Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Consistent Models and Efficient Algorithms for Genomic Duplications

2017/27/B/ST6/02720

Keywords:

genomic duplication genome phylogenetic tree comparative genomics

Descriptors:

  • ST6_12: Scientific computing, simulation and modelling tools
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • ST6_6: Algorithms, parallel, distributed and network algorithms, algorithmic game theory

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

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. Paweł Górecki 

Number of co-investigators in the project: 6

Call: OPUS 14 - announced on 2017-09-15

Amount awarded: 798 440 PLN

Project start date (Y-m-d): 2018-07-23

Project end date (Y-m-d): 2023-07-22

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

Project status: Project settled

Project description

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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. Integer Linear Programming Formulation for the Unified Duplication-Loss-Coalescence Model
    Authors:
    Javad Ansarifar, Alexey Markin, Paweł Górecki, Oliver Eulenstein
    Academic press:
    Lecture Notes in Computer Science (rok: 2020, tom: 12304, strony: 229-242), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/978-3-030-57821-3_20 - link to the publication
  2. The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost
    Authors:
    Paweł Górecki ; Oliver Eulenstein ; Jerzy Tiuryn
    Academic press:
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (rok: 2021, tom: 18, strony: 2125-2135), Wydawca: IEEE/ACM
    Status:
    Published
    DOI:
    10.1109/TCBB.2019.2919617 - link to the publication
  3. Unifying duplication episode clustering and gene-species mapping inference
    Authors:
    Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka & Jarosław Paszek
    Academic press:
    Algorithms for Molecular Biology (rok: 2024, tom: 19, strony: 45311), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s13015-024-00252-8 - link to the publication
  4. Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming
    Authors:
    J Paszek, A Markin, P Górecki, O Eulenstein
    Academic press:
    Journal of Computational Biology (rok: 2021, tom: 28, strony: 758-773), Wydawca: Mary Ann Liebert, Inc.,
    Status:
    Published
    DOI:
    10.1089/cmb.2021.0011 - link to the publication
  5. Asymmetric Cluster-Based Measuresfor Comparative Phylogenetics
    Authors:
    Sanket Wagle, Alexey Markin, Paweł Górecki, Tavis K. Anderson and Oliver Eulenstein
    Academic press:
    Journal of Computational Biology (rok: 2024, tom: 31, strony: 312 - 327), Wydawca: Mary Ann Liebert, Inc., publishers
    Status:
    Published
    DOI:
    10.1089/cmb.2023.0338 - link to the publication
  6. Feasibility Algorithms for the Duplication-Loss Cost
    Authors:
    Paweł Górecki, Alexey Markin, Oliver Eulenstein
    Academic press:
    Lecture Notes in Computer Science (rok: 2019, tom: 11653, strony: 206-218), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/978-3-030-26176-4_17 - link to the publication
  7. Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings
    Authors:
    P. Górecki, N. Rutecka, A.Mykowiecka, J.Paszek
    Academic press:
    Leibniz International Proceedings in Informatics (LIPIcs) (rok: 2023, tom: 242, strony: 6:1-6:18), Wydawca: Leibniz International Proceedings in Informatics (LIPIcs)
    Status:
    Published
    DOI:
    10.4230/LIPIcs.WABI.2023.6 - link to the publication
  8. Exact median-tree inference for unrooted reconciliation costs
    Authors:
    Paweł Górecki, Alexey Markin, Oliver Eulenstein
    Academic press:
    BMC Evolutionary Biology (rok: 2020, tom: 20, strony: 136), Wydawca: BMC/Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12862-020-01700-w - link to the publication
  9. Minimizing genomic duplication episodes
    Authors:
    Jarosław Paszek, Jerzy Tiuryn, Paweł Górecki
    Academic press:
    Computational Biology and Chemistry (rok: 2020, tom: 89, strony: 107260), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.compbiolchem.2020.107260 - link to the publication
  1. Novel Genomic Duplication Models through Integer Linear Programming
    Authors:
    Paszek, Eulenstein, Gorecki
    Conference:
    ACM BCB 2021 (rok: 2021, ), Wydawca: ACM
    Data:
    konferencja August 1–4
    Status:
    Published

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