{"id":98,"date":"2021-02-04T14:39:08","date_gmt":"2021-02-04T13:39:08","guid":{"rendered":"http:\/\/localhost\/mSzachniuk\/?page_id=98"},"modified":"2026-06-22T13:35:13","modified_gmt":"2026-06-22T11:35:13","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<h1 class=\"wp-block-heading\">Publications<\/h1>\n\n\n\nH-index: 26 (<a href=\"https:\/\/www.scopus.com\/authid\/detail.uri?authorId=55933445600\" target=\"_blank\" rel=\"noopener noreferrer\">Scopus<\/a>\/<a href=\"https:\/\/www.webofscience.com\/wos\/author\/rid\/N-1991-2014\" target=\"_blank\" rel=\"noopener noreferrer\">Web of Science<\/a>), 30 (<a href=\"http:\/\/scholar.google.pl\/citations?user=cm7tTlIAAAAJ\" target=\"_blank\" rel=\"noopener noreferrer\">Google Scholar<\/a>)\n<br><br>\n<div align=\"left\"><a href=\"#Editorial\">Editoral boards<\/a> | <a href=\"#Books 2\">Books &#038; book chapters<\/a> | <a href=\"#Papers\">Papers<\/a> | <a href=\"#Reports\">Scientific reports<\/a> | <a href=\"#Misc\">Monographs<\/a> | <a href=\"#Pate\">Patents<\/a> |<a href=\"#Reviewer\">Reviewer for journals<\/a> <\/div>\n\n<a name=\"Editorial\"><\/a>\n<h3>Editorial Boards<\/h3>\n<ul>\n<li><p align=\"justify\"><a href=\"https:\/\/academic.oup.com\/nar\/pages\/editorial_board\" target=\"_blank\" rel=\"noopener noreferrer\">Nucleic Acids Research<\/a> (since 2024)<\/p><\/li>\n\n<li><p align=\"justify\">European Journal of Operational Research &#8211; Guest Editor for the Special Issue: EURO 2024 Conference for European Journal of Operational Research<\/p><\/li>\n\n<li><p align=\"justify\">RAIRO Operations Research &#8211; Guest Editor for the Special Issue: Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine (RAIRO Operations Research 50(2), 2016; doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1051\/ro\/2015036\" rel=\"noopener noreferrer\">10.1051\/ro\/2015036<\/a>)<\/p><\/li>\n\n<\/ul>\n\n<a name=\"Books\"><\/a>\n<h3>Books, book chapters<\/h3>\n<ol reversed=\"\">\n<li><p align=\"justify\">\nAntczak M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2025<\/strong>) Toward increasing the credibility of RNA design, in Churkin A, Barash D (eds.) <em>RNA Design. Methods in Molecular Biology<\/em> 2847, Humana New York, NY, 137\u2013151 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1007\/978-1-0716-4079-1_9\" rel=\"noopener noreferrer\">10.1007\/978-1-0716-4079-1_9<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBiesiada M, Purzycka KJ, <u>Szachniuk M<\/u>, Blazewicz J, Adamiak RW (<strong>2016<\/strong>)\nAutomated RNA 3D structure prediction with RNAComposer, \nin Turner D, Mathews D (eds.) <em>RNA Structure Determination. Methods in Molecular Biology <\/em>1490, Humana Press, New York, NY, 199\u2013215 (doi:<a target=\"_blank\" href=\"http:\/\/link.springer.com\/protocol\/10.1007%2F978-1-4939-6433-8_13\" rel=\"noopener noreferrer\">10.1007\/978-1-4939-6433-8<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPurzycka KJ, Popenda M, <u>Szachniuk M<\/u>, Antczak M, Lukasiak P, Blazewicz J, Adamiak RW (<strong>2015<\/strong>)\nAutomated 3D RNA structure prediction using the RNAComposer method for riboswitches, in Chen S-J, Burke-Aguero DH (eds.) <em>Methods in Enzymology: Computational Methods for Understanding Riboswitches<\/em> 553, Academic Press, 3\u201334 (doi: <a target=\"blank\" href=\"http:\/\/dx.doi.org\/10.1016\/bs.mie.2014.10.050\" rel=\"noopener noreferrer\"> 10.1016\/bs.mie.2014.10.050<\/a>).\n<\/p><\/li>\n<\/ol>\n\n\n<a name=\"Papers\"><\/a>\n<h3>Peer reviewed papers<\/h3>\n<ol reversed=\"\">\n\n<!---<li><p align=\"justify\">\nAbel J, Zok T, Kaden M, Weber M, Reuss LV, Bohnsack KS, Justyna M, Antczak M, <u>Szachniuk M<\/u>, Villmann T (2025) Challenges in G4 structure prediction: a Machine Learning approach, <em>submitted<\/em>.\n<\/p><\/li>--->\n\n<li><p align=\"justify\">\nDziel D, Fidelis K, <u>Szachniuk M<\/u>, Antczak M (2026) <em>working paper<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMlynarczyk M, Poblete S, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (2026) <em>working paper<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nJustyna M, Rog K, Gorska A, Urbanski F, Pawlowski T, Skrzypczak B, Kelar P, Antczak M, <u>Szachniuk M<\/u> (2026) <em>working paper<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nCerny J, Justyna M, Biedermannova L, Antczak M, <u>Szachniuk M<\/u>, Schneider B (2026) <em>working paper<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAdamczyk B, <u>Szachniuk M<\/u>, Antczak M (2026) <em>working paper<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nHladki P, Stachowiak D, Justyna M, Antczak M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (2026) <em>working paper<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nKubis J, Boinski P, Antczak M, Figlerowicz MM, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Figiel M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (2026) BIOREDIS: rapid and customizable design of nucleic acid therapeutics, <em>submitted<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBelter A, Synak J, Mackowiak M, Kotowska-Zimmer A, Figlerowicz M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Olejniczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (2026) Machine learning-guided design of artificial microRNAs for targeted gene silencing, <em>submitted<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBernard C, Justyna M, Postic G, Antczak M, Tahi F<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (2026) Meta-scoring approach to curate synthetic RNA 3D structures: the RNA-SyntHub+ dataset, <em>submitted<\/em>.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPielesiak J, Niznik K, Snioszek P, Wachowski G, Zurawski M, Antczak M, <u>Szachniuk M<\/u>, Zok T (<strong>2026<\/strong>) RNApdbee 3.0: A unified web server for comprehensive RNA secondary structure annotation from 3D coordinates,  <em>Journal of Molecular Biology<\/em> 438():169795 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1016\/j.jmb.2026.169795\" rel=\"noopener noreferrer\"> 10.1016\/j.jmb.2026.169795<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAdamczyk B, Boinski P, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2026<\/strong>) RNAsolo 2.0: multimodal database to study RNAs, their structural families and intermolecular interfaces, <em>Journal of Molecular Biology<\/em> 438():169570 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1016\/j.jmb.2025.169570\" rel=\"noopener noreferrer\"> 10.1016\/j.jmb.2025.169570<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nGumna-Mikina J, Andrzejewska-Romanowska A, Antczak M, Tykwinska E, <u>Szachniuk M<\/u>, Pachulska-Wieczorek K (<strong>2026<\/strong>) A retroelement-derived mammalian Arc protein exhibits selective RNA recognition and nucleic acid chaperone functions, <em>Nucleic Acids Research<\/em> 54(5):gkag207 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkag207\" rel=\"noopener noreferrer\">10.1093\/nar\/gkag207<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nWeber M, Erichson F, Antczak M, Schumann V, Meitzner J, Zok T, Steffen FD, <u>Szachniuk M<\/u>, Borner R (<strong>2026<\/strong>) FRET-guided selection of RNA 3D structures, <em>Nucleic Acids Research<\/em> 54(5):gkag147 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkag147\" rel=\"noopener noreferrer\">10.1093\/nar\/gkag147<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPielesiak J, Antczak M, <u>Szachniuk M<\/u>, Zok T (<strong>2025<\/strong>) RNAtive to recognize native-like structure in a set of RNA 3D models, <em>Bioinformatics<\/em> 41(11):btaf601 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf601\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btaf601<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZurkowski M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Marusic M, Gudanis-Sobocinska D, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2025<\/strong>) Detecting polynucleotide motifs: pentads, hexads, and beyond, <em>PLoS Computational Biology<\/em> 21(10):e1013633 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1013633\" rel=\"noopener noreferrer\">10.1371\/journal.pcbi.1013633<\/a>).\n\n<\/p><\/li>\n\n<li><p align=\"justify\">\nJustyna M, Zirbel CL, Antczak M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2025<\/strong>) Graph Neural Network and Diffusion Model for modeling RNA interatomic interactions, <em>Bioinformatics<\/em> 41(9):btaf515 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf515\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btaf515<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nLudwiczak O, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2025<\/strong>) Assessing interface accuracy in macromolecular complexes, <em>PLoS ONE<\/em> 20(4):e0319917 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1371\/journal.pone.0319917\" rel=\"noopener noreferrer\">10.1371\/journal.pone.0319917<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPoblete S<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Mlynarczyk M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2025<\/strong>) Unknotting RNA: a method to resolve computational artifacts, <em>PLoS Computational Biology<\/em> 21(3):e1012843 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1012843\" rel=\"noopener noreferrer\">10.1371\/journal.pcbi.1012843<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBu F, Adam Y, 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 WK, DiMaio F, Ding F, Dock-Bregeon A-C, Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferr\u00e9-D\u2019Amar\u00e9 AR, Geniesse C, Ghanim GE, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC, Kurcinski M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN, Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, <u>Szachniuk M<\/u>, Townshend R, Trachman III RJ, Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J, Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T, Zhang D, Zhang S, Zyla A, Westhof E, Miao Z (<strong>2025<\/strong>) RNA-Puzzles Round V: blind predictions of 23 RNA structures, <em>Nature Methods<\/em> 22:399\u2013411 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1038\/s41592-024-02543-9\" rel=\"noopener noreferrer\">10.1038\/s41592-024-02543-9<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMackowiak M, Adamczyk B, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Zok T<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2024<\/strong>) RNAtango: analysing and comparing RNA 3D structures via torsional angles, <em>PLoS Computational Biology<\/em> 20(10):e1012500 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1012500\" rel=\"noopener noreferrer\">10.1371\/journal.pcbi.1012500<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nGren BA, Antczak M, Zok T, Sulkowska JI<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2024<\/strong>) Knotted artifacts in predicted 3D RNA structures, <em>PLoS Computational Biology<\/em> 20(6):e1011959 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1011959\" rel=\"noopener noreferrer\">10.1371\/journal.pcbi.1011959<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nWitek W, Ragin W, Tran HL, Po\u0142omska E, Podlewski M, Paw\u0142owicz A, Cioch-Binia\u015b A, Wo\u015b A, Andra\u0142oj\u0107 W, <u>Szachniuk M<\/u>, Ruszkowski M (<strong>2024<\/strong>) Post\u0119py biologii strukturalnej \u2013 jak zobaczy\u0107 cz\u0105steczki \u017cycia?, <em>Post\u0119py Biochemii<\/em> 70(2):128\u2013138 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.18388\/pb.2021_533\" rel=\"noopener noreferrer\">10.18388\/pb.2021_533<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZurkowski M, Swiercz M, Wozny F, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2024<\/strong>) RNAhugs web server for customized 3D RNA structure alignment, <em>Nucleic Acids Research<\/em> 52(W1):W348\u2013W353 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkae259\" rel=\"noopener noreferrer\">10.1093\/nar\/gkae259<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nSchneider B, Sweeney B, Bateman A, Cerny J, Zok T, <u>Szachniuk M<\/u> (<strong>2023<\/strong>) When will RNA get its AlphaFold moment?, <em>Nucleic Acids Research<\/em> 51(18):9522\u20139532 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkad726\" rel=\"noopener noreferrer\">10.1093\/nar\/gkad726<\/a>).<\/p><\/li>\n\n<li><p align=\"justify\">\nSarzynska J, Popenda M, Antczak M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2023<\/strong>) RNA tertiary structure prediction using RNAComposer in CASP15, <em>PROTEINS: Structure, Function, and Bioinformatics<\/em> 91(12):1790\u20131799 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1002\/prot.26578\" rel=\"noopener noreferrer\">10.1002\/prot.26578<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nKryshtafovych A, Antczak M, <u>Szachniuk M<\/u>, 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 (<strong>2023<\/strong>) New prediction categories in CASP15, <em>PROTEINS: Structure, Function, and Bioinformatics<\/em> 91(12):1550\u20131557 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1002\/prot.26515\" rel=\"noopener noreferrer\">10.1002\/prot.26515<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZurkowski M, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2023<\/strong>) High-quality, customizable heuristics for RNA 3D structure alignment, <em>Bioinformatics<\/em> 39(5):btad315 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btad315\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btad315<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAdamczyk B, Zurkowski M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Zok T<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2023<\/strong>) WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures, <em>Nucleic Acids Research<\/em> 51(W1):W607\u2013W612 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkad346\" rel=\"noopener noreferrer\">10.1093\/nar\/gkad346<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nJustyna M, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2023<\/strong>) Machine learning for RNA 2D structure prediction benchmarked on experimental data, <em>Briefings in Bioinformatics<\/em> 24(3):bbad153 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bib\/bbad153\" rel=\"noopener noreferrer\">110.1093\/bib\/bbad153<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nWiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2022<\/strong>) RNAloops: a database of RNA multiloops, <em>Bioinformatics<\/em> 38(17):4200\u20134205 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btac484\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btac484<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nGumna 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<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u>, Rybarczyk A<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2022<\/strong>) Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models, <em>International Journal of Molecular Sciences<\/em> 23(17):9630 (doi: <a target=\"_blank\" href=\"https:\/\/doi.org\/10.3390\/ijms23179630\" rel=\"noopener noreferrer\">10.3390\/ijms23179630<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZurkowski M, Zok T, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2022<\/strong>) DrawTetrado to create layer diagrams of G4 structures, <em>Bioinformatics<\/em> 38(15):3835\u20133836 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btac394\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btac394<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAdamczyk B, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2022<\/strong>) RNAsolo: a repository of cleaned PDB-derived RNA 3D structures, <em>Bioinformatics<\/em> 38(14):3668\u20133670 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btac386\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btac386<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nLuwanski K, Hlushchenko V, Popenda M, Zok T, Sarzynska J, Martsich D, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Antczak M<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2022<\/strong>) RNAspider: a webserver to analyze entanglements in RNA 3D structures, <em>Nucleic Acids Research<\/em> 50(W1):W663\u2013W669 (doi:<a target=\"_blank\" href=\"https:\/\/dx.doi.org\/10.1093\/nar\/gkac218\" rel=\"noopener noreferrer\">10.1093\/nar\/gkac218<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nCarrascoza F, Antczak M, Miao Z, Westhof E, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2022<\/strong>) Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions, <em>RNA<\/em> 28(2):250\u2013262 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1261\/rna.078685.121\" rel=\"noopener noreferrer\">10.1261\/rna.078685.121<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, Kraszewska N, Miskiewicz J, Pielacinska P, Zurkowski M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2022<\/strong>) ONQUADRO: a database of experimentally determined quadruplex structures, <em>Nucleic Acids Research<\/em> 50(D1):D253\u2013D258 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkab1118\" rel=\"noopener noreferrer\">10.1093\/nar\/gkab1118<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBelter A, Popenda M, Sajek M, Wozniak T, Naskret-Barciszewska MZ, <u>Szachniuk M<\/u>, Jurga S, Barciszewski J (<strong>2022<\/strong>) A new molecular mechanism of RNA circularization and the microRNA sponge formation, <em>Journal of Biomolecular Structure and Dynamics<\/em> 40(7):3038\u20133045 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1080\/07391102.2020.1844802\" rel=\"noopener noreferrer\">10.1080\/07391102.2020.1844802<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPopenda M, Zok T, Sarzynska J, Korpeta A, Adamiak RW, Antczak M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2021<\/strong>) Entanglements of structure elements revealed in RNA 3D models, <em>Nucleic Acids Research<\/em> 49(17):9625\u20139632 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkab716\" rel=\"noopener noreferrer\">10.1093\/nar\/gkab716<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMiskiewicz J, Sarzynska J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2021<\/strong>) How bioinformatics resources work with G4 RNAs, <em>Briefings in Bioinformatics<\/em> 22(3):bbaa201 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bib\/bbaa201\" rel=\"noopener noreferrer\">10.1093\/bib\/bbaa201<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nKudla M, Gutowska K, Synak J, Weber M, Bohnsack KS, Lukasiak P, Villmann T, Blazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2020<\/strong>) Virxicon: a lexicon of viral sequences, <em>Bioinformatics<\/em> 36(22-23):5507\u20135513 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa1066\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btaa1066<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nLehmann TP<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Miskiewicz J, Szostak N, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Grodecka-Gazdecka S, Jagodzinski PP (<strong>2020<\/strong>) In vitro and in silico analysis of miR-125a with rs12976445 polymorphism in breast cancer patients, <em>Applied Sciences<\/em> 10(20):7275 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.3390\/app10207275\" rel=\"noopener noreferrer\">10.3390\/app10207275<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nGumna J, Zok T, Figurski K, Pachulska-Wieczorek K<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2020<\/strong>) RNAthor &#8211; fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis, <em>PLOS ONE<\/em> 15(10):e0239287 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1371\/journal.pone.0239287\" rel=\"noopener noreferrer\">10.1371\/journal.pone.0239287<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMiao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, \nDing F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piatkowski P, Pluta R, \nPopenda M, Sarzynska J, Sun L, <u>Szachniuk M<\/u>, Tian S, Wang J, Watkins AM, Wiedemann J, Xu X, Yesselman JD, \nZhang 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, \nPatel DJ, Westhof E (<strong>2020<\/strong>) RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, <em>RNA<\/em> 26(8):982\u2013995 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1261\/rna.075341.120\" rel=\"noopener noreferrer\">10.1261\/rna.075341.120<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, Popenda M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2020<\/strong>) ElTetrado: a tool for identification and classification of tetrads and quadruplexes, <em>BMC Bioinformatics<\/em> 21:40 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1186\/s12859-020-3385-1\" rel=\"noopener noreferrer\">10.1186\/s12859-020-3385-1<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPopenda M, Miskiewicz J, Sarzynska J, Zok T, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2020<\/strong>) Topology-based classification of tetrads and quadruplex structures, <em>Bioinformatics<\/em> 36(4):1129\u20131134 (doi:<a target=\"_blank\" href=\"http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btz738\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btz738<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMagnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Miao Z<sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2020<\/strong>) RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools, <em>Nucleic Acids Research<\/em> 48(2):576\u2013588 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkz1108\" rel=\"noopener noreferrer\">10.1093\/nar\/gkz1108<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2019<\/strong>) RNApolis: computational platform for RNA structure analysis, <em>Foundations of Computing and Decision Sciences<\/em> 44(2):241\u2013257 \n(doi:<a target=\"_blank\" href=\"http:\/\/dx.doi.org\/10.2478\/fcds-2019-0012\" rel=\"noopener noreferrer\">10.2478\/fcds-2019-0012<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAntczak M, Zablocki M, Zok T, Rybarczyk A, Blazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2019<\/strong>) RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs, <em>Bioinformatics<\/em> 35(1):152\u2013155 \n(doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/bty609\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/bty609<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAntczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2018<\/strong>) RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures, <em>BMC Bioinformatics<\/em> 19(1):304 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1186\/s12859-018-2317-9\" rel=\"noopener noreferrer\">10.1186\/s12859-018-2317-9<\/a>). \n<\/p><\/li>\n\n<li><p align=\"justify\">\nMiskiewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2018<\/strong>) Discovering structural motifs in miRNA precursors from Viridiplantae kingdom, <em>Molecules<\/em> 23(6):1367 (doi:<a target=\"_blank\" href=\"http:\/\/www.mdpi.com\/1420-3049\/23\/6\/1367\" rel=\"noopener noreferrer\">10.3390\/molecules23061367<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, Antczak M, Zurkowski M, Popenda M, Blazewicz J, Adamiak RW, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2018<\/strong>) RNApdbee 2.0: multifunctional tool for RNA structure annotation, <em>Nucleic Acids Research<\/em> 46(W1):W30\u2013W35 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gky314\" rel=\"noopener noreferrer\">10.1093\/nar\/gky314<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAntczak M, Popenda M, Zok T, Zurkowski M, Adamiak RW, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2018<\/strong>) New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation, <em>Bioinformatics<\/em> 34(8):1304\u20131312 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btx783\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/btx783<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nWiedemann J, Zok T, Milostan M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2017<\/strong>) LCS-TA to identify similar fragments in RNA 3D structures, <em>BMC Bioinformatics<\/em> 18:456 (doi:<a target=\"_blank\" href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1867-6\" rel=\"noopener noreferrer\">10.1186\/s12859-017-1867-6<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMiao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, \nChou FC, Ferre-D&#8217;Amare AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, \nKladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, \nPopenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, <u>Szachniuk M<\/u>, Tandon A, Trausch JJ, \nTian S, Wang J, Weeks KM, Williams II B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E (<strong>2017<\/strong>) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme, <em>RNA<\/em> 23(5):655\u2013672 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1261\/rna.060368.116\" rel=\"noopener noreferrer\">10.1261\/rna.060368.116<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMiskiewicz J, Tomczyk K, Mickiewicz A, Sarzynska J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2017<\/strong>) Bioinformatics study of structural patterns in plant microRNA precursors, <em>BioMed Research International<\/em> 2017:6783010  (doi:<a target=\"_&quot;blank&quot;\" href=\"https:\/\/www.hindawi.com\/journals\/bmri\/2017\/6783010\/\" rel=\"noopener noreferrer\">10.1155\/2017\/6783010<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAntczak M, Popenda M, Zok T, Sarzynska J, Ratajczak T, Tomczyk K, Adamiak RW, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2016<\/strong>) New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure, <em>Acta Biochimica Polonica<\/em> 63(4):737\u2013744 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.18388\/abp.2016_1329\" rel=\"noopener noreferrer\">10.18388\/abp.2016_1329<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nTurkay M, Felici G, <u>Szachniuk M<\/u>, Lukasiak P (<strong>2016<\/strong>) Recent advances in operations research in computational biology, bioinformatics and medicine, <em>RAIRO &#8211; Operations Research<\/em> 50(2):327\u2013330 (doi:<a target=\"_blank\" href=\"http:\/\/dx.doi.org\/10.1051\/ro\/2015036\" rel=\"noopener noreferrer\">10.1051\/ro\/2015036<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nRybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak RW, Blazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2015<\/strong>) New in silico approach to assessing RNA secondary structures with non-canonical base pairs, <em>BMC Bioinformatics<\/em> 16:276 (doi:<a target=\"_blank\" href=\"http:\/\/www.biomedcentral.com\/1471-2105\/16\/276\" rel=\"noopener noreferrer\">10.1186\/s12859-015-0718-6<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nLukasiak P, Antczak M, Ratajczak T, <u>Szachniuk M<\/u>, Popenda M, Adamiak RW, Blazewicz J (<strong>2015<\/strong>) RNAssess &#8211; a webserver for quality assessment of RNA 3D structures, <em>Nucleic Acids Research<\/em> 43(W1):W502\u2013W506 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkv557\" rel=\"noopener noreferrer\">10.1093\/nar\/gkv557<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, Antczak M, Riedel M, Nebel D, Villmann T, Lukasiak P, Blazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2015<\/strong>) Building the library of RNA 3D nucleotide conformations using clustering approach, <em>International Journal of Applied Mathematics and Computer Science<\/em> 25(3):689\u2013700 (doi:<a target=\"_blank\" href=\"https:\/\/www.amcs.uz.zgora.pl\/?action=paper&amp;paper=852\" rel=\"noopener noreferrer\">10.1515\/amcs-2015-0050<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nMiao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, \nCruz JA, Ferre-D&#8217;Amare AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, \nMagnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, \nStasiewicz J, <u>Szachniuk M<\/u>, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E (<strong>2015<\/strong>) RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures, <em>RNA<\/em> 21(6):1066\u20131084 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1261\/rna.049502.114\" rel=\"noopener noreferrer\">10.1261\/rna.049502.114<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2015<\/strong>) Assigning NMR Spectra of Irregular RNAs by Heuristic Algorithms, <em>Bulletin of the Polish Academy of Sciences Technical Sciences<\/em> 63(1):329\u2013338 (doi:<a target=\"_blank\" href=\"http:\/\/www.degruyter.com\/view\/j\/bpasts.2015.63.issue-1\/bpasts-2015-0037\/bpasts-2015-0037.xml?format=INT\" rel=\"noopener noreferrer\">10.1515\/bpasts-2015-0037<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, De Cola MC, Felici G, de Werra D, Blazewicz J (<strong>2015<\/strong>) Optimal pathway reconstruction on 3D NMR maps, <em>Discrete Applied Mathematics<\/em> 182:134\u2013149 (doi:<a target=\"_blank\" href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0166218X1400170X\" rel=\"noopener noreferrer\">10.1016\/j.dam.2014.04.010<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nSzostak N, Royo F, Rybarczyk A, <u>Szachniuk M<\/u>, Blazewicz J, del Sol A, Falcon-Perez JM (<strong>2014<\/strong>) Sorting signal targeting mRNA into hepatic extracellular vesicles, <em>RNA Biology<\/em> 11(7):836\u2013844 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.4161\/rna.29305\" rel=\"noopener noreferrer\">10.4161\/rna.29305<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAntczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2014<\/strong>) RNApdbee &#8211; a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs, <em>Nucleic Acids Research<\/em> 42(W1):W368\u2013W372 (doi:<a href=\"https:\/\/doi.org\/10.1093\/nar\/gku330\" target=\"blank\" rel=\"noopener noreferrer\">10.1093\/nar\/gku330<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, De Cola MC, Felici G, Blazewicz J (<strong>2014<\/strong>) The Orderly Colored Longest Path Problem &#8211; a survey of applications and new algorithms, <em>RAIRO &#8211; Operations Research<\/em> 48(1):25\u201351 (doi:<a target=\"blank\" href=\"https:\/\/doi.org\/10.1051\/ro\/2013046\" rel=\"noopener noreferrer\">10.1051\/ro\/2013046<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, Popenda M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2014<\/strong>) MCQ4Structures to compute similarity of molecule structures, <em>Central European Journal of Operations Research<\/em> 22(3):457\u2013474 (doi:<a target=\"blank\" href=\"http:\/\/link.springer.com\/article\/10.1007%2Fs10100-013-0296-5\" rel=\"noopener noreferrer\">10.1007\/s10100-013-0296-5<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Malaczynski M, Pesch E, Burke EK, Blazewicz J (<strong>2013<\/strong>) MLP accompanied beam search for the resonance assignment problem, <em>Journal of Heuristics<\/em> 19(3):443\u2013464 (doi:<a target=\"blank\" href=\"http:\/\/link.springer.com\/article\/10.1007\/s10732-013-9220-3\" rel=\"noopener noreferrer\">10.1007\/s10732-013-9220-3<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nLukasiak P, Antczak M, Ratajczak T, Bujnicki JM, <u>Szachniuk M<\/u>, Popenda M, Adamiak RW, Blazewicz J (<strong>2013<\/strong>) RNAlyzer \u2013 novel approach for quality analysis of RNA structural models, <em>Nucleic Acids Research<\/em> 41(12):5978\u20135990 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkt318\" rel=\"noopener noreferrer\">10.1093\/nar\/gkt318<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPopenda M, <u>Szachniuk M<\/u>, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW (<strong>2012<\/strong>) Automated 3D structure composition for large RNAs, <em>Nucleic Acids Research<\/em> 40(14):e112 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gks339\" rel=\"noopener noreferrer\">10.1093\/nar\/gks339<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nRadom M, Rybarczyk A, Kottmann R, Formanowicz P, <u>Szachniuk M<\/u>, Gloeckner FO, Rebholz-Schuhmann D, Blazewicz J (<strong>2012<\/strong>) Poseidon: an information retrieval and extraction system for metagenomic marine science, <em>Ecological Informatics<\/em> 12:10\u201315 (doi:<a target=\"_blank\" href=\"http:\/\/dx.doi.org\/10.1016\/j.ecoinf.2012.07.003\" rel=\"noopener noreferrer\">10.1016\/j.ecoinf.2012.07.003<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nRadom M, Kottmann R, Rybarczyk A, Formanowicz P, <u>Szachniuk M<\/u>, Gloeckner FO, Blazewicz J (<strong>2010<\/strong>) Cerberus: a new information retrieval tool for marine metagenomics, <em>Foundations of Computing and Decision Sciences<\/em> 35(2):107\u2013126.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPopenda M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW (<strong>2010<\/strong>) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, \n<em>BMC Bioinformatics<\/em> 11:231 (doi:<a target=\"_blank\" href=\"http:\/\/www.biomedcentral.com\/1471-2105\/11\/231\" rel=\"noopener noreferrer\">10.1186\/1471-2105-11-231<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Popenda M, Adamiak RW, Blazewicz J (<strong>2009<\/strong>) An assignment walk through 3D NMR spectrum, <em>Proceedings of the 2009 IEEE Symposium on Computational Intelligence\nin Bioinformatics and Computational Biology<\/em>, 215\u2013219 (doi:10.1109\/CIBCB.2009.4925731).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPopenda M, Blazewicz M, <u>Szachniuk M<\/u>, Adamiak RW (<strong>2008<\/strong>) RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures, <em>Nucleic Acids Research<\/em> 36(D1):D386\u2013D391 \n(doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/nar\/gkm786\" rel=\"noopener noreferrer\">10.1093\/nar\/gkm786<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBlazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Wojtowicz A (<strong>2005<\/strong>) RNA tertiary structure determination: NOE pathway construction by tabu search, <em>Bioinformatics<\/em> 21(10):2356\u20132361 (doi:<a target=\"_blank\" href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/bti351\" rel=\"noopener noreferrer\">10.1093\/bioinformatics\/bti351<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Popenda L, Gdaniec Z, Adamiak RW, Blazewicz J (<strong>2005<\/strong>) NMR analysis of RNA bulged structures: tabu search application in NOE signal assignment, <em>Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology<\/em>, 172\u2013178 (doi:10.1109\/CIBCB.2005.1594914).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBlazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Wojtowicz A (<strong>2004<\/strong>) Evolutionary approach to NOE paths assignment in RNA structure elucidation, <em>Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology<\/em>, 206\u2013213 (doi:10.1109\/CIBCB.2004.1393955).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBlazewicz J, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup>, Wojtowicz A (<strong>2004<\/strong>) Evolutionary algorithm for a reconstruction of NOE paths in NMR spectra of RNA chains, <em>Bulletin of the Polish Academy of Sciences Technical Sciences<\/em> 52(3):221\u2013230 (<a target=\"_blank\" href=\"https:\/\/journals.pan.pl\/dlibra\/publication\/128178\/edition\/111826\/content\/evolutionary-algorithm-for-a-reconstruction-of-noe-paths-in-nmr-spectra-of-rna-chains-blazewicz-j-szachniuk-m-wojtowicz-a?language=en\" rel=\"noopener noreferrer\">paper<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nAdamiak RW, Blazewicz J, Formanowicz P, Gdaniec Z, Kasprzak M, Popenda M, <u>Szachniuk M<\/u><sup><img decoding=\"async\" src=\"..\/wp-content\/uploads\/2021\/02\/envelope.jpg\"><\/sup> (<strong>2004<\/strong>) An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes, <em>Journal of Computational Biology<\/em> 11(1):163\u2013180 (doi:<a target=\"_blank\" href=\"http:\/\/online.liebertpub.com\/doi\/abs\/10.1089\/106652704773416948\" rel=\"noopener noreferrer\">10.1089\/106652704773416948<\/a>).\n<\/p><\/li>\n<\/ol>\n\n\n\n<a name=\"Reports\"><\/a>\n<h3>Scientific reports, abstracts and short peer reviewed papers<\/h3>\n<ol reversed=\"\">\n\n<li><p align=\"justify\">\nGumna 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, <u>Szachniuk M<\/u>, Miao Z, Rybarczyk A (<strong>2022<\/strong>), Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions, (<a target=\"_blank\" href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2021.12.17.473170v1\" rel=\"noopener noreferrer\">bioRxiv<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Popenda M, Zok T (<strong>2019<\/strong>) ElTetrado captures topological features of nucleic acid quadruplexes, <em>F1000Research<\/em> 8(ISCB Comm J):1973 (poster) (doi: <a target=\"_blank&quot;\" href=\"https:\/\/f1000research.com\/posters\/8-1973\" rel=\"noopener noreferrer\">10.7490\/f1000research.1117688.1<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Blazewicz J (<strong>2018<\/strong>) Virtual RNA biology: from sequence to high quality 3D structure model, <em>Proceedings of IASTEM International Conference<\/em>, 9-11.<\/p><\/li>\n\n<li><p align=\"justify\">\nKowalska JA, Tomczyk K, Sarzynska J, <u>Szachniuk M<\/u> (<strong>2016<\/strong>) Bioinformatic analysis of motifs in microRNA vicinity in plants, <em>Acta Biochimica Polonica 63(2) Supplement<\/em>, 173 (<a taget=\"_blank\" href=\"http:\/\/www.actabp.pl\/pdf\/Supl2_16\/Session_20.pdf\">on-line<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nCeranek P, Zok T, Antczak A, <u>Szachniuk M<\/u> (<strong>2015<\/strong>) RNAsprite &#8211; a concept of tool to calculate RNA structural data, <em>Machine Learning Reports<\/em> 04\/2015:14 (<a taget=\"_blank\" href=\"http:\/\/www.techfak.uni-bielefeld.de\/~fschleif\/mlr\/mlr_04_2015.pdf\">on-line<\/a>).\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, Antczak M, Riedel M, Nebel D, Villmann T, Lukasiak P, Blazewicz J, <u>Szachniuk M<\/u> (<strong>2015<\/strong>) Clustering approach to create libraries of representative RNA conformers, <em>Machine Learning Reports<\/em> 04\/2015:18.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nSzostak N, Rybarczyk A, Antczak M, Zok T, Popenda M, Adamiak RW, Blazewicz J, <u>Szachniuk M<\/u> (<strong>2015<\/strong>) New in silico approach to assess RNA secondary structures with noncanonical base pairs, <em>Machine Learning Reports<\/em> 04\/2015:13.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Sarzynska J, Blazewicz J (<strong>2013<\/strong>) Turning data into folds using RNAComposer, <em>AIP Conference Proceedings<\/em> 1559(1):353-354.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nDe Cola M, Felici G, <u>Szachniuk M<\/u> (<strong>2012<\/strong>) The Orderly Colored Longest Path Problem, <em>CNR-IASI Technical Report<\/em> 29\/2012.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Popenda M, Antczak M, Purzycka KJ, Lukasiak P, Blazewicz J, Adamiak RW (<strong>2011<\/strong>) RNAComposer: the art of composing RNA structures, <em>Machine Learning Reports<\/em> 01\/2011:26-29.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, <u>Szachniuk M<\/u>, Antczak M (<strong>2011<\/strong>) Comparison of RNA structures in torsional angle space, <em>Machine Learning Reports<\/em> 01\/2011:14-18.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Popenda M, Popenda L (<strong>2009<\/strong>) Graphs in NMR analysis of RNAs, <em>TU Clausthal Technical Report Series<\/em> IfI-09-12:52-59.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nZok T, Popenda M, <u>Szachniuk M<\/u> (<strong>2008<\/strong>) Comparison of RNA structures &#8211; concepts and measures, <em>TU Clausthal Technical Report Series<\/em> IfI-08-03:42-44.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBlazewicz J, Adamiak RW, Lukasiak P, Popenda M, <u>Szachniuk M<\/u>, Antczak M, Palik G (<strong>2008<\/strong>) 3D-RNA-Pred: an automatic building of the three-dimensional RNA structures, <em>TU Clausthal Technical Report Series<\/em> IfI-08-03:45-48.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Radom M, Rybarczyk A, Formanowicz P, Blazewicz J (<strong>2008<\/strong>) From document processing to an identification of marine microorganisms&#8217; habitat specificity, <em>TU Clausthal Technical Report Series<\/em> IfI-08-03:61-63.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Popenda M, Popenda L, Blazewicz J (<strong>2008<\/strong>) Constructing transfer pathways in multidimensional NMR spectra of RNAs, <em>RECOMB&#8217;08 poster book<\/em>, 62-63.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Blazewicz M, Popenda M, Adamiak RW (<strong>2008<\/strong>) On the design of RNA fragments structural database, <em>RECOMB&#8217;08 poster book<\/em>, 18-19.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Popenda M, Klemczak S, Blazewicz J (<strong>2007<\/strong>) An analysis of three-dimensional NMR spectra in RNA structure determination process, <em>Research report<\/em> RA-001\/2007, Poznan Supercomputing and Networking Center.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nBlazewicz M, Popenda M, Adamiak RW, <u>Szachniuk M<\/u> (<strong>2007<\/strong>) Project of RNA fragments database, <em>TU Clausthal Technical Report Series<\/em> IfI-07-03:25-27.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Popenda M, Popenda L (<strong>2007<\/strong>) Strategies of signal assignment in NMR spectra of RNAs with different structural motifs, <em>TU Clausthal Technical Report Series<\/em> IfI-07-03:12-14.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nPaczkowski W, Milawski M, Popenda L, <u>Szachniuk M<\/u> (<strong>2007<\/strong>) A new tool for fundamental analysis of NMR spectra, <em>TU Clausthal Technical Report Series<\/em> IfI-07-03:8-11.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Adamiak RW, Formanowicz P, Gdaniec Z, Kasprzak M, Popenda M, Blazewicz J (<strong>2003<\/strong>) A combinatorial analysis of 2D NMR spectra of RNA duplexes, <em>Currents in Computational Molecular Biology<\/em>, 345-346.\n<\/p><\/li>\n<\/ol>\n\n\n<a name=\"Misc\"><\/a>\n<h3>Monographs<\/h3>\n<ol reversed=\"\">\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u> (<strong>2005<\/strong>) Combinatorial Analysis of 2D-NOESY Spectra in Nuclear Magnetic Resonance Spectroscopy of RNA Molecules, <em>PhD thesis<\/em>, Institute of Computing Science, Poznan University of Technology. (<a target=\"_top\" href=\"..\/wp-content\/uploads\/2021\/02\/MXSphdthesis.pdf\" rel=\"noopener noreferrer\">pdf<\/a>)\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u> (<strong>1999<\/strong>) Selected problems of contemporary topology, <em>MSc thesis<\/em>, Institute of Mathematics, Poznan University of Technology.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u> (<strong>1998<\/strong>) Optical character recognition &#8211; analysis of methods, <em>MSc thesis<\/em>, Institute of Computing Science, Poznan University of Technology.\n<\/p><\/li>\n<\/ol>\n\n<a name=\"Pate\"><\/a>\n<h3>Patents<\/h3>\n<ol reversed=\"\">\n<li><p align=\"justify\">\nBelter A, Olejniczak M, Synak J, <u>Szachniuk M<\/u> (<strong>2025<\/strong>) Cz\u0105steczka kwasu nukleinowego do wyciszania ekspresji genu koduj\u0105cego bia\u0142ko TMPRSS-2, kaseta ekspresyjna, wektor ekspresyjny, kompozycja farmaceutyczna, cz\u0105steczka kwasu nukleinowego do zastosowania w terapii, cz\u0105steczka kwasu nukleinowego do zastosowania w leczeniu i\/lub profilaktyce choroby wirusowej zale\u017cnej od TMPRSS-2 oraz spos\u00f3b in vitro wyciszania ekspresji genu koduj\u0105cego bia\u0142ko TMPRSS-2 (Nucleic acid molecule for silencing the expression of the gene encoding the TMPRSS-2 protein, expression cassette, expression vector, pharmaceutical composition, nucleic acid molecule for use in therapy, nucleic acid molecule for use in the treatment and\/or prevention of TMPRSS-2-dependent viral disease, and method for in vitro silencing of the expression of the gene encoding the protein TMPRSS-2), P.452059, 16.05.2025, The Patent Office of the Republic of Poland.<\/p><\/li>\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u>, Popenda M, Adamiak RW, Blazewicz J (<strong>2004<\/strong>) Spos\u00f3b wyznaczania \u015bcie\u017cki przekazywania magnetyzacji \nmi\u0119dzy protonami H6\/H8-H1&#8217;na dwuwymiarowych widmach NOESY\nw spektroskopii magnetycznego rezonansu j\u0105drowego \nkwas\u00f3w nukleinowych (The method of an assignment of the magnetization transfer pathway between H6\/H8-H1&#8242; protons in the 2-dimensional NOESY spectra in Nuclear Magnetic Resonance spectroscopy of nucleic acids), P.364736, 03.02.2004, The Patent Office of the Republic of Poland.<\/p><\/li>\n<\/ol>\n\n<h3>Other works (posters, popular science &amp; non-scientific articles)<\/h3>\n<ol reversed=\"\">\n<li><p align=\"justify\">\nBlazewicz J, <u>Szachniuk M<\/u>, Szostak N, Weber GW (<strong>2014<\/strong>) Historic Venue for a Young Group of an Emerging Field, <em>IFORS NEWS<\/em> 8(3):9.\n<\/p><\/li>\n\n<li><p align=\"justify\">\nSzostak N, <u>Szachniuk M<\/u> (<strong>2014<\/strong>) CBBM 2014: Badania operacyjne, biologia i medycyna w palacowych salonach, <em>Glos Politechniki<\/em> 4(182):20-21.\n<\/p><\/li>\n\n<li><p align=\"justify\">\n<u>Szachniuk M<\/u> (<strong>2010<\/strong>) Gora nasi, czyli bioinformatycy z Politechniki Poznanskiej w Ustroniu, <em>Glos Politechniki<\/em> 10(154):14-15.\n<\/p><\/li>\n<\/ol>\n\n<a name=\"Reviewer\"><\/a>\n<h3>Reviewer for journals<\/h3>\nActa Crystallographica Section D Structural Biology &bull; \nAlgorithms for Molecular Biology &bull; \nAnnals of Operations Research &bull; \nBiochemistry and Biophysics Reports &bull;\nBioinformatics &bull; \nBioinformatics Advances &bull;\nBiology &bull; \nBiomedicines &bull; \nBiophysical Journal &bull; \nBiophysics Reviews &bull; \nBMC Bioinformatics &bull; \nBMC Musculoskeletal Disorders &bull; \nBMC Structural Biology &bull; \nBMC Supplements &bull; \nBriefings in Bioinformatics &bull; \nCentral European Journal of Operations Research (CJOR) &bull; \nChemical Communications &bull; \nCommunications Biology &bull; \nComputational and Structural Biotechnology Journal &bull; \nComputational Biology and Chemistry &bull; \nComputers &#038; Operations Research &bull; \nDiscrete Applied Mathematics &bull; \nEuropean Journal of Operational Research (EJOR) &bull; \nF1000Research &bull; \nFrontiers in Molecular Biosciences &bull; \nGenes &bull; \nGenome Research &bull;\nIEEE\/ACM Transactions on Computational Biology and Bioinformatics &bull; \nInternational Journal of Molecular Sciences &bull; \nInternational Journal of Optimization and Control: Theories &#038; Applications (IJOCTA) &bull; \nJournal of Chemical Information and Modeling &bull; \nJournal of Computational Biology &bull; \nJournal of Computer-Aided Molecular Design &bull; \nJournal of Medicinal Chemistry &bull; \nJournal of Personalized Medicine &bull; \nJournal of Scientific Research and Reports &bull; \nMolecular Diversity &bull;\nNature Communications &bull;\nNature Machine Intelligence &bull;\nNature Methods &bull;\nNAR Genomics and Bioinformatics &bull; \nNucleic Acids Research &bull; \nPLOS Computational Biology &bull; \nPLOS ONE &bull; \nPROTEINS: Structure, Function, and Bioinformatics &bull;\nRNA &bull; \nSoft Computing (SOCO) &bull; \nSource Code for Biology and Medicine &bull; \nTop &#8211; Journal of the Spanish Society of Statistics and Operations Research\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Publications H-index: 26 (Scopus\/Web of Science), 30 (Google Scholar) Editoral boards | Books &#038; book chapters | Papers | Scientific reports | Monographs | Patents |Reviewer for journals Editorial Boards Nucleic Acids Research (since 2024) European Journal of Operational Research &#8211; Guest Editor for the Special Issue: EURO 2024 Conference for European Journal of Operational [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"custom-page.php","meta":{"footnotes":""},"class_list":["post-98","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages\/98","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/comments?post=98"}],"version-history":[{"count":657,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages\/98\/revisions"}],"predecessor-version":[{"id":3129,"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/pages\/98\/revisions\/3129"}],"wp:attachment":[{"href":"https:\/\/www.cs.put.poznan.pl\/mszachniuk\/site\/wp-json\/wp\/v2\/media?parent=98"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}