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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Formal linguistics for proteomics - modeling, analysis and hypotheses testing

2015/17/D/ST6/04054

Keywords:

protein sequences probabilistic grammars context-free grammars machine learning

Descriptors:

  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • NZ2_7: Bioinformatics

Panel:

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

Host institution :

Politechnika Wrocławska, Wydział Podstawowych Problemów Techniki

woj. dolnośląskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Witold Dyrka 

Number of co-investigators in the project: 8

Call: SONATA 9 - announced on 2015-03-16

Amount awarded: 472 200 PLN

Project start date (Y-m-d): 2016-02-15

Project end date (Y-m-d): 2019-06-14

Project duration:: 40 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. 2 monitory.
  2. Komputer przenośny (6 000 PLN)
  3. Zestaw komputerowy (wydajny komputer stacjonarny + monitor) (2 szt.) (12 000 PLN)

Information in the final report

  • Publication in academic press/journals (4)
  • Articles in post-conference publications (3)
  • Book publications / chapters in book publications (1)
  1. Estimating probabilistic context-free grammars for proteins using contact map constraints
    Authors:
    Witold Dyrka, Mateusz Pyzik, François Coste, Hugo Talibart
    Academic press:
    PeerJ (rok: 2019, tom: 7, strony: e6559), Wydawca: PeerJ, Inc
    Status:
    Published
    DOI:
    10.7717/peerj.6559 - link to the publication
  2. Quantiprot - a Python package for quantitative analysis of protein sequences
    Authors:
    Bogumił M. Konopka, Marta Marciniak, Witold Dyrka
    Academic press:
    BMC Bioinformatics (rok: 2017, tom: 18, strony: 339), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-017-1751-4 - link to the publication
  3. Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes
    Authors:
    Witold Dyrka, Virginie Coustou, Asen Daskalov, Alons Lends, Thierry Bardin, Mélanie Berbon, Brice Kauffmann, Corinne Blancard, Bénédicte Salin, Antoine Loquet, Sven J Saupe
    Academic press:
    Journal of Molecular Biology (rok: 2020, tom: 432, strony: 6005-6027), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.004 - link to the publication
  4. Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars
    Authors:
    Witold Dyrka, Marlena Gąsior-Głogowska, Natalia Szulc
    Academic press:
    BMC Bioinformatics (rok: 2021, tom: 22, strony: 222), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-021-04139-y - link to the publication
  1. How to measure the topological quality of protein grammars?
    Authors:
    Witold Dyrka, François Coste, Olgierd Unold, Łukasz Culer, Agnieszka Kaczmarek
    Conference:
    The 13th International Conference on Grammatical Inference (ICGI 2016) (rok: 2016, ), Wydawca: arXiv.org
    Data:
    konferencja 40305
    Status:
    Published
  2. How to measure the topological quality of protein parse trees?
    Authors:
    Mateusz Pyzik, François Coste, Witold Dyrka
    Conference:
    The 14th International Conference on Grammatical Inference (ICGI 2018) (rok: 2018, ), Wydawca: PMLR
    Data:
    konferencja 39940
    Status:
    Published
  3. Towards Improved Evolutionary Learning of Probabilistic Context-Free Grammars for Protein Sequences
    Authors:
    Robert Kowalski, Mateusz Pyzik, Witold Dyrka
    Conference:
    EVO* 2019 -- Late-Breaking Abstracts Volume (rok: 2019, ), Wydawca: arXiv.org
    Data:
    konferencja 24-26/04
    Status:
    Published
  1. NLR Function in Fungi as Revealed by the Study of Self/Non-self Recognition Systems
    Authors:
    Asen Daskalov, Witold Dyrka, Sven J. Saupe
    Book:
    Genetics and Biotechnology. The Mycota (A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research) (rok: 2020, tom: 2, strony: 123-141), Wydawca: Springer, Cham.
    Status:
    Published

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