 

Number of co-investigators in the project: 5

Call: OPUS 17 - announced on 2019-03-15

Amount awarded: 816 520 PLN

Project start date (Y-m-d): 2020-02-06

Project end date (Y-m-d): 2023-02-05

Project duration:: 36 months (the same as in the proposal)

Project status: Project settled

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 (9)
  • Articles in post-conference publications (1)
  1. Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues
    Authors:
    S. Darvish Shafighi, A. Geras, B. Jurzysta, I. Filipiuk, L. Raczkowski, H. Toosi, L. Koperski, K. Thrane, C. Engblom, J. Mold, X. Chen, J. Hartman, D. Nowis, A. Carbone, J. Lagergren, E. Szczurek
    Academic press:
    Nature Communications (rok: 2022, tom: -, strony: -), Wydawca: Springer Nature
    Status:
    Submitted
  2. Interpretable deep recommender system model for prediction of kinase inhibitor efficacy across cancer cell lines.
    Academic press:
    Scientific Reports (rok: 2021, tom: 11, strony: 15993)
    Status:
    Published
    DOI:
    10.1038/s41598-021-94564-z - link to the publication
  3. CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells.
    Authors:
    Shafighi SD, Kiełbasa SM, Sepúlveda-Yáñez J, Monajemi R, Cats D, Mei H, Menafra R, Kloet S, Veelken H, van Bergen CAM, Szczurek E
    Academic press:
    Genome Medicine (rok: 2021, tom: 13, strony: 45), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s13073-021-00842-w - link to the publication
  4. Synthetic lethality prediction in DNA damage repair, chromatin remodeling and the cell cycle using multi-omics data from cell lines and patients
    Authors:
    M. Markowska, M. A. Budzinska, A. Coenen-Stass, S. Kang, E. Kizling, K. Kolmus, K. Koras, E. Staub, E. Szczurek,
    Academic press:
    Scientific Reports (rok: 2023, tom: 13, strony: 7049), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-023-34161-4 - link to the publication
  5. Celloscope: a probabilistic model for marker-gene driven cell type deconvolution in spatial transcriptomics data
    Authors:
    A. Geras, S. Darvish Shafighi, K. Domżał, I. Filipiuk, A. Rączkowska, P. Szymczak, H. Toosi, L. Kaczmarek, L. Koperski, J. Lagergren, D. Nowis, E. Szczurek
    Academic press:
    Genome Biology (rok: 2023, tom: 24, strony: 120), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s13059-023-02951-8 - link to the publication
  6. Interpretable deep recommender system model for prediction of kinase inhibitor efficacy across cancer cell lines.
    Authors:
    Koras K, Kizling E, Juraeva D, Staub E, Szczurek E
    Academic press:
    Scientific Reports (rok: 2021, tom: 11, strony: 15993), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-021-94564-z - link to the publication
  7. CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells.
    Authors:
    Shafighi SD, Kiełbasa SM, Sepúlveda-Yáñez J, Monajemi R, Cats D, Mei H, Menafra R, Kloet S, Veelken H, van Bergen CAM, Szczurek E
    Academic press:
    Genome Medicine (rok: 2021, tom: 13, 45, strony: )
    Status:
    Published
    DOI:
    10.1186/s13073-021-00842-w - link to the publication
  8. CONET: copy number event tree model of evolutionary tumor history for single-cell data
    Authors:
    Magda Markowska, Tomasz Cąkała, BłaŻej Miasojedow, Bogac Aybey, Dilafruz Juraeva, Johanna Mazur, Edith Ross, Eike Staub, Ewa Szczurek
    Academic press:
    Genome Biology (rok: 2022, tom: 23, strony: 128), Wydawca: Biomed Central
    Status:
    Published
    DOI:
    10.1186/s13059-022-02693-z - link to the publication
  9. Deep learning-based tumor microenvironment segmentation is predictive of tumor mutations and patient survival in non-small-cell lung cancer
    Authors:
    L. Raczkowski, I. Pasnik, M. Kukielka, M. Nicos, M. A. Budzinska, T. Kucharczyk, J. Szumilo, P. Krawczyk, N. Crosetto, E. Szczurek
    Academic press:
    BMC Cancer (rok: 2022, tom: 22, strony: 1001), Wydawca: BioMed Cental
    Status:
    Published
    DOI:
    10.1186/s12885-022-10081-w - link to the publication
  1. A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction
    Authors:
    Krzysztof Koras, Marcin Możejko, Paulina Szymczak, Adam Izdebski, Eike Staub, Ewa Szczurek
    Conference:
    Proceedings of the 17th Machine Learning in Computational Biology meeting (rok: 2022, tom: Machine Learning in Computational Biology, strony: 61-73), Wydawca: Proceedings of Machine Learning Research
    Data:
    konferencja Listopad 21-22
    Status:
    Published
    DOI:
    10.48550/arXiv.2206.03555 - link to the publication

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