Publications

ResearcherID/Publons, ORCID
Google Scholar Profile
PubMed
h-index: 15 (Web of Science), 17 (Google Scholar)


Editorial Boards



Books, book chapters

  1. Biesiada M, Purzycka KJ, Szachniuk M, Blazewicz J, Adamiak RW
    Automated RNA 3D structure prediction with RNAComposer, in Doug H. Turner, David H. Mathews (eds.) RNA Structure Determination: Methods and Protocols (Methods in Molecular Biology 1490), Springer, Humana Press, 2016, 199-215 (doi:10.1007/978-1-4939-6433-8).

  2. Purzycka KJ, Popenda M, Szachniuk M, Antczak M, Lukasiak P, Blazewicz J, Adamiak RW
    Automated 3D RNA structure prediction using the RNAComposer method for riboswitches, in Shi-Jie Chen, Donald H. Burke-Aguero (eds.) Methods in Enzymology: Computational Methods for Understanding Riboswitches 553, Elsevier, 2014, 3-34 (doi: 10.1016/bs.mie.2014.10.050).


Peer reviewed papers

  1. Wozniak T, Sajek M, Antczak M, Zurkowski M, Jaruzelska J, Szachniuk M
    submission

  2. Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen S-J, Ding F, Li J, Pachulska-Wieczorek K, Popenda M, Sarzynska J, Zhang D, Zhang S, Zok T, Szachniuk M, Miao Z, Westhof E
    work in progress

  3. Wiedemann J, Kaczor J, Antczak M, Milostan M, Zok T, Szachniuk M
    submission

  4. Zok T, Miskiewicz J, Kraszewska N, Pielacinska P, Szachniuk M
    ONQUADRO: a database of tetrads and quadruplexes, submission

  5. Popenda M, Zok T, Sarzynska J, Antczak M, Korpeta A, Adamiak RW, Szachniuk M
    submission

  6. Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M
    submitted

  7. Kudla M, Gutowska K, Synak J, Weber M, Bohnsack KS, Lukasiak P, Villmann T, Blazewicz J, Szachniuk M
    Virxicon: a lexicon of viral sequences, Bioinformatics, 2021, online publication: 26 December 2020 (doi:10.1093/bioinformatics/btaa1066).

  8. Belter A, Popenda M, Sajek M, Wozniak T, Naskret-Barciszewska MZ, Szachniuk M, Jurga S, Barciszewski J
    A new molecular mechanism of RNA circularization and the microRNA sponge formation, Journal of Biomolecular Structure and Dynamics, 2020, online publication: 17 November 2020 (doi:10.1080/07391102.2020.1844802).

  9. Miskiewicz J, Sarzynska J, Szachniuk M
    How bioinformatics resources work with G4 RNAs, Briefings in Bioinformatics, 2020, online publication: 8 September 2020 (doi:10.1093/bib/bbaa201).

  10. Lehmann TP, Miskiewicz J, Szostak N, Szachniuk M, Grodecka-Gazdecka S, Jagodzinski PP
    In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients, Applied Sciences 10(20), 2020, 7275 (doi:10.3390/app10207275).

  11. Gumna J, Zok T, Figurski K, Pachulska-Wieczorek K, Szachniuk M
    RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis, PLOS ONE 15(10), 2020, e0239287 (doi:10.1371/journal.pone.0239287).

  12. Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piatkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Watkins AM, Wiedemann J, Xu X, Yesselman JD, Zhang D, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Zyla A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E
    RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, RNA 26(8), 2020, 982-995 (doi:10.1261/rna.075341.120).

  13. Zok T, Popenda M, Szachniuk M
    ElTetrado: a tool for identification and classification of tetrads and quadruplexes, BMC Bioinformatics 21, 2020, 40 (doi:10.1186/s12859-020-3385-1).

  14. Popenda M, Miskiewicz J, Sarzynska J, Zok T, Szachniuk M
    Topology-based classification of tetrads and quadruplex structures, Bioinformatics 36(4), 2020, 1129–1134, online publication: 7 October 2019 (doi:10.1093/bioinformatics/btz738).

  15. Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z
    RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, Nucleic Acids Research 48(2), 2020, 576–588, online publication: 4 Dec 2019 (doi: 10.1093/nar/gkz1108).

  16. Szachniuk M
    RNApolis: computational platform for RNA structure analysis, Foundations of Computing and Decision Sciences 44(2), 2019, 241-257 (doi:10.2478/fcds-2019-0012).

  17. Antczak M, Zablocki M, Zok T, Rybarczyk A, Blazewicz J, Szachniuk M
    RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs, Bioinformatics 35(1), 2019, 152-155 (doi:10.1093/bioinformatics/bty609).

  18. Antczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, Szachniuk M
    RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, BMC Bioinformatics 19(1), 2018, 304 (doi:10.1186/s12859-018-2317-9).

  19. Miskiewicz J, Szachniuk M
    Discovering structural motifs in miRNA precursors from Viridiplantae kingdom, Molecules 23(6), 2018, 1367 (doi:10.3390/molecules23061367).

  20. Zok T, Antczak M, Zurkowski M, Popenda M, Blazewicz J, Adamiak RW, Szachniuk M
    RNApdbee 2.0: multifunctional tool for RNA structure annotation, Nucleic Acids Research 46(W1), 2018, W30-W35 (doi:10.1093/nar/gky314).

  21. Antczak M, Popenda M, Zok T, Zurkowski M, Adamiak RW, Szachniuk M
    New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation, Bioinformatics 34(8), 2018, 1304-1312 (doi:10.1093/bioinformatics/btx783).

  22. Wiedemann J, Zok T, Milostan M, Szachniuk M
    LCS-TA to identify similar fragments in RNA 3D structures, BMC Bioinformatics 18, 2017, 456 (doi:10.1186/s12859-017-1867-6).

  23. Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferre-D'Amare AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams II B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E
    RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme, RNA 23(5), 2017, 655-672 (doi:10.1261/rna.060368.116).

  24. Miskiewicz J, Tomczyk K, Mickiewicz A, Sarzynska J, Szachniuk M
    Bioinformatics study of structural patterns in plant microRNA precursors, BioMed Research International vol. 2017, article ID 6783010, 8 pages, 2017 (doi:10.1155/2017/6783010).

  25. Antczak M, Popenda M, Zok T, Sarzynska J, Ratajczak T, Tomczyk K, Adamiak RW, Szachniuk M
    New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure, Acta Biochimica Polonica 63(4), 2016, 737-744 (doi:10.18388/abp.2016_1329).

  26. Turkay M, Felici G, Szachniuk M, Lukasiak P
    Recent advances in operations research in computational biology, bioinformatics and medicine, RAIRO - Operations Research 50(2), 2016, 327-330 (doi:10.1051/ro/2015036).

  27. Rybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak RW, Blazewicz J, Szachniuk M
    New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics 16, 2015, 276 (doi:10.1186/s12859-015-0718-6).

  28. Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J
    RNAssess - a webserver for quality assessment of RNA 3D structures, Nucleic Acids Research 43(W1), 2015, W502-W506 (doi:10.1093/nar/gkv557).

  29. Zok T, Antczak M, Riedel M, Nebel D, Villmann T, Lukasiak P, Blazewicz J, Szachniuk M
    Building the library of RNA 3D nucleotide conformations using clustering approach, International Journal of Applied Mathematics and Computer Science 25(3), 2015, 689-700 (doi:10.1515/amcs-2015-0050).

  30. Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferre-D'Amare AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E
    RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures, RNA 21(6), 2015, 1066-1084 (doi:10.1261/rna.049502.114).

  31. Szachniuk M
    Assigning NMR Spectra of Irregular RNAs by Heuristic Algorithms, Bulletin of the Polish Academy of Sciences Technical Sciences 63(1), 2015, 329-338 (doi:10.1515/bpasts-2015-0037).

  32. Szachniuk M, De Cola MC, Felici G, de Werra D, Blazewicz J
    Optimal pathway reconstruction on 3D NMR maps, Discrete Applied Mathematics 182, 2015, 134-149 (doi:10.1016/j.dam.2014.04.010).

  33. Szostak N, Royo F, Rybarczyk A, Szachniuk M, Blazewicz J, del Sol A, Falcon-Perez JM
    Sorting signal targeting mRNA into hepatic extracellular vesicles, RNA Biology 11(7), 2014, 836-844 (doi:10.4161/rna.29305).

  34. Antczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M
    RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, Nucleic Acids Research 42(W1), 2014, W368-W372 (doi:10.1093/nar/gku330).

  35. Szachniuk M, De Cola MC, Felici G, Blazewicz J
    The Orderly Colored Longest Path Problem - a survey of applications and new algorithms, RAIRO - Operations Research 48(1), 2014, 25-51 (doi:10.1051/ro/2013046).

  36. Zok T, Popenda M, Szachniuk M
    MCQ4Structures to compute similarity of molecule structures, Central European Journal of Operations Research 22(3), 2014, 457-474 (doi:10.1007/s10100-013-0296-5).

  37. Szachniuk M, Malaczynski M, Pesch E, Burke EK, Blazewicz J
    MLP accompanied beam search for the resonance assignment problem, Journal of Heuristics 19(3), 2013, 443-464 (doi:10.1007/s10732-013-9220-3).

  38. Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J
    RNAlyzer – novel approach for quality analysis of RNA structural models, Nucleic Acids Research 41(12), 2013, 5978-5990 (doi:10.1093/nar/gkt318).

  39. Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW
    Automated 3D structure composition for large RNAs, Nucleic Acids Research 40(14), 2012, e112 (doi:10.1093/nar/gks339).

  40. Radom M, Rybarczyk A, Kottmann R, Formanowicz P, Szachniuk M, Gloeckner FO, Rebholz-Schuhmann D, Blazewicz J
    Poseidon: an information retrieval and extraction system for metagenomic marine science, Ecological Informatics 12, 2012, 10-15 (doi:10.1016/j.ecoinf.2012.07.003).

  41. Radom M, Kottmann R, Rybarczyk A, Formanowicz P, Szachniuk M, Gloeckner FO, Blazewicz J
    Cerberus: a new information retrieval tool for marine metagenomics, Foundations of Computing and Decision Sciences 35(2), 2010, 107-126.

  42. Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW
    RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, BMC Bioinformatics 11, 2010, 231 (doi:10.1186/1471-2105-11-231).

  43. Szachniuk M, Popenda M, Adamiak RW, Blazewicz J
    An assignment walk through 3D NMR spectrum, Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2009, 215-219 (doi:10.1109/CIBCB.2009.4925731).

  44. Popenda M, Blazewicz M, Szachniuk M, Adamiak RW
    RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures, Nucleic Acids Research 36(1), 2008, D386-D391 (doi:10.1093/nar/gkm786).

  45. Blazewicz J, Szachniuk M, Wojtowicz A
    RNA tertiary structure determination: NOE pathway construction by tabu search, Bioinformatics 21(10), 2005, 2356-2361 (doi:10.1093/bioinformatics/bti351).

  46. Szachniuk M, Popenda L, Gdaniec Z, Adamiak RW, Blazewicz J
    NMR analysis of RNA bulged structures: tabu search application in NOE signal assignment, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005, 172-178 (doi:10.1109/CIBCB.2005.1594914).

  47. Blazewicz J, Szachniuk M, Wojtowicz A
    Evolutionary approach to NOE paths assignment in RNA structure elucidation, Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2004, 206-213 (doi:10.1109/CIBCB.2004.1393955).

  48. Blazewicz J, Szachniuk M, Wojtowicz A
    Evolutionary algorithm for a reconstruction of NOE paths in NMR spectra of RNA chains, Bulletin of the Polish Academy of Sciences Technical Sciences 52(3), 2004, 221-230.

  49. Adamiak RW, Blazewicz J, Formanowicz P, Gdaniec Z, Kasprzak M, Popenda M, Szachniuk M
    An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes, Journal of Computational Biology 11(1), 2004, 163-180 (doi:10.1089/106652704773416948).


Scientific reports, abstracts and short peer reviewed papers

  1. M. Szachniuk, J. Blazewicz
    Virtual RNA biology: from sequence to high quality 3D structure model, Proceedings of IASTEM International Conference, 2018, 9-11.

  2. J.A. Kowalska, K. Tomczyk, J. Sarzynska, M. Szachniuk
    Bioinformatic analysis of motifs in microRNA vicinity in plants, Acta Biochimica Polonica 63(2) Supplement, 2016, 173 (on-line).

  3. P. Ceranek, T. Zok, M. Antczak, M. Szachniuk
    RNAsprite - a concept of tool to calculate RNA structural data, Machine Learning Reports 04/2015, 2015, 14 (on-line).

  4. T. Zok, M. Antczak, M. Riedel, D. Nebel, T. Villmann, P. Lukasiak, J. Blazewicz, M. Szachniuk
    Clustering approach to create libraries of representative RNA conformers, Machine Learning Reports 04/2015, 2015, 18.

  5. N. Szostak, A. Rybarczyk, M. Antczak, T. Zok, M. Popenda, R. Adamiak, J. Blazewicz, M. Szachniuk
    New in silico approach to assess RNA secondary structures with noncanonical base pairs, Machine Learning Reports 04/2015, 2015, 13.

  6. M. Szachniuk, J. Sarzynska, J. Blazewicz
    Turning data into folds using RNAComposer, AIP Conference Proceedings 1559(1), 2013, 353-354.

  7. M. De Cola, G. Felici, M. Szachniuk
    The Orderly Colored Longest Path Problem, CNR-IASI Technical Report 29/2012, 2012.

  8. M. Szachniuk, M. Popenda, M. Antczak, K.J. Purzycka, P. Lukasiak, J. Blazewicz, R.W. Adamiak
    RNAComposer: the art of composing RNA structures, Machine Learning Reports 01/2011, 2011, 26-29.

  9. T. Zok, M. Szachniuk, M. Antczak
    Comparison of RNA structures in torsional angle space, Machine Learning Reports 01/2011, 2011, 14-18.

  10. M. Szachniuk, M. Popenda, L. Popenda
    Graphs in NMR analysis of RNAs, TU Clausthal Technical Report Series IfI-09-12, 2009, 52-59.

  11. T. Zok, M. Popenda, M. Szachniuk
    Comparison of RNA structures - concepts and measures, TU Clausthal Technical Report Series IfI-08-03, 2008, 42-44.

  12. J. Blazewicz, R.W. Adamiak, P. Lukasiak, M. Popenda, M. Szachniuk, M. Antczak, G. Palik
    3D-RNA-Pred: an automatic building of the three-dimensional RNA structures, TU Clausthal Technical Report Series IfI-08-03, 2008, 45-48.

  13. M. Szachniuk, M. Radom, A. Rybarczyk, P. Formanowicz, J. Blazewicz
    From document processing to an identification of marine microorganisms' habitat specificity, TU Clausthal Technical Report Series IfI-08-03, 2008, 61-63.

  14. M. Szachniuk, M. Popenda, L. Popenda, J. Blazewicz
    Constructing transfer pathways in multidimensional NMR spectra of RNAs, RECOMB'08 poster book, 2008, 62-63.

  15. M. Szachniuk, M. Blazewicz, M. Popenda, R.W. Adamiak
    On the design of RNA fragments structural database, RECOMB'08 poster book, 2008, 18-19.

  16. M. Szachniuk, M. Popenda, S. Klemczak, J. Blazewicz
    An analysis of three-dimensional NMR spectra in RNA structure determination process, Research report RA-001/2007, 2007, Poznan Supercomputing and Networking Center.

  17. M. Blazewicz, M. Popenda, R.W. Adamiak, M. Szachniuk
    Project of RNA fragments database, TU Clausthal Technical Report Series IfI-07-03, 2007, 25-27.

  18. M. Szachniuk, M. Popenda, L. Popenda
    Strategies of signal assignment in NMR spectra of RNAs with different structural motifs, TU Clausthal Technical Report Series IfI-07-03, 2007, 12-14.

  19. W. Paczkowski, M. Milawski, L. Popenda, M. Szachniuk
    A new tool for fundamental analysis of NMR spectra, TU Clausthal Technical Report Series IfI-07-03, 2007, 8-11.

  20. M. Szachniuk, R.W. Adamiak, P. Formanowicz, Z. Gdaniec, M. Kasprzak, M. Popenda, J. Blazewicz
    A combinatorial analysis of 2D NMR spectra of RNA duplexes, Currents in Computational Molecular Biology, 2003, 345-346.


Monographs

  1. M. Szachniuk
    Combinatorial Analysis of 2D-NOESY Spectra in Nuclear Magnetic Resonance Spectroscopy of RNA Molecules, PhD thesis, 2005, Institute of Computing Science, Poznan University of Technology. (pdf)

  2. M. Szachniuk
    Selected problems of contemporary topology, MSc thesis, 1999, Institute of Mathematics, Poznan University of Technology.

  3. M. Szachniuk
    Optical character recognition - analysis of methods, MSc thesis, 1998, Institute of Computing Science, Poznan University of Technology.


Patents

  1. M. Szachniuk, M. Popenda, R.W. Adamiak, J. Blazewicz
    The Method of an Assignment of the Magnetization Transfer Pathway Between H6/H8-H1' Protons in the 2-Dimensional NOESY Spectra in Nuclear Magnetic Resonance Spectroscopy of Nucleic Acids, Polish patent pending application P 364 736, 03.02.2004, The Patent Office of the Republic of Poland.

Other works (posters, popular science & non-scientific articles)

  1. M. Szachniuk, M. Popenda, T. Zok
    ElTetrado captures topological features of nucleic acid quadruplexes, F1000Research 8(ISCB Comm J), 2019, 1973 (poster) (doi: 10.7490/f1000research.1117688.1).

  2. J. Blazewicz, M. Szachniuk, N. Szostak, G.-W. Weber
    Historic Venue for a Young Group of an Emerging Field, IFORS NEWS 8(3), 2014, 9.

  3. N. Szostak, M. Szachniuk
    CBBM 2014: Badania operacyjne, biologia i medycyna w palacowych salonach, Glos Politechniki 4(182), 2014, 20-21.

  4. M. Szachniuk
    Gora nasi, czyli bioinformatycy z Politechniki Poznanskiej w Ustroniu, Glos Politechniki 10(154), 2010, 14-15.