Marta Szachniuk

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 18

Top Topics

Secondary Structure

Structural Motifs

Experimentally Determined

Machine Learning

Top Venues

Nucleic Acids Res.

RAIRO Oper. Res.

Publications

Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok
WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. Nucleic Acids Res. 51 (W1) (2023)
Michal Zurkowski, Maciej Antczak, Marta Szachniuk
High-quality, customizable heuristics for RNA 3D structure alignment. Bioinform. 39 (5) (2023)
Marek Justyna, Maciej Antczak, Marta Szachniuk
Machine learning for RNA 2D structure prediction benchmarked on experimental data. Briefings Bioinform. 24 (3) (2023)
Tomasz Zok, Natalia Kraszewska, Joanna Miskiewicz, Paulina Pielacinska, Michal Zurkowski, Marta Szachniuk
ONQUADRO: a database of experimentally determined quadruplex structures. Nucleic Acids Res. 50 (D1) (2022)
Jakub Wiedemann, Jacek Kaczor, Maciej Milostan, Tomasz Zok, Jacek Blazewicz, Marta Szachniuk, Maciej Antczak
RNAloops: a database of RNA multiloops. Bioinform. 38 (17) (2022)
Bartosz Adamczyk, Maciej Antczak, Marta Szachniuk
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures. Bioinform. 38 (14) (2022)
Michal Zurkowski, Tomasz Zok, Marta Szachniuk
DrawTetrado to create layer diagrams of G4 structures. Bioinform. 38 (15) (2022)
Kamil Luwanski, Vladyslav Hlushchenko, Mariusz Popenda, Tomasz Zok, Joanna Sarzynska, Daniil Martsich, Marta Szachniuk, Maciej Antczak
RNAspider: a webserver to analyze entanglements in RNA 3D structures. Nucleic Acids Res. 50 (W1) (2022)
Mateusz Kudla, Kaja Gutowska, Jaroslaw Synak, Mirko Weber, Katrin Sophie Bohnsack, Piotr Lukasiak, Thomas Villmann, Jacek Blazewicz, Marta Szachniuk
Virxicon: a lexicon of viral sequences. Bioinform. 36 (22-23) (2021)
Joanna Miskiewicz, Joanna Sarzynska, Marta Szachniuk
How bioinformatics resources work with G4 RNAs. Briefings Bioinform. 22 (3) (2021)
Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk
Topology-based classification of tetrads and quadruplex structures. Bioinform. 36 (4) (2020)
Tomasz Zok, Mariusz Popenda, Marta Szachniuk
ElTetrado: a tool for identification and classification of tetrads and quadruplexes. BMC Bioinform. 21 (1) (2020)
Maciej Antczak, Marcin Zablocki, Tomasz Zok, Agnieszka Rybarczyk, Jacek Blazewicz, Marta Szachniuk
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs. Bioinform. 35 (1) (2019)
Maciej Antczak, Mariusz Popenda, Tomasz Zok, Michal Zurkowski, Ryszard W. Adamiak, Marta Szachniuk
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. Bioinform. 34 (8) (2018)
Tomasz Zok, Maciej Antczak, Michal Zurkowski, Mariusz Popenda, Jacek Blazewicz, Ryszard W. Adamiak, Marta Szachniuk
RNApdbee 2.0: multifunctional tool for RNA structure annotation. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak, Marta Szachniuk
RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. BMC Bioinform. 19 (1) (2018)
Jakub Wiedemann, Tomasz Zok, Maciej Milostan, Marta Szachniuk
LCS-TA to identify similar fragments in RNA 3D structures. BMC Bioinform. 18 (1) (2017)
Metin Türkay, Giovanni Felici, Marta Szachniuk, Piotr Lukasiak
Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine. RAIRO Oper. Res. 50 (2) (2016)
Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk
New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinform. 16 (2015)
Tomasz Zok, Maciej Antczak, Martin Riedel, David Nebel, Thomas Villmann, Piotr Lukasiak, Jacek Blazewicz, Marta Szachniuk
Building the Library of Rna 3D Nucleotide Conformations Using the Clustering Approach. Int. J. Appl. Math. Comput. Sci. 25 (3) (2015)
Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, Marta Szachniuk, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz
RNAssess - a web server for quality assessment of RNA 3D structures. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Dominique de Werra, Jacek Blazewicz
Optimal pathway reconstruction on 3D NMR maps. Discret. Appl. Math. 182 (2015)
Maciej Antczak, Tomasz Zok, Mariusz Popenda, Piotr Lukasiak, Ryszard W. Adamiak, Jacek Blazewicz, Marta Szachniuk
RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Tomasz Zok, Mariusz Popenda, Marta Szachniuk
MCQ4Structures to compute similarity of molecule structures. Central Eur. J. Oper. Res. 22 (3) (2014)
Marta Szachniuk, Maria Cristina De Cola, Giovanni Felici, Jacek Blazewicz
The Orderly Colored Longest Path Problem - a survey of applications and new algorithms. RAIRO Oper. Res. 48 (1) (2014)
Marta Szachniuk, Mikolaj Malaczynski, Erwin Pesch, Edmund K. Burke, Jacek Blazewicz
MLP accompanied beam search for the resonance assignment problem. J. Heuristics 19 (3) (2013)
Marcin Radom, Agnieszka Rybarczyk, Renzo Kottmann, Piotr Formanowicz, Marta Szachniuk, Frank Oliver Glöckner, Dietrich Rebholz-Schuhmann, Jacek Blazewicz
Poseidon: An information retrieval and extraction system for metagenomic marine science. Ecol. Informatics 12 (2012)
Mariusz Popenda, Marta Szachniuk, Marek Blazewicz, Szymon Wasik, Edmund K. Burke, Jacek Blazewicz, Ryszard W. Adamiak
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinform. 11 (2010)
Marta Szachniuk, Mariusz Popenda, Ryszard W. Adamiak, Jacek Blazewicz
An assignment walk through 3D NMR spectrum. CIBCB (2009)
Mariusz Popenda, Marek Blazewicz, Marta Szachniuk, Ryszard W. Adamiak
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res. 36 (Database-Issue) (2008)
Marta Szachniuk, Lukasz Popenda, Zofia Gdaniec, Ryszard W. Adamiak, Jacek Blazewicz
NMR Analysis of RNA Bulged structures: Tabu Search Application in NOE Signal Assignment. CIBCB (2005)
Jacek Blazewicz, Marta Szachniuk, Adam Wójtowicz
RNA tertiary structure determination: NOE pathways construction by tabu search. Bioinform. 21 (10) (2005)
Ryszard W. Adamiak, Jacek Blazewicz, Piotr Formanowicz, Zofia Gdaniec, Marta Kasprzak, Mariusz Popenda, Marta Szachniuk
An Algorithm for an Automatic NOE Pathways Analysis of 2D NMR Spectra of RNA Duplexes. J. Comput. Biol. 11 (1) (2004)
Jacek Blazewicz, Marta Szachniuk, Adam Wójtowicz
Evolutionary approach to NOE paths assignment in RNA structure elucidation. CIBCB (2004)