Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Development of methods for bias correction of gene expression measurements

2016/23/D/ST7/03665

Keywords:

gene expression microarrays deep sequencing PCR

Descriptors:

  • ST7_11: Electronic, optoelectronic and photonic components and systems for applications (e.g. in biomedical engineering)
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • NZ2_10: Biological systems analysis, modelling and simulation

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):

dr Roman Jaksik 

Number of co-investigators in the project: 3

Call: SONATA 12 - announced on 2016-09-15

Amount awarded: 536 900 PLN

Project start date (Y-m-d): 2017-09-26

Project end date (Y-m-d): 2022-09-25

Project duration:: 60 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 (12)
  • Articles in post-conference publications (3)
  • Book publications / chapters in book publications (1)
  1. Circuits Regulating Superoxide and Nitric Oxide Production and Neutralization in Different Cell Types: Expression of Participating Genes and Changes Induced by Ionizing Radiation
    Authors:
    Bil P, Ciesielska S, Jaksik R, Rzeszowska-Wolny J
    Academic press:
    Antioxidants (rok: 2020, tom: 9, strony: 701), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/antiox9080701 - link to the publication
  2. Effect of the unfolded protein response and oxidative stress on mutagenesis in CSF3R: a model for evolution of severe congenital neutropenia to myelodysplastic syndrome/acute myeloid leukemia
    Authors:
    Sapra A, Jaksik R, Mehta H, Biesiadny S, Kimmel M, Corey S
    Academic press:
    Mutagenesis (rok: 2021, tom: 35, strony: 381–389), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/mutage/geaa027 - link to the publication
  3. GaMRed - adaptive filtering of high-throughput biological data
    Authors:
    Marczyk M, Jaksik R, Polanski A, Polanska J
    Academic press:
    IEEE-ACM Transactions On Computational Biology and Bioinformatics (rok: 2018, tom: 1, strony: 45300), Wydawca: IEEE
    Status:
    Published
    DOI:
    10.1109/TCBB.2018.2858825 - link to the publication
  4. Heuristic search of exact biclusters in binary data
    Authors:
    Michalak M, Jaksik R, Ślęzak D
    Academic press:
    International Journal of Applied Mathematics and Computer Science, (rok: 2020, tom: 30, strony: 161–171), Wydawca: Uniwersytet Zielonogórski
    Status:
    Published
    DOI:
    10.34768/amcs-2020-0013 - link to the publication
  5. Interferon Gamma Mediates Hematopoietic Stem Cell Activation and Niche Relocalization through 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
  6. Small RNA-Seq Reveals Similar miRNA Transcriptome in Children and Young Adults with T-ALL and Indicates miR-143-3p as Novel Candidate Tumor Suppressor in This Leukemia
    Authors:
    3.Dawidowska M, Maćkowska-Maślak N, Drobna-Śledzińska M, Kosmalska M, Jaksik R, Szymczak D, Jarmuż-Szymczak M, Sadowska-Klasa A, Wojtaszewska M, Sędek Ł, Wróbel T, Zaucha J, Szczepański T, Lewandowski K, Giebel S, Witt M
    Academic press:
    International Journal of Molecular Sciences (rok: 2022, tom: 23, strony: 10117), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms231710117 - 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. Chronic infection drives Dnmt3a-loss-of-functionclonal hematopoiesis via IFNgsignaling
    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
  9. Involvement of miRNAs in cellular responses to radiation
    Authors:
    Rzeszowska-Wolny J, Hudy D, Biernacki K, Ciesielska S, Jaksik R
    Academic press:
    International Journal of Radiation Biology (rok: 2022, tom: 98, strony: 479-488), Wydawca: Informa
    Status:
    Published
    DOI:
    10.1080/09553002.2022.2028923 - link to the publication
  10. RNA-seq library preparation for comprehensive transcriptome analysis in cancer cells: The impact of insert size
    Authors:
    Jaksik R, Drobna M, Dawidowska M
    Academic press:
    Genomics (rok: 2021, tom: 113, strony: 4149-4162), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.018 - link to the publication
  11. 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
    Status:
    Published
    DOI:
    10.1002/cso2.1026 - link to the publication
  12. The origin of bladder cancer from mucosal field effects
    Authors:
    2.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
  1. Analysis of factors affecting the precision of gene expression measurement methods
    Authors:
    Lalik A, Puszynski K, Jaksik R
    Conference:
    13th International Conference on Signal Processing and Communication Systems (rok: 2019, ), Wydawca: IEEE
    Data:
    konferencja 43815
    Status:
    Published
  2. Nucleotide composition bias in high throughput gene expression measurement methods
    Authors:
    Jaksik R, Lalik A, Puszynski K
    Conference:
    13th International Conference on Signal Processing and Communication Systems (rok: 2019, ), Wydawca: IEEE
    Data:
    konferencja 43815
    Status:
    Published
  3. Correction of the genes expression measurements based on the probes design features
    Authors:
    Puszynski K, Lalik A, Jaksik R
    Conference:
    13th International Conference on Signal Processing and Communication Systems (rok: 2019, ), Wydawca: IEEE
    Data:
    konferencja 43815
    Status:
    Published
  1. Identification of factors that affect reproducibility of mutation calling methods in data originating from the next-generation sequencing
    Authors:
    Jaksik R, Psiuk-Maksymowicz K, Swierniak A
    Book:
    Computer and Information Sciences (rok: 2018, tom: 935, strony: 264-271), Wydawca: Springer International Publishing
    Status:
    Published

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