LinkProt: a database collecting information about biological links. - Pawel Dabrowski-Tumanski; Aleksandra I. Jarmolinska; Wanda Niemyska; Eric J. Rawdon; Kenneth C. Millett; Joanna I. Sulkowska (Nucleic Acids Res., 2017)

GapRepairer: a server to model a structural gap and validate it using topological analysis. - Aleksandra I. Jarmolinska; Michal Kadlof; Pawel Dabrowski-Tumanski; Joanna I. Sulkowska (Bioinform., 2018)

KnotGenome: a server to analyze entanglements of chromosomes. - Joanna I. Sulkowska; Szymon Niewieczerzal; Aleksandra I. Jarmolinska; Jonathan T. Siebert; Peter Virnau; Wanda Niemyska (Nucleic Acids Res., 2018)

DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings. - Aleksandra I. Jarmolinska; Qin Zhou; Joanna I. Sulkowska; Faruck Morcos (J. Chem. Inf. Model., 2019)

Knot_pull - python package for biopolymer smoothing and knot detection. - Aleksandra I. Jarmolinska; Anna Gambin; Joanna I. Sulkowska (Bioinform., 2020)

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. - Vasilina Zayats; Agata P. Perlinska; Aleksandra I. Jarmolinska; Borys Jastrzebski; Stanislaw Dunin-Horkawicz; Joanna I. Sulkowska (PLoS Comput. Biol., 2021)