Marta Szachniuk

41 papers C 4Journal 37

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Detecting polynucleotide motifs: Pentads, hexads, and beyond. PLoS Comput. Biol. Michal Zurkowski, Maja Marusic, Dorota Gudanis-Sobocinska, Marta Szachniuk
2025	J	`jnl`	Graph neural network and diffusion model for modeling RNA interatomic interactions. Bioinform. Marek Justyna, Craig L. Zirbel, Maciej Antczak, Marta Szachniuk
2025	C	`conf`	OR for the Nanoworld: Insights into RNA Structure Modeling. ICORES Marta Szachniuk
2025	J	`jnl`	RNAtive to recognize native-like structure in a set of RNA 3D models. Bioinform. Jan Pielesiak, Maciej Antczak, Marta Szachniuk, Tomasz Zok
2025	J	`jnl`	Unknotting RNA: A method to resolve computational artifacts. PLoS Comput. Biol. Simón Poblete, Mikolaj Mlynarczyk, Marta Szachniuk
2024	J	`jnl`	Knotted artifacts in predicted 3D RNA structures. PLoS Comput. Biol. Bartosz Ambrozy Gren, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk
2024	J	`jnl`	RNAtango: Analysing and comparing RNA 3D structures via torsional angles. PLoS Comput. Biol. Marta Mackowiak, Bartosz Adamczyk, Marta Szachniuk, Tomasz Zok
2023	J	`jnl`	High-quality, customizable heuristics for RNA 3D structure alignment. Bioinform. Michal Zurkowski, Maciej Antczak, Marta Szachniuk
2023	J	`jnl`	Machine learning for RNA 2D structure prediction benchmarked on experimental data. Briefings Bioinform. Marek Justyna, Maciej Antczak, Marta Szachniuk
2023	J	`jnl`	WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. Nucleic Acids Res. Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok
2022	J	`jnl`	DrawTetrado to create layer diagrams of G4 structures. Bioinform. Michal Zurkowski, Tomasz Zok, Marta Szachniuk
2022	J	`jnl`	ONQUADRO: a database of experimentally determined quadruplex structures. Nucleic Acids Res. Tomasz Zok, Natalia Kraszewska, Joanna Miskiewicz, Paulina Pielacinska, Michal Zurkowski, Marta Szachniuk
2022	J	`jnl`	RNAloops: a database of RNA multiloops. Bioinform. Jakub Wiedemann, Jacek Kaczor, Maciej Milostan, Tomasz Zok, Jacek Blazewicz, Marta Szachniuk, Maciej Antczak
2022	J	`jnl`	RNAsolo: a repository of cleaned PDB-derived RNA 3D structures. Bioinform. Bartosz Adamczyk, Maciej Antczak, Marta Szachniuk
2022	J	`jnl`	RNAspider: a webserver to analyze entanglements in RNA 3D structures. Nucleic Acids Res. Kamil Luwanski, Vladyslav Hlushchenko, Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Daniil Martsich, Marta Szachniuk, Maciej Antczak
2021	J	`jnl`	How bioinformatics resources work with G4 RNAs. Briefings Bioinform. Joanna Miskiewicz, Joanna Sarzynska, Marta Szachniuk
2021	J	`jnl`	Virxicon: a lexicon of viral sequences. Bioinform. Mateusz Kudla, Kaja Gutowska, Jaroslaw Synak, Mirko Weber, Katrin Sophie Bohnsack, Piotr Lukasiak, Thomas Villmann, Jacek Blazewicz, Marta Szachniuk
2020	J	`jnl`	ElTetrado: a tool for identification and classification of tetrads and quadruplexes. BMC Bioinform. Tomasz Zok, Mariusz Popenda, Marta Szachniuk
2020	J	`jnl`	Topology-based classification of tetrads and quadruplex structures. Bioinform. Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk
2019	J	`jnl`	RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. Bioinform. Maciej Antczak, Marcin Zablocki, Tomasz Zok, Agnieszka Rybarczyk, Jacek Blazewicz, Marta Szachniuk
2018	J	`jnl`	New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. Bioinform. Maciej Antczak, Mariusz Popenda, Tomasz Zok, Michal Zurkowski, Ryszard W. Adamiak, Marta Szachniuk
2018	J	`jnl`	RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. BMC Bioinform. Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk
2018	J	`jnl`	RNApdbee 2.0: multifunctional tool for RNA structure annotation. Nucleic Acids Res. Tomasz Zok, Maciej Antczak, Michal Zurkowski, Mariusz Popenda, Jacek Blazewicz, Ryszard W. Adamiak, Marta Szachniuk
2017	J	`jnl`	LCS-TA to identify similar fragments in RNA 3D structures. BMC Bioinform. Jakub Wiedemann, Tomasz Zok, Maciej Milostan, Marta Szachniuk
2016	J	`jnl`	Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine. RAIRO Oper. Res. Metin Türkay, Giovanni Felici, Marta Szachniuk, Piotr Lukasiak
2015	J	`jnl`	Building the Library of Rna 3D Nucleotide Conformations Using the Clustering Approach. Int. J. Appl. Math. Comput. Sci. Tomasz Zok, Maciej Antczak, Martin Riedel, David Nebel, Thomas Villmann, Piotr Lukasiak, Jacek Blazewicz, Marta Szachniuk
2015	J	`jnl`	New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinform. Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk
2015	J	`jnl`	Optimal pathway reconstruction on 3D NMR maps. Discret. Appl. Math. Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Dominique de Werra, Jacek Blazewicz
2015	J	`jnl`	RNAssess - a web server for quality assessment of RNA 3D structures. Nucleic Acids Res. Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, Marta Szachniuk, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz
2014	J	`jnl`	MCQ4Structures to compute similarity of molecule structures. Central Eur. J. Oper. Res. Tomasz Zok, Mariusz Popenda, Marta Szachniuk
2014	J	`jnl`	RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Res. Maciej Antczak, Tomasz Zok, Mariusz Popenda, Piotr Lukasiak, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk
2014	J	`jnl`	The Orderly Colored Longest Path Problem - a survey of applications and new algorithms. RAIRO Oper. Res. Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Jacek Blazewicz
2013	J	`jnl`	MLP accompanied beam search for the resonance assignment problem. J. Heuristics Marta Szachniuk, Mikolaj Malaczynski, Erwin Pesch, Edmund K. Burke, Jacek Blazewicz
2012	J	`jnl`	Poseidon: An information retrieval and extraction system for metagenomic marine science. Ecol. Informatics Marcin Radom, Agnieszka Rybarczyk, Renzo Kottmann, Piotr Formanowicz, Marta Szachniuk, Frank Oliver Glöckner, Dietrich Rebholz-Schuhmann, Jacek Blazewicz
2010	J	`jnl`	RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinform. Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K. Burke, Jacek Blazewicz, Ryszard W. Adamiak
2009	C	`conf`	An assignment walk through 3D NMR spectrum. CIBCB Marta Szachniuk, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz
2008	J	`jnl`	RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res. Mariusz Popenda, Marek Blazewicz, Marta Szachniuk, Ryszard W. Adamiak
2005	C	`conf`	NMR Analysis of RNA Bulged structures: Tabu Search Application in NOE Signal Assignment. CIBCB Marta Szachniuk, Lukasz Popenda, Zofia Gdaniec, Ryszard W. Adamiak, Jacek Blazewicz
2005	J	`jnl`	RNA tertiary structure determination: NOE pathways construction by tabu search. Bioinform. Jacek Blazewicz, Marta Szachniuk, Adam Wójtowicz
2004	J	`jnl`	An Algorithm for an Automatic NOE Pathways Analysis of 2D NMR Spectra of RNA Duplexes. J. Comput. Biol. Ryszard W. Adamiak, Jacek Blazewicz, Piotr Formanowicz, Zofia Gdaniec, Marta Kasprzak, Mariusz Popenda, Marta Szachniuk
2004	C	`conf`	Evolutionary approach to NOE paths assignment in RNA structure elucidation. CIBCB Jacek Blazewicz, Marta Szachniuk, Adam Wójtowicz