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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RNApolis - methods and algorithms to model and analyse the RNA structure

2016/23/B/ST6/03931

Keywords:

bioinformatic algorithms RNA structure 3D structure modeling structure evaluation computational technologies

Descriptors:

  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • ST6_12: Scientific computing, simulation and modelling tools

Panel:

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

Host institution :

Politechnika Poznańska, Wydział Informatyki i Telekomunikacji

woj. wielkopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Marta Szachniuk 

Number of co-investigators in the project: 10

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

Amount awarded: 632 450 PLN

Project start date (Y-m-d): 2017-07-20

Project end date (Y-m-d): 2020-11-19

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.

Information in the final report

  • Publication in academic press/journals (20)
  1. Discovering structural motifs in miRNA precursors from Viridiplantae kingdom
    Authors:
    J. Miskiewicz, M. Szachniuk
    Academic press:
    Molecules (rok: 2018, tom: 23(6), strony: 1367), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/molecules23061367 - link to the publication
  2. In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients
    Authors:
    T. P. Lehmann, J. Miskiewicz, N. Szostak, M. Szachniuk, S. Grodecka-Gazdecka, P. Jagodziński
    Academic press:
    Applied Sciences (rok: 2020, tom: 10(20), strony: 7275), Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
    Status:
    Published
    DOI:
    10.3390/app10207275 - link to the publication
  3. RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures
    Authors:
    M. Antczak, T. Zok, M. Osowiecki, M. Popenda, R.W. Adamiak, M. Szachniuk
    Academic press:
    BMC Bioinformatics (rok: 2018, tom: 19(1), strony: 304), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12859-018-2317-9 - link to the publication
  4. RNApolis: Computational Platform for RNA Structure Analysis
    Authors:
    M. Szachniuk
    Academic press:
    Foundations of Computing and Decision Sciences (rok: 2019, tom: 44(2), strony: 241-257), Wydawca: Poznań University of Technology
    Status:
    Published
    DOI:
    10.2478/fcds-2019-0012 - link to the publication
  5. RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
    Authors:
    M. Antczak, M. Zablocki, T. Zok, A. Rybarczyk, J. Blazewicz, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2019, tom: 35(1), strony: 152–155), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty609 - link to the publication
  6. Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA
    Authors:
    J. Gumna, K.J. Purzycka, H.W. Ahn, D.J. Garfinkel, K. Pachulska-Wieczorek
    Academic press:
    RNA Biology (rok: 2019, tom: 16(12), strony: 1749-1763), Wydawca: Taylor & Francis Group
    Status:
    Published
    DOI:
    10.1080/15476286.2019.1657370 - link to the publication
  7. A new molecular mechanism of RNA circularization and the microRNA sponge formation
    Authors:
    A. Belter, M. Popenda, M. Sajek, T. Woźniak, M. Z. Naskręt-Barciszewska, M. Szachniuk, S. Jurga, J. Barciszewski
    Academic press:
    Journal of Biomolecular Structure and Dynamics (rok: 2020, tom: w druku, strony: w druku), Wydawca: Taylor & Francis
    Status:
    Published
    DOI:
    10.1080/07391102.2020.1844802 - link to the publication
  8. ElTetrado: a tool for identification and classification of tetrads and quadruplexes
    Authors:
    T. Zok, M. Popenda, M. Szachniuk,
    Academic press:
    BMC Bioinformatics (rok: 2020, tom: 21, strony: 40), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12859-020-3385-1 - link to the publication
  9. New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
    Authors:
    M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R.W. Adamiak, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2018, tom: 34(8), strony: 1304-1312), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btx783 - link to the publication
  10. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
    Authors:
    Z. Miao, R. Adamiak, M. Antczak, M. Boniecki, J. M. Bujnicki, S. Chen, C. Y. Cheng, Y. Cheng, F. Chou, R.Das, N. V. Dokholyan, F. Ding, C. Geniesse, Y. Jiang, A. Joshi, A. Krokhotin, M. Magnus, O. Mailhot, F. Major, T. H. Mann, P. Piątkowski, R. Pluta, M. Popenda, J. Sarzyńska, L. Sun, M. Szachniuk, S. Tian, J. Wang, A. M. Watkins, J. Wiedemann, X. Xu, J. D. Yesselman, D. Zhang, Z. Zhang, C. Zhao, P. Zhao, Y. Zhou, T. Zok, A. Żyła, A. Ren, R.t T. Batey, B. L. Golden, L. Huang, D. M. Lilley, Y. Liu, Di. J. Patel, E. Westhof
    Academic press:
    RNA (rok: 2020, tom: 26(12), strony: 982-995), Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Published
    DOI:
    10.1261/rna.075341.120 - link to the publication
  11. RNApdbee 2.0: multifunctional tool for RNA structure annotation
    Authors:
    T. Zok, M. Antczak, M. Zurkowski, M. Popenda, J. Blazewicz, R.W. Adamiak, M. Szachniuk
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 46, strony: W30-W35), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gky314 - link to the publication
  12. BioCommons: a robust Java library for RNA structural bioinformatics
    Authors:
    T. Żok
    Academic press:
    Bioinformatics (rok: 2021, ), Wydawca: Oxford University Press
    Status:
    Accepted for publication
    DOI:
    10.1093/bioinformatics/btab069 - link to the publication
  13. Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions
    Authors:
    F. Carrascoza, M. Antczak, Z. Miao, E. Westhof, M. Szachniuk
    Academic press:
    RNA , Wydawca: Cold Spring Harbor Laboratory Press
    Status:
    Submitted
    DOI:
    brak - link to the publication
  14. New models and algorithms for RNA pseudoknot order assignment
    Authors:
    T. Zok, J. Badura, S. Swat, K. Figurski, M. Popenda, M. Antczak
    Academic press:
    International Journal of Applied Mathematics and Computer Science (rok: 2020, tom: 30(2), strony: 315-324), Wydawca: University of Zielona Góra
    Status:
    Published
    DOI:
    10.34768/amcs-2020-0024 - link to the publication
  15. Topology-based classification of tetrads and quadruplex structures
    Authors:
    M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2020, tom: 36(4), strony: 1129-1134), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btz738 - link to the publication
  16. How bioinformatics resources work with G4 RNAs
    Authors:
    J. Miśkiewicz, J. Sarzyńska, M. Szachniuk
    Academic press:
    Briefings in Bioinformatics (rok: 2020, tom: w druku, strony: 45305), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bib/bbaa201 - link to the publication
  17. Virxicon: a lexicon of viral sequences
    Authors:
    M. Kudla, K. Gutowska, J. Synak, M. Weber, K.S. Bohnsack, P. Lukasiak, T. Villmann, J. Blazewicz, M. Szachniuk
    Academic press:
    Bioinformatics (rok: 2020, tom: 36(22-23), strony: 5507-5513), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    brak - link to the publication
  18. LCS-TA to identify similar fragments in RNA 3D structures
    Authors:
    J. Wiedemann, T. Zok, M. Milostan, M. Szachniuk
    Academic press:
    BMC Bioinformatics (rok: 2018, tom: 18, strony: 456), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12859-017-1867-6 - link to the publication
  19. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools
    Authors:
    M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J.M. Bujnicki, E. Westhof, M. Szachniuk, Z. Miao
    Academic press:
    Nucleic Acids Research (rok: 2020, tom: 48(2), strony: 576–588), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkz1108 - link to the publication
  20. RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis
    Authors:
    J. Gumna, T. Zok, K. Figurski, K. Pachulska-Wieczorek, M. Szachniuk
    Academic press:
    PLOS ONE (rok: 2020, tom: 15(10), strony: 239287), Wydawca: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0239287 - link to the publication

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