Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields. - Indrajit Deb; Joanna Sarzynska; Lennart Nilsson; Ansuman Lahiri (J. Chem. Inf. Model., 2014)

Reparameterizations of the χ Torsion and Lennard-Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines. - Indrajit Deb; Rupak Pal; Joanna Sarzynska; Ansuman Lahiri (J. Comput. Chem., 2016)

Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. - Agnieszka Mickiewicz; Joanna Sarzynska; Maciej Milostan; Anna Kurzynska-Kokorniak; Agnieszka Rybarczyk; Piotr Lukasiak; Tadeusz Kulinski; Marek Figlerowicz; Jacek Blazewicz (Comput. Biol. Chem., 2017)

Topology-based classification of tetrads and quadruplex structures. - Mariusz Popenda; Joanna Miskiewicz; Joanna Sarzynska; Tomasz Zok; Marta Szachniuk (Bioinform., 2020)

Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space. - Nivedita Dutta; Joanna Sarzynska; Ansuman Lahiri (J. Chem. Inf. Model., 2020)

How bioinformatics resources work with G4 RNAs. - Joanna Miskiewicz; Joanna Sarzynska; Marta Szachniuk (Briefings Bioinform., 2021)

Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives. - Nivedita Dutta; Indrajit Deb; Joanna Sarzynska; Ansuman Lahiri (J. Comput. Aided Mol. Des., 2022)

RNAspider: a webserver to analyze entanglements in RNA 3D structures. - Kamil Luwanski; Vladyslav Hlushchenko; Mariusz Popenda; Tomasz Zok; Joanna Sarzynska; Daniil Martsich; Marta Szachniuk; Maciej Antczak (Nucleic Acids Res., 2022)