Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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Computational Genomics: Problems, Algorithms and Models

2015/19/B/ST6/00726

Keywords:

tree reconciliation genomics metagenomics algorithmics gene duplication gene transfer B-cells leukemia

Descriptors:

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

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: 7

Call: OPUS 10 - announced on 2015-09-15

Amount awarded: 580 740 PLN

Project start date (Y-m-d): 2016-06-28

Project end date (Y-m-d): 2020-02-27

Project duration:: 44 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.

Equipment purchased [PL]

  1. Przenośny komputer osobisty (laptop) (2 szt.) (6 002 PLN)
  2. Ipad Pro 12.9 (6 203 PLN)
  3. Drukarka wielofunkcyjna (2 500 PLN)
  4. Przenośny komputer osobisty (ultrabook) (7 000 PLN)
  5. Monitor DELL.
  6. Serwer obliczeniowy (75 000 PLN)
  7. Komputer osobisty (4 000 PLN)
  8. Komputer osobisty (2 szt.) (4 738 PLN)

Information in the final report

  • Publication in academic press/journals (12)
  • Articles in post-conference publications (7)
  1. Credibility of Evolutionary Events in Gene Trees
    Authors:
    Agnieszka Mykowiecka and Paweł Górecki
    Academic press:
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (rok: 2019, tom: 16/3, strony: 713 - 726), Wydawca: IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
    Status:
    Published
    DOI:
    10.1109/TCBB.2017.2788888 - link to the publication
  2. Inferring duplication episodes from unrooted gene trees
    Authors:
    Jarosław Paszek, Paweł Górecki
    Academic press:
    BMC Genomics (rok: 2018, tom: 19, strony: 288), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12864-018-4623-z - link to the publication
  3. Locus-aware decomposition of gene trees with respect to polytomous species trees
    Authors:
    Michał Aleksander Ciach, Anna Muszewska and Paweł Górecki
    Academic press:
    Algorithms for Molecular Biology (rok: 2018, tom: 13/1, strony: 11), Wydawca: BMC
    Status:
    Published
    DOI:
    10.1186/s13015-018-0128-1 - link to the publication
  4. Cophenetic Distances in Near-linear Time
    Authors:
    Paweł Górecki, Alexey Markin, Oliver Eulenstein
    Academic press:
    Journal of ACM (rok: 2020, tom: n/a, strony: n/a), Wydawca: ACM
    Status:
    Submitted
    DOI:
    brak - link to the publication
  5. Consensus of all Solutions for Intractable Phylogenetic Tree Inference
    Authors:
    Paweł Tabaszewski, Paweł Górecki, Alexey Markin, Tavis Anderson, Oliver Eulenstein
    Academic press:
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (rok: 2021, tom: 18, strony: 149 - 161), Wydawca: IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
    Status:
    Published
    DOI:
    10.1109/TCBB.2019.2947051 - link to the publication
  6. Inferring gene-species assignments in the presence of horizontal gene transfer
    Authors:
    Agnieszka Mykowiecka, Paweł Szczęsny, and Paweł Górecki
    Academic press:
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (rok: 2018, tom: 15/5, strony: 1571-1578), Wydawca: 1,8IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
    Status:
    Published
    DOI:
    10.1109/TCBB.2017.2707083 - link to the publication
  7. The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost
    Authors:
    Paweł Górecki, Oliver Eulenstein and Jerzy Tiuryn
    Academic press:
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (rok: 2021, tom: 18, strony: 2125 - 2135), Wydawca: IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
    Status:
    Published
    DOI:
    10.1109/TCBB.2019.2919617 - link to the publication
  8. Bijective Diameters of Gene Tree Parsimony Costs
    Authors:
    Paweł Górecki and Oliver Eulenstein
    Academic press:
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (rok: 2018, tom: 15/5, strony: 1723-1727), Wydawca: IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
    Status:
    Published
    DOI:
    10.1109/TCBB.2017.2735968 - link to the publication
  9. Efficient Algorithms for Genomic Duplication Models
    Authors:
    Jarosław Paszek, Paweł Górecki
    Academic press:
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (rok: 2018, tom: 15/5, strony: 1515 - 1524), Wydawca: IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
    Status:
    Published
    DOI:
    10.1109/ - link to the publication
  10. Exact Median-tree Inference for Unrooted Reconciliation Costs
    Authors:
    Paweł Górecki, Alexey Markin and Oliver Eulenstein
    Academic press:
    BMC Bioinformatics (rok: 2020, tom: 20, strony: 136), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12862-020-01700-w - link to the publication
  11. Minimizing the deep coalescence cost
    Authors:
    Dawid Dąbkowski; Paweł Tabaszewski; Paweł Górecki
    Academic press:
    Journal of Bioinformatics and Computational Biology (rok: 2018, tom: 16/5, strony: 1840021), Wydawca: Imperial College Press
    Status:
    Published
    DOI:
    10.1142/S0219720018400218 - link to the publication
  12. Mathematical properties of the gene duplication cost
    Authors:
    Paweł Górecki, Agnieszka Mykowiecka, Jarosław Paszek, Oliver Eulenstein
    Academic press:
    Discrete Applied Mathematics (rok: 2019, tom: 258, strony: 114-122), Wydawca: North-Holland
    Status:
    Published
    DOI:
    10.1016/j.dam.2018.11.014 - link to the publication
  1. Inferring time-consistent and well-supported horizontal gene transfers
    Authors:
    Agnieszka Mykowiecka, Anna Muszewska, Paweł Górecki
    Conference:
    IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (rok: 2018, ), Wydawca: IEEE
    Data:
    konferencja 2018/12
    Status:
    Published
  2. Varcatch: an efficient method to reduce preferential alignment of reference over alternative alleles in next-generation sequencing data
    Authors:
    Szymon M. Kiełbasa, Ramin Monajemi, Harmen H.M. Draisma, Kristina Gagalova, Paweł Górecki, BIOS Consortium, Lude Franke, and Peter A.C. Hoen
    Conference:
    BIOSB 2017 (rok: 2017, ), Wydawca: n/a
    Data:
    konferencja 2017
    Status:
    Published
  3. Phylogenetic Consensus for Exact Median Trees
    Authors:
    Pawel Tabaszewski, Pawel Górecki, Oliver Eulenstein
    Conference:
    ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (rok: 2018, ), Wydawca: ACM
    Data:
    konferencja 2018/8
    Status:
    Published
  4. Minimising the Deep Coalescence
    Authors:
    Dawid Dąbkowski and Paweł Górecki
    Conference:
    BICOB 2018 (rok: 2018, ), Wydawca: n/a
    Data:
    konferencja Marzec 2018
    Status:
    Published
  5. Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Tree
    Authors:
    Paweł Górecki, Alexey Markin, Agnieszka Mykowiecka, Jarosław Paszek, Oliver Eulenstein
    Conference:
    ISBRA 2017 (rok: 2017, ), Wydawca: Springer
    Data:
    konferencja 29 May - 2 June
    Status:
    Published
  6. Detecting Locus Acquisition Events in Gene Trees
    Authors:
    Michał Aleksander Ciach, Anna Muszewska,Paweł Górecki
    Conference:
    WABI 2017 (rok: 2017, ), Wydawca: Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik
    Data:
    konferencja 2017
    Status:
    Published
    DOI:
    link to the publication
  7. New Algorithms for the Genomic Duplication Problem
    Authors:
    Jarosław Paszek and Paweł Górecki
    Conference:
    RECOMB Comparative Genomics 2017 (rok: 2017, ), Wydawca: Springer
    Data:
    konferencja 4-6 October
    Status:
    Published

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