Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Systems approach to cancer progression and prognosis: New models and statistics for analysis of genomic data

2018/29/B/ST7/02550

Keywords:

Systems Coalescent theory Epithelial mesenchymal transition Breast cancer Head and neck cancer Genome modeling Dynamics of immunity Metastasis Mutation distributions

Descriptors:

  • ST7_12:
  • ST7_3:
  • ST7_4:

Panel:

ST7 - Systems and communication engineering: electronics, communication, optoelectronics

Host institution :

Politechnika Śląska, Wydział Automatyki, Elektroniki i Informatyki

woj. śląskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Marek Kimmel 

Number of co-investigators in the project: 5

Call: OPUS 15 - announced on 2018-03-15

Amount awarded: 1 418 100 PLN

Project start date (Y-m-d): 2019-02-25

Project end date (Y-m-d): 2023-08-24

Project duration:: 54 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 (13)
  • Book publications / chapters in book publications (2)
  1. Heat Shock Factor 1 (HSF1) cooperates with estrogen receptor α (ERα) in the regulation of estrogen action in breast cancer cells
    Authors:
    1.Vydra N, Janus P, Kuś P, Stokowy T, Mrowiec K, Toma-Jonik A, Krzywon A, Cortez A, Wojtas B, Gielnewski B, Jaksik R, Kimmel M, Widlak W
    Academic press:
    eLife (rok: 2021, tom: 10, strony: e69843), Wydawca: eLife Sciences Publications, Ltd
    Status:
    Published
    DOI:
    10.7554/eLife.69843 - link to the publication
  2. A general calculus of fitness landscapes finds genes under selection in cancers.
    Authors:
    Hsu TK, Asmussen J, Koire A, Choi BK, Gadhikar MA, Huh E, Lin CH, Konecki DM, Kim YW, Pickering CR, Kimmel M, Donehower LA, Frederick MJ, Myers JN, Katsonis P, Lichtarge O.
    Academic press:
    Genome Research (rok: 2022, tom: 32, strony: 916-929), Wydawca: Cold Spring Harbor Lab Press
    Status:
    Published
    DOI:
    10.1101/gr.275811.121 - link to the publication
  3. Genomic Analysis of SARS-CoV-2 Alpha, Beta and Delta Variants of Concern Uncovers Signatures of Neutral and Non-Neutral Evolution
    Authors:
    Kurpas M, Jaksik R, Kuś P, Kimmel M
    Academic press:
    Viruses (rok: 2022, tom: 14, strony: 2375), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/v14112375 - link to the publication
  4. Interferon Gamma Mediates Hematopoietic StemCell Activation and Niche Relocalizationthrough BST2
    Authors:
    Florez M, Matatall KA, Jeong Y, Ortinau L, Shafer P, Lynch A, Jaksik R, Kimmel M, Park D, King KY
    Academic press:
    Cell Reports (rok: 2020, tom: 33, strony: 108530), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.celrep.2020.108530 - link to the publication
  5. Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon
    Authors:
    Jaksik R, Wheeler D, Kimmel M
    Academic press:
    BMC Biology (rok: 2023, tom: 21, strony: 41), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12915-023-01527-z - link to the publication
  6. Alternatively spliced CSF3R isoforms in SRSF2 P95H mutated myeloid neoplasms
    Authors:
    Borwyn A. Wang, Hrishikesh M. Mehta, Srinivasa R. Penumutchu, Blanton S. Tolbert, Chonghui Cheng, Marek Kimmel, Torsten Haferlach, Jaroslaw P. Maciejewski & Seth J. Corey
    Academic press:
    Leukemia (rok: 2022, tom: 36, strony: 2499–2508), Wydawca: nature
    Status:
    Published
    DOI:
    10.1038/s41375-022-01672-4 - link to the publication
  7. Statistical Inference for the Evolutionary History of Cancer Genomes
    Authors:
    Khanh N. Dinh, Roman Jaksik, Marek Kimmel, Amaury Lambert, and Simon Tavaré
    Academic press:
    Statistical Science (rok: 2020, tom: 35, strony: 129–144), Wydawca: The Institute of Mathematical Statistics
    Status:
    Published
    DOI:
    10.1214/19-STS7561 - link to the publication
  8. Moran process version of the tug-of-war model: Behavior revealed by mathematical analysis and simulation studies
    Authors:
    Adam Bobrowski, Marek Kimmel, Monika K. Kurpas, Elżbieta Ratajczyk
    Academic press:
    Discrete and Continuous Dynamical Systems - B (rok: 2023, tom: 28, strony: 4532-4563), Wydawca: American Institute of Mathematical Sciences
    Status:
    Published
    DOI:
    10.3934/dcdsb.2023029 - link to the publication
  9. Modes of Selection in Tumors as Reflected by Two Mathematical Models and Site Frequency Spectra
    Authors:
    Kurpas M, Kimmel M
    Academic press:
    Frontiers in Ecology and Evolution (rok: 2022, tom: 10, strony: 889438), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fevo.2022.889438 - link to the publication
  10. Chronic infection drives Dnmt3a-loss-of-functionclonal hematopoiesis via IFNg signaling
    Authors:
    Agulla D, Matatall KA, Le D, Kain B, Long X, Kuś P, Jaksik R, Challen G, Kimmel M, King KY
    Academic press:
    Cell Stem Cell (rok: 2021, tom: S1934-5909, strony: 00108-9), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.stem.2021.03.002 - link to the publication
  11. The origin of bladder cancer from mucosal field effects
    Authors:
    1.Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh K, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kuś P, Chen H, Weinstein J, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo C, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B
    Academic press:
    iScience (rok: 2022, tom: 25, strony: 104551), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.isci.2022.104551 - link to the publication
  12. Predicting time to relapse in acute myeloid leukemia through stochastic modeling of minimal residual disease based on clonality data
    Authors:
    Dinh K, Jaksik R, Corey S, Kimmel M
    Academic press:
    Computational and Systems Oncology (rok: 2021, tom: 1, strony: e1026), Wydawca: Wiley Periodicals LLC
    Status:
    Published
    DOI:
    10.1002/cso2.1026 - link to the publication
  13. Mathematical model predicts response to chemotherapy in advanced non-resectable non-small cell lung cancer patients treated with platinum-based doublet
    Authors:
    Emilia Kozłowska, Rafał Suwiński, Monika Giglok, Andrzej Świerniak, Marek Kimmel
    Academic press:
    PLOS Computational Biology (rok: 2020, tom: 16, strony: e1008234), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1008234 - link to the publication
  1. Tumor subclonal reconstruction pipelines - comparison of results
    Authors:
    Kuś Paweł, Jaksik Roman, Kimmel Marek
    Book:
    Recent advances in computational oncology and personalized medicine (rok: 2021, tom: 1, strony: 137-147), Wydawca: Wydawnictwo Politechniki Śląskiej
    Status:
    Published
  2. Biological models' parameter estimation based on discrete measurements and adjoint sensitivity analysis
    Authors:
    Fujarewicz K, Łakomiec K
    Book:
    Advanced, Contemporary Control. Advances in Intelligent Systems and Computing (rok: 2020, tom: 1196, strony: 567-578), Wydawca: Springer, Cham
    Status:
    Published

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