Publications
H-index: 20 (Scopus/Web of Science), 22 (Google Scholar)Editorial Boards
Nucleic Acids Research (since 2024)
European Journal of Operational Research – Guest Editor for the Special Issue: EURO 2024 Conference for European Journal of Operational Research
RAIRO Operations Research – Guest Editor for the Special Issue: Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine (RAIRO Operations Research 50(2), 2016; doi:10.1051/ro/2015036)
Books, book chapters
Antczak M
, Szachniuk M (2024) Towards increasing the credibility of RNA design, in Danny Barash (ed.) RNA Design (Methods in Molecular Biology), Springer, Humana Press.
Biesiada M, Purzycka KJ, Szachniuk M, Blazewicz J, Adamiak RW (2016) 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, 199-215 (doi:10.1007/978-1-4939-6433-8).
Purzycka KJ, Popenda M, Szachniuk M, Antczak M, Lukasiak P, Blazewicz J, Adamiak RW (2015) 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, 3-34 (doi: 10.1016/bs.mie.2014.10.050).
Peer reviewed papers
Wozniak T, Sajek M, Antczak M, Zurkowski M, Jaruzelska J, Szachniuk M, working paper.
Abel J, Zok T, Kaden M, Weber M, Reuss LV, Bohnsack KS, Justyna M, Antczak M, Szachniuk M, Villmann T (2024) How successful are machine learning models in the G4 secondary structure prediction?, working paper.
Boinski P, Kubis J, Antczak M, Szachniuk M, Figiel M (2024), working paper.
Poblete S, Mlynarczyk M, Szachniuk M (2024), working paper.
Gren BA, Antczak M, Zok T, Sulkowska JI, Szachniuk M (2024) Knotted artifacts in predicted 3D RNA structures, submitted.
Bu F, Miao Z, Trachman III RJ, Adam YAI, Adamiak RW, Antczak M, de Aquino BRH, Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ, Bujnicki JM, Carpenter KA, Chacon J, Chen S-J, Chiu W, Cordero P, Das NK, Das R, Dawson W, Dimaio F, Ding F, Dock-Bregeon A-C, Dokholyan NV, Dror R, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferré-D’Amaré AR, Geniesse C, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kretsch R, Kurcinski M, Lee S-Y, Li S, Li J, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Perez A, Pham P, Piccirilli JA, Pilla SP, Nayaka PJ IP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda L, Popenda M, Pucci F, Rangan R, Ray A, Ren A, Sanbonmatsu K, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Wang W, Wang J, Watkins A, Wirecki T, Xiao Y, Xiong Y, Xiong P, Yang J, Yesselman JD, Zhang J, Zhang S, Zhang D, Zhang Y, Zhang Z, Zhou Y, Zok T, Zyla A, Westhof E (2024) RNA-Puzzles Round V: the blind predictions of 23 RNA structures, submitted.
Ragin W, Tran HL, Witek W, Połomska E, Podlewski M, Pawłowicz A, Cioch-Biniaś A, Woś A, Andrałojć W, Szachniuk M, Ruszkowski M (2024) Postępy biologii strukturalnej – jak zobaczyć cząsteczki życia?, Postępy Biochemii.
Zurkowski M, Swiercz M, Wozny F, Antczak M
, Szachniuk M (2024) RNAhugs web server for customized 3D RNA structure alignment, Nucleic Acids Research 52(W1) (doi: 10.1093/nar/gkae259).
Schneider B, Sweeney B, Bateman A, Cerny J, Zok T, Szachniuk M (2023), When will RNA get its AlphaFold moment?, Nucleic Acids Research 51(18):9522-9532 (doi: 10.1093/nar/gkad726).
Sarzynska J, Popenda M, Antczak M, Szachniuk M
(2023) RNA tertiary structure prediction using RNAComposer in CASP15, PROTEINS: Structure, Function, and Bioinformatics 91(12):1790-1799 (doi: 10.1002/prot.26578).
Kryshtafovych A, Antczak M, Szachniuk M, Zok T, Kretsch RC, Rangan R, Pham P, Das R, Robin X, Studer G, Durairaj J, Eberhardt J, Sweeney A, Topf M, Schwede T, Fidelis K, Moult J (2023) New prediction categories in CASP15, PROTEINS: Structure, Function, and Bioinformatics 91(12):1550-1557 (doi: 10.1002/prot.26515).
Zurkowski M, Antczak M
, Szachniuk M (2023) High-quality, customizable heuristics for RNA 3D structure alignment, Bioinformatics 39(5):btad315 (doi: 10.1093/bioinformatics/btad315), published online: 11 May 2023.
Adamczyk B, Zurkowski M, Szachniuk M
, Zok T (2023) WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures, Nucleic Acids Research 51(W1):W607-W612 (doi: 10.1093/nar/gkad346).
Justyna M, Antczak M
, Szachniuk M (2023) Machine learning for RNA 2D structure prediction benchmarked on experimental data, Briefings in Bioinformatics 24(3):bbad153 (doi: 110.1093/bib/bbad153), published online: 24 April 2023.
Wiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, Szachniuk M
, Antczak M (2022) RNAloops: a database of RNA multiloops, Bioinformatics 38(17):4200-4205 (doi: 10.1093/bioinformatics/btac484).
Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen S-J, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z
, Szachniuk M, Rybarczyk A (2022) Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models, International Journal of Molecular Sciences 23(17):9630 (doi: 10.3390/ijms23179630).
Zurkowski M, Zok T, Szachniuk M
(2022) DrawTetrado to create layer diagrams of G4 structures, Bioinformatics 38(15):3835-3836 (doi:10.1093/bioinformatics/btac394).
Adamczyk B, Antczak M
, Szachniuk M (2022) RNAsolo: a repository of cleaned PDB-derived RNA 3D structures, Bioinformatics 38(14):3668-3670 (doi:10.1093/bioinformatics/btac386).
Luwanski K, Hlushchenko V, Popenda M, Zok T, Sarzynska J, Martsich D, Szachniuk M
, Antczak M (2022) RNAspider: a webserver to analyze entanglements in RNA 3D structures, Nucleic Acids Research 50(W1):W663-W669 (doi:10.1093/nar/gkac218).
Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M
(2022) Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions, RNA 28(2):250-262 (doi:10.1261/rna.078685.121), published online: 24 November 2021.
Zok T, Kraszewska N, Miskiewicz J, Pielacinska P, Zurkowski M, Szachniuk M
(2022) ONQUADRO: a database of experimentally determined quadruplex structures, Nucleic Acids Research 50(D1):D253-D258 (doi:10.1093/nar/gkab1118), published online: 19 November 2021.
Belter A, Popenda M, Sajek M, Wozniak T, Naskret-Barciszewska MZ, Szachniuk M, Jurga S, Barciszewski J (2022) A new molecular mechanism of RNA circularization and the microRNA sponge formation, Journal of Biomolecular Structure and Dynamics 40(7):3038-3045 (doi:10.1080/07391102.2020.1844802), published online: 17 November 2020.
Popenda M, Zok T, Sarzynska J, Korpeta A, Adamiak RW, Antczak M, Szachniuk M
(2021) Entanglements of structure elements revealed in RNA 3D models, Nucleic Acids Research 49(17):9625-9632 (doi:10.1093/nar/gkab716).
Miskiewicz J, Sarzynska J, Szachniuk M
(2021) How bioinformatics resources work with G4 RNAs, Briefings in Bioinformatics 22(3):bbaa201 (doi:10.1093/bib/bbaa201), published online: 8 September 2020.
Kudla M, Gutowska K, Synak J, Weber M, Bohnsack KS, Lukasiak P, Villmann T, Blazewicz J, Szachniuk M
(2020) Virxicon: a lexicon of viral sequences, Bioinformatics 36(22-23):5507-5513 (doi:10.1093/bioinformatics/btaa1066).
Lehmann TP
, Miskiewicz J, Szostak N, Szachniuk M, Grodecka-Gazdecka S, Jagodzinski PP (2020) In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients, Applied Sciences 10(20):7275 (doi:10.3390/app10207275).
Gumna J, Zok T, Figurski K, Pachulska-Wieczorek K
, Szachniuk M (2020) RNAthor – fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis, PLOS ONE 15(10):e0239287 (doi:10.1371/journal.pone.0239287).
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 (2020) RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, RNA 26(8):982-995 (doi:10.1261/rna.075341.120).
Zok T, Popenda M, Szachniuk M
(2020) ElTetrado: a tool for identification and classification of tetrads and quadruplexes, BMC Bioinformatics 21:40 (doi:10.1186/s12859-020-3385-1).
Popenda M, Miskiewicz J, Sarzynska J, Zok T, Szachniuk M
(2020) Topology-based classification of tetrads and quadruplex structures, Bioinformatics 36(4):1129-1134 (doi:10.1093/bioinformatics/btz738), published online: 7 October 2019.
Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M
, Miao Z (2020) RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, Nucleic Acids Research 48(2):576–588 (doi:10.1093/nar/gkz1108), published online: 4 Dec 2019.
Szachniuk M
(2019) RNApolis: computational platform for RNA structure analysis, Foundations of Computing and Decision Sciences 44(2):241-257
(doi:10.2478/fcds-2019-0012).
Antczak M, Zablocki M, Zok T, Rybarczyk A, Blazewicz J, Szachniuk M
(2019) RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs, Bioinformatics 35(1):152-155
(doi:10.1093/bioinformatics/bty609).
Antczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, Szachniuk M
(2018) RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, BMC Bioinformatics 19(1):304 (doi:10.1186/s12859-018-2317-9).
Miskiewicz J, Szachniuk M
(2018) Discovering structural motifs in miRNA precursors from Viridiplantae kingdom, Molecules 23(6):1367 (doi:10.3390/molecules23061367).
Zok T, Antczak M, Zurkowski M, Popenda M, Blazewicz J, Adamiak RW, Szachniuk M
(2018) RNApdbee 2.0: multifunctional tool for RNA structure annotation, Nucleic Acids Research 46(W1):W30-W35 (doi:10.1093/nar/gky314).
Antczak M, Popenda M, Zok T, Zurkowski M, Adamiak RW, Szachniuk M
(2018) New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation, Bioinformatics 34(8):1304-1312 (doi:10.1093/bioinformatics/btx783).
Wiedemann J, Zok T, Milostan M, Szachniuk M
(2017) LCS-TA to identify similar fragments in RNA 3D structures, BMC Bioinformatics 18:456 (doi:10.1186/s12859-017-1867-6).
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 (2017) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme, RNA 23(5):655-672 (doi:10.1261/rna.060368.116).
Miskiewicz J, Tomczyk K, Mickiewicz A, Sarzynska J, Szachniuk M
(2017) Bioinformatics study of structural patterns in plant microRNA precursors, BioMed Research International 2017:6783010 (doi:10.1155/2017/6783010).
Antczak M, Popenda M, Zok T, Sarzynska J, Ratajczak T, Tomczyk K, Adamiak RW, Szachniuk M
(2016) New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure, Acta Biochimica Polonica 63(4):737-744 (doi:10.18388/abp.2016_1329).
Turkay M, Felici G, Szachniuk M, Lukasiak P (2016) Recent advances in operations research in computational biology, bioinformatics and medicine, RAIRO – Operations Research 50(2):327-330 (doi:10.1051/ro/2015036).
Rybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak RW, Blazewicz J, Szachniuk M
(2015) New in silico approach to assessing RNA secondary structures with non-canonical base pairs, BMC Bioinformatics 16:276 (doi:10.1186/s12859-015-0718-6).
Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J (2015) RNAssess – a webserver for quality assessment of RNA 3D structures, Nucleic Acids Research 43(W1):W502-W506 (doi:10.1093/nar/gkv557).
Zok T, Antczak M, Riedel M, Nebel D, Villmann T, Lukasiak P, Blazewicz J, Szachniuk M
(2015) Building the library of RNA 3D nucleotide conformations using clustering approach, International Journal of Applied Mathematics and Computer Science 25(3):689-700 (doi:10.1515/amcs-2015-0050).
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 (2015) RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures, RNA 21(6):1066-1084 (doi:10.1261/rna.049502.114).
Szachniuk M
(2015) Assigning NMR Spectra of Irregular RNAs by Heuristic Algorithms, Bulletin of the Polish Academy of Sciences Technical Sciences 63(1):329-338 (doi:10.1515/bpasts-2015-0037).
Szachniuk M
, De Cola MC, Felici G, de Werra D, Blazewicz J (2015) Optimal pathway reconstruction on 3D NMR maps, Discrete Applied Mathematics 182:134-149 (doi:10.1016/j.dam.2014.04.010).
Szostak N, Royo F, Rybarczyk A, Szachniuk M, Blazewicz J, del Sol A, Falcon-Perez JM (2014) Sorting signal targeting mRNA into hepatic extracellular vesicles, RNA Biology 11(7):836-844 (doi:10.4161/rna.29305).
Antczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M
(2014) RNApdbee – a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, Nucleic Acids Research 42(W1):W368-W372 (doi:10.1093/nar/gku330).
Szachniuk M
, De Cola MC, Felici G, Blazewicz J (2014) The Orderly Colored Longest Path Problem – a survey of applications and new algorithms, RAIRO – Operations Research 48(1):25-51 (doi:10.1051/ro/2013046).
Zok T, Popenda M, Szachniuk M
(2014) MCQ4Structures to compute similarity of molecule structures, Central European Journal of Operations Research 22(3):457-474 (doi:10.1007/s10100-013-0296-5).
Szachniuk M
, Malaczynski M, Pesch E, Burke EK, Blazewicz J (2013) MLP accompanied beam search for the resonance assignment problem, Journal of Heuristics 19(3):443-464 (doi:10.1007/s10732-013-9220-3).
Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J (2013) RNAlyzer – novel approach for quality analysis of RNA structural models, Nucleic Acids Research 41(12):5978-5990 (doi:10.1093/nar/gkt318).
Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW (2012) Automated 3D structure composition for large RNAs, Nucleic Acids Research 40(14):e112 (doi:10.1093/nar/gks339).
Radom M, Rybarczyk A, Kottmann R, Formanowicz P, Szachniuk M, Gloeckner FO, Rebholz-Schuhmann D, Blazewicz J (2012) Poseidon: an information retrieval and extraction system for metagenomic marine science, Ecological Informatics 12:10-15 (doi:10.1016/j.ecoinf.2012.07.003).
Radom M, Kottmann R, Rybarczyk A, Formanowicz P, Szachniuk M, Gloeckner FO, Blazewicz J (2010) Cerberus: a new information retrieval tool for marine metagenomics, Foundations of Computing and Decision Sciences 35(2):107-126.
Popenda M, Szachniuk M
, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW (2010) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures,
BMC Bioinformatics 11:231 (doi:10.1186/1471-2105-11-231).
Szachniuk M
, Popenda M, Adamiak RW, Blazewicz J (2009) An assignment walk through 3D NMR spectrum, Proceedings of the 2009 IEEE Symposium on Computational Intelligence
in Bioinformatics and Computational Biology, 215-219 (doi:10.1109/CIBCB.2009.4925731).
Popenda M, Blazewicz M, Szachniuk M, Adamiak RW (2008) 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):D386-D391 (doi:10.1093/nar/gkm786).
Blazewicz J, Szachniuk M
, Wojtowicz A (2005) RNA tertiary structure determination: NOE pathway construction by tabu search, Bioinformatics 21(10):2356-2361 (doi:10.1093/bioinformatics/bti351).
Szachniuk M
, Popenda L, Gdaniec Z, Adamiak RW, Blazewicz J (2005) 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, 172-178 (doi:10.1109/CIBCB.2005.1594914).
Blazewicz J, Szachniuk M
, Wojtowicz A (2004) Evolutionary approach to NOE paths assignment in RNA structure elucidation, Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 206-213 (doi:10.1109/CIBCB.2004.1393955).
Blazewicz J, Szachniuk M
, Wojtowicz A (2004) 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):221-230.
Adamiak RW, Blazewicz J, Formanowicz P, Gdaniec Z, Kasprzak M, Popenda M, Szachniuk M
(2004) An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes, Journal of Computational Biology 11(1):163-180 (doi:10.1089/106652704773416948).
Scientific reports, abstracts and short peer reviewed papers
Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen S-J, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Szachniuk M, Miao Z, Rybarczyk A (2022), Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions, (bioRxiv).
Szachniuk M, Popenda M, Zok T (2019) ElTetrado captures topological features of nucleic acid quadruplexes, F1000Research 8(ISCB Comm J):1973 (poster) (doi: 10.7490/f1000research.1117688.1).
Szachniuk M, Blazewicz J (2018) Virtual RNA biology: from sequence to high quality 3D structure model, Proceedings of IASTEM International Conference, 9-11.
Kowalska JA, Tomczyk K, Sarzynska J, Szachniuk M (2016) Bioinformatic analysis of motifs in microRNA vicinity in plants, Acta Biochimica Polonica 63(2) Supplement, 173 (on-line).
Ceranek P, Zok T, Antczak A, Szachniuk M (2015) RNAsprite – a concept of tool to calculate RNA structural data, Machine Learning Reports 04/2015:14 (on-line).
Zok T, Antczak M, Riedel M, Nebel D, Villmann T, Lukasiak P, Blazewicz J, Szachniuk M (2015) Clustering approach to create libraries of representative RNA conformers, Machine Learning Reports 04/2015:18.
Szostak N, Rybarczyk A, Antczak M, Zok T, Popenda M, Adamiak RW, Blazewicz J, Szachniuk M (2015) New in silico approach to assess RNA secondary structures with noncanonical base pairs, Machine Learning Reports 04/2015:13.
Szachniuk M, Sarzynska J, Blazewicz J (2013) Turning data into folds using RNAComposer, AIP Conference Proceedings 1559(1):353-354.
De Cola M, Felici G, Szachniuk M (2012) The Orderly Colored Longest Path Problem, CNR-IASI Technical Report 29/2012.
Szachniuk M, Popenda M, Antczak M, Purzycka KJ, Lukasiak P, Blazewicz J, Adamiak RW (2011) RNAComposer: the art of composing RNA structures, Machine Learning Reports 01/2011:26-29.
Zok T, Szachniuk M, Antczak M (2011) Comparison of RNA structures in torsional angle space, Machine Learning Reports 01/2011:14-18.
Szachniuk M, Popenda M, Popenda L (2009) Graphs in NMR analysis of RNAs, TU Clausthal Technical Report Series IfI-09-12:52-59.
Zok T, Popenda M, Szachniuk M (2008) Comparison of RNA structures – concepts and measures, TU Clausthal Technical Report Series IfI-08-03:42-44.
Blazewicz J, Adamiak RW, Lukasiak P, Popenda M, Szachniuk M, Antczak M, Palik G (2008) 3D-RNA-Pred: an automatic building of the three-dimensional RNA structures, TU Clausthal Technical Report Series IfI-08-03:45-48.
Szachniuk M, Radom M, Rybarczyk A, Formanowicz P, Blazewicz J (2008) From document processing to an identification of marine microorganisms’ habitat specificity, TU Clausthal Technical Report Series IfI-08-03:61-63.
Szachniuk M, Popenda M, Popenda L, Blazewicz J (2008) Constructing transfer pathways in multidimensional NMR spectra of RNAs, RECOMB’08 poster book, 62-63.
Szachniuk M, Blazewicz M, Popenda M, Adamiak RW (2008) On the design of RNA fragments structural database, RECOMB’08 poster book, 18-19.
Szachniuk M, Popenda M, Klemczak S, Blazewicz J (2007) An analysis of three-dimensional NMR spectra in RNA structure determination process, Research report RA-001/2007, Poznan Supercomputing and Networking Center.
Blazewicz M, Popenda M, Adamiak RW, Szachniuk M (2007) Project of RNA fragments database, TU Clausthal Technical Report Series IfI-07-03:25-27.
Szachniuk M, Popenda M, Popenda L (2007) Strategies of signal assignment in NMR spectra of RNAs with different structural motifs, TU Clausthal Technical Report Series IfI-07-03:12-14.
Paczkowski W, Milawski M, Popenda L, Szachniuk M (2007) A new tool for fundamental analysis of NMR spectra, TU Clausthal Technical Report Series IfI-07-03:8-11.
Szachniuk M, Adamiak RW, Formanowicz P, Gdaniec Z, Kasprzak M, Popenda M, Blazewicz J (2003) A combinatorial analysis of 2D NMR spectra of RNA duplexes, Currents in Computational Molecular Biology, 345-346.
Monographs
Szachniuk M (2005) Combinatorial Analysis of 2D-NOESY Spectra in Nuclear Magnetic Resonance Spectroscopy of RNA Molecules, PhD thesis, Institute of Computing Science, Poznan University of Technology. (pdf)
Szachniuk M (1999) Selected problems of contemporary topology, MSc thesis, Institute of Mathematics, Poznan University of Technology.
Szachniuk M (1998) Optical character recognition – analysis of methods, MSc thesis, Institute of Computing Science, Poznan University of Technology.
Patents
Szachniuk M, Popenda M, Adamiak RW, Blazewicz J (2004) 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)
Blazewicz J, Szachniuk M, Szostak N, Weber GW (2014) Historic Venue for a Young Group of an Emerging Field, IFORS NEWS 8(3):9.
Szostak N, Szachniuk M (2014) CBBM 2014: Badania operacyjne, biologia i medycyna w palacowych salonach, Glos Politechniki 4(182):20-21.
Szachniuk M (2010) Gora nasi, czyli bioinformatycy z Politechniki Poznanskiej w Ustroniu, Glos Politechniki 10(154):14-15.