Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Models and methods of computer science in cell biology

2012/05/B/ST6/03026

Keywords:

bioinformatics algorithms

Descriptors:

  • 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 :

Politechnika Poznańska, Wydział Informatyki

woj. wielkopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Marta Kasprzak 

Number of co-investigators in the project: 22

Call: OPUS 3 - announced on 2012-03-15

Amount awarded: 960 180 PLN

Project start date (Y-m-d): 2013-01-31

Project end date (Y-m-d): 2016-01-30

Project duration:: 36 months (the same as in the proposal)

Project status: Project settled

Information in the final report

  • Publication in academic press/journals (32)
  • Articles in post-conference publications (2)
  1. Assigning NMR spectra of irregular RNAs by heuristic algorithms
    Authors:
    Marta Szachniuk
    Academic press:
    Bulletin of the Polish Academy of Sciences - Technical Sciences (rok: 2015, tom: 63, strony: 329-338), Wydawca: Polska Akademia Nauk, Wydział IV Nauk Technicznych
    Status:
    Published
    DOI:
    10.1515/bpasts-2015-0037 - link to the publication
  2. Building the library of RNA 3D nucleotide conformations using the clustering approach
    Authors:
    Tomasz Żok, Maciej Antczak, Martin Riedel, David Nebel, Thomas Villmann, Piotr Łukasiak, Jacek Błażewicz, Marta Szachniuk
    Academic press:
    International Journal of Applied Mathematics and Computer Science (rok: 2015, tom: 25, strony: 689-700), Wydawca: Uniwersytet Zielonogórski
    Status:
    Published
    DOI:
    10.1515/amcs-2015-0050 - link to the publication
  3. Classification of de Bruijn-based labeled digraphs
    Authors:
    Marta Kasprzak
    Academic press:
    Discrete Applied Mathematics (rok: 2018, tom: 234, strony: 86-92), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.014 - link to the publication
  4. G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads
    Authors:
    Wojciech Frohmberg, Michał Kierzynka, Jacek Błażewicz, Piotr Gawron, Paweł Wojciechowski
    Academic press:
    Bulletin of the Polish Academy of Sciences - Technical Sciences (rok: 2013, tom: 61, strony: 989-992), Wydawca: Polska Akademia Nauk, Wydział IV Nauk Technicznych
    Status:
    Published
    DOI:
    10.2478/bpasts-2013-0106 - link to the publication
  5. RNAlyzer - novel approach for quality analysis of RNA structural models
    Authors:
    Piotr Łukasiak, Maciej Antczak, Tomasz Ratajczak, Janusz M. Bujnicki, Marta Szachniuk, Ryszard W. Adamiak, Mariusz Popenda, Jacek Błażewicz
    Academic press:
    Nucleic Acids Research (rok: 2013, tom: 41, strony: 5978-5990), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkt318 - link to the publication
  6. Sorting signal targeting mRNA into hepatic extracellular vesicles
    Authors:
    Natalia Szóstak, Felix Royo, Agnieszka Rybarczyk, Marta Szachniuk, Jacek Błażewicz, Antonio del Sol, Juan M. Falcon-Perez
    Academic press:
    RNA Biology (rok: 2014, tom: 11, strony: 836-844), Wydawca: Landes Bioscience
    Status:
    Published
    DOI:
    10.4161/rna.29305 - link to the publication
  7. Computer Representations of Bioinformatics Models
    Authors:
    Tomasz Prejzendanc, Szymon Wąsik, Jacek Błażewicz
    Academic press:
    Current Bioinformatics (rok: 2016, tom: 11, strony: 551-560), Wydawca: Bentham Science Publishers
    Status:
    Published
    DOI:
    10.2174/1574893610666150928193510 - link to the publication
  8. DNA sequence assembly involving an acyclic graph model
    Authors:
    Jacek Błażewicz, Wojciech Frohmberg, Piotr Gawron, Marta Kasprzak, Michał Kierzynka, Aleksandra Świercz, Paweł Wojciechowski
    Academic press:
    Foundations of Computing and Decision Sciences (rok: 2013, tom: 38, strony: 25-34), Wydawca: Politechnika Poznańska
    Status:
    Published
    DOI:
    10.2478/v10209-011-0019-4 - link to the publication
  9. DomGen - graph based method for protein domain delineation
    Authors:
    Maciej Miłostan, Piotr Łukasiak
    Academic press:
    RAIRO Operations Research (rok: 2016, tom: 50, strony: online), Wydawca: EDP Sciences
    Status:
    Published
    DOI:
    10.1051/ro/2015040 - link to the publication
  10. G-MAPSEQ - a new method for mapping reads to a reference genome
    Authors:
    Paweł Wojciechowski, Wojciech Frohmberg, Michał Kierzynka, Piotr Żurkowski, Jacek Błażewicz
    Academic press:
    Foundations of Computing and Decision Sciences (rok: 2016, tom: 41, strony: 123-142), Wydawca: Politechnika Poznańska
    Status:
    Published
    DOI:
    10.1515/fcds-2016-0007 - link to the publication
  11. Inferring mathematical equations using crowdsourcing
    Authors:
    Szymon Wąsik, Filip Frątczak, Jakub Krzyśków, Jarosław Wulnikowski
    Academic press:
    PLoS ONE (rok: 2015, tom: 10, strony: Article ID e0145557), Wydawca: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0145557 - link to the publication
  12. MLP accompanied beam search for the resonance assignment problem
    Authors:
    Marta Szachniuk, Mikołaj Małaczyński, Erwin Pesch, Edmund K. Burke, Jacek Błażewicz
    Academic press:
    Journal of Heuristics (rok: 2013, tom: 19, strony: 443-464), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s10732-013-9220-3 - link to the publication
  13. New in silico approach to assessing RNA secondary structures with non-canonical base pairs
    Authors:
    Agnieszka Rybarczyk, Natalia Szóstak, Maciej Antczak, Tomasz Żok, Mariusz Popenda, Ryszard Adamiak, Jacek Błażewicz, Marta Szachniuk
    Academic press:
    BMC Bioinformatics (rok: 2015, tom: 16, strony: Article ID 276), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12859-015-0718-6 - link to the publication
  14. Optimal pathway reconstruction on 3D NMR maps
    Authors:
    Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Dominique de Werra, Jacek Błażewicz
    Academic press:
    Discrete Applied Mathematics (rok: 2015, tom: 182, strony: 134-149), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.dam.2014.04.010 - link to the publication
  15. Selection of reference genes for qPCR- and ddPCR-based analyses of gene expression in senescing barley leaves
    Authors:
    Agnieszka Żmieńko, Anna Samelak-Czajka, Michał Góralski, Ewa Sobieszczuk- Nowicka, Piotr Kozłowski, Marek Figlerowicz
    Academic press:
    PLoS ONE (rok: 2015, tom: 10, strony: Article ID e0118226), Wydawca: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0118226 - link to the publication
  16. Tabu search for the RNA Partial Degradation Problem
    Authors:
    Agnieszka Rybarczyk, Alain Hertz, Marta Kasprzak, Jacek Błażewicz
    Academic press:
    International Journal of Applied Mathematics and Computer Science (rok: 2017, tom: 27, strony: 401-415), Wydawca: Uniwersytet Zielonogórski
    Status:
    Published
    DOI:
    10.1515/amcs-2017-0028 - link to the publication
  17. A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly
    Authors:
    Michał Góralski, Paula Sobieszczańska, Aleksandra Obrępalska-Stęplowska, Aleksandra Świercz, Agnieszka Żmieńko, Marek Figlerowicz
    Academic press:
    Plant Methods (rok: 2016, tom: 12, strony: Article ID 28), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s13007-016-0128-4 - link to the publication
  18. AmiRNA Designer - new method of artificial miRNA design
    Authors:
    Agnieszka Mickiewicz, Agnieszka Rybarczyk, Joanna Sarzyńska, Marek Figlerowicz, Jacek Błażewicz
    Academic press:
    Acta Biochimica Polonica (rok: 2016, tom: 63, strony: Article ID 2015_989), Wydawca: Polskie Towarzystwo Biochemiczne
    Status:
    Published
    DOI:
    10.18388/abp.2015_989 - link to the publication
  19. An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: application on Arabidopsis thaliana
    Authors:
    Daniele Santoni, Aleksandra Świercz, Agnieszka Żmieńko, Marta Kasprzak, Marek Błażewicz, Paola Bertolazzi, Giovanni Felici
    Academic press:
    OMICS A Journal of Integrative Biology (rok: 2014, tom: 18, strony: 155-165), Wydawca: Mary Ann Liebert
    Status:
    Published
    DOI:
    10.1089/omi.2013.0050 - link to the publication
  20. Graph algorithms for DNA sequencing - origins, current models and the future
    Authors:
    Jacek Błażewicz, Marta Kasprzak, Michał Kierzynka, Wojciech Frohmberg, Aleksandra Świercz, Paweł Wojciechowski, Piotr Żurkowski
    Academic press:
    European Journal of Operational Research (rok: 2018, tom: 264, strony: 799-812), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ejor.2016.06.043 - link to the publication
  21. RNAssess - a web server for quality assessment of RNA 3D structures
    Authors:
    Piotr Łukasiak, Maciej Antczak, Tomasz Ratajczak, Marta Szachniuk, Mariusz Popenda, Ryszard W. Adamiak, Jacek Błażewicz
    Academic press:
    Nucleic Acids Research (rok: 2015, tom: 43, strony: W502-W506), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkv557 - link to the publication
  22. Reference alignment based methods for quality evaluation of multiple sequence alignment - a survey
    Authors:
    Paweł Wojciechowski, Piotr Formanowicz, Jacek Błażewicz
    Academic press:
    Current Bioinformatics (rok: 2014, tom: 9, strony: 44-56), Wydawca: Bentham Science Publishers
    Status:
    Published
    DOI:
    10.2174/15748936113080990005 - link to the publication
  23. Computational prediction of non-enzymatic RNA degradation patterns
    Authors:
    Agnieszka Rybarczyk, Paulina Jackowiak, Marek Figlerowicz, Jacek Błażewicz
    Academic press:
    Acta Biochimica Polonica (rok: 2016, tom: 63, strony: 745-751), Wydawca: Polskie Towarzystwo Biochemiczne
    Status:
    Published
    DOI:
    10.18388/abp.2016_1331 - link to the publication
  24. ModeLang: A New Approach for Experts-Friendly Viral Infections Modeling
    Authors:
    Szymon Wąsik, Tomasz Prejzendanc, Jacek Błażewicz
    Academic press:
    Computational and Mathematical Methods in Medicine (rok: 2013, tom: 2013, strony: Article ID 320715), Wydawca: Hindawi Publishing Corporation
    Status:
    Published
    DOI:
    10.1155/2013/320715 - link to the publication
  25. Multi-agent model of hepatitis C virus infection
    Authors:
    Szymon Wąsik, Paulina Jackowiak, Marek Figlerowicz, Jacek Błażewicz
    Academic press:
    Artificial Intelligence in Medicine (rok: 2014, tom: 60, strony: 123-131), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.artmed.2013.11.001 - link to the publication
  26. Preprocessing and storing high-throughput sequencing data
    Authors:
    Aleksandra Świercz, Bartosz Bosak, Marek Chłopkowski, Arkadiusz Hoffa, Marta Kasprzak, Krzysztof Kurowski, Tomasz Piontek, Jacek Błażewicz
    Academic press:
    Computational Methods in Science and Technology (rok: 2014, tom: 20, strony: 45555), Wydawca: Ośrodek Wydawnictw Naukowych
    Status:
    Published
    DOI:
    10.12921/cmst.2014.20.01.9-20 - link to the publication
  27. The orderly colored longest path problem – a survey of applications and new algorithms
    Authors:
    Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Jacek Błażewicz
    Academic press:
    RAIRO - Operations Research (rok: 2014, tom: 48, strony: 25-51), Wydawca: EDP Sciences
    Status:
    Published
    DOI:
    10.1051/ro/2013046 - link to the publication
  28. Unified encoding for hyper-heuristics with application to bioinformatics
    Authors:
    Aleksandra Świercz, Edmund K. Burke, Mateusz Cicheński, Grzegorz Pawlak, Sanja Petrovic, Tomasz Żurkowski, Jacek Błażewicz
    Academic press:
    Central European Journal of Operations Research (rok: 2014, tom: 22, strony: 567-589), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s10100-013-0321-8 - link to the publication
  29. High-order statistical compressor for long-term storage of DNA sequencing data
    Authors:
    Marek Chłopkowski, Maciej Antczak, Michał Ślusarczyk, Aleksander Wdowiński, Michał Zajączkowski, Marta Kasprzak
    Academic press:
    RAIRO Operations Research (rok: 2016, tom: 50, strony: online), Wydawca: EDP Sciences
    Status:
    Published
    DOI:
    10.1051/ro/2015039 - link to the publication
  30. MCQ4Structures to compute similarity of molecule structures
    Authors:
    Tomasz Żok, Mariusz Popenda, Marta Szachniuk
    Academic press:
    Central European Journal of Operations Research (rok: 2014, tom: 22, strony: 457-473), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s10100-013-0296-5 - link to the publication
  31. Structural alignment of protein descriptors - a combinatorial model
    Authors:
    Maciej Antczak, Marta Kasprzak, Piotr Łukasiak, Jacek Błażewicz
    Academic press:
    BMC Bioinformatics (rok: 2016, tom: 17, strony: Article ID 383), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12859-016-1237-9 - link to the publication
  32. Parallel GPU algorithms for phylogenetic tree construction
    Authors:
    Jacek Błażewicz, Paweł Kędziora, Marcin Nowaczyk
    Academic press:
    BioTechnologia (rok: 2016, tom: -, strony: -), Wydawca: Instytut Chemii Bioorganicznej PAN
    Status:
    Submitted
    DOI:
    brak - link to the publication
  1. Turning data into folds using RNAComposer
    Authors:
    Marta Szachniuk, Joanna Sarzyńska, Jacek Błażewicz
    Conference:
    2013 International Symposium on Computational Models for Life Sciences (rok: 2013, ), Wydawca: AIP Publishing, DOI: 10.1063/1.4825029
    Data:
    konferencja 27–29.11.2013
    Status:
    Published
  2. SphereGrinder - reference structure-based tool for quality assessment of protein structural models
    Authors:
    Piotr Łukasiak, Maciej Antczak, Tomasz Ratajczak, Jacek Błażewicz
    Conference:
    2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (rok: 2015, ), Wydawca: IEEE (Institute of Electrical and Electronics Engineers)
    Data:
    konferencja 9-12.11.2015
    Status:
    Published

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