Ion flux through membrane channels - An enhanced algorithm for the Poisson-Nernst-Planck model. - Witold Dyrka; Andy T. Augousti; Malgorzata Kotulska (J. Comput. Chem., 2008)

Accuracy in Predicting Secondary Structure of Ionic Channels. - Bogumil Konopka; Witold Dyrka; Jean-Christophe Nebel; Malgorzata Kotulska (ICCCI (SCI Volume), 2009)

Towards 3D Modeling of Interacting TM Helix Pairs Based on Classification of Helix Pair Sequence. - Witold Dyrka; Jean-Christophe Nebel; Malgorzata Kotulska (PRIB, 2010)

Quality assessment of protein model-structures based on structural and functional similarities. - Bogumil Konopka; Jean-Christophe Nebel; Malgorzata Kotulska (BMC Bioinform., 2012)

Probabilistic grammatical model for helix-helix contact site classification. - Witold Dyrka; Jean-Christophe Nebel; Malgorzata Kotulska (Algorithms Mol. Biol., 2013)

On the amyloid datasets used for training PAFIG - how (not) to extend the experimental dataset of hexapeptides. - Malgorzata Kotulska; Olgierd Unold (BMC Bioinform., 2013)

Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides. - Jerzy Stanislawski; Malgorzata Kotulska; Olgierd Unold (BMC Bioinform., 2013)

FISH Amyloid - a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids. - Pawel Gasior; Malgorzata Kotulska (BMC Bioinform., 2014)

Evaluating the Significance of Protein Functional Similarity Based on Gene Ontology. - Bogumil Konopka; Tomasz Golda; Malgorzata Kotulska (J. Comput. Biol., 2014)

Automated Analysis of Images from Confocal Laser Scanning Microscopy Applied to Observation of Calcium Channel Subunits in Nerve Cell Model Line Subjected Electroporation and Calcium. - Julita Kulbacka; Marek Kulbacki; Jakub Segen; Anna Choromanska; Jolanta Saczko; Magda Dubinska-Magiera; Malgorzata Kotulska (ACIIDS (2), 2015)

AmyLoad: website dedicated to amyloidogenic protein fragments. - Pawel P. Wozniak; Malgorzata Kotulska (Bioinform., 2015)

Database of Peptides Susceptible to Aggregation as a Tool for Studying Mechanisms of Diseases of Civilization. - Pawel P. Wozniak; Jean-Christophe Nebel; Malgorzata Kotulska (ACIIDS (1), 2016)

Forecasting residue-residue contact prediction accuracy. - Pawel P. Wozniak; Bogumil Konopka; J. Xu; Gert Vriend; Malgorzata Kotulska (Bioinform., 2017)

Correlated mutations select misfolded from properly folded proteins. - Pawel P. Wozniak; Gert Vriend; Malgorzata Kotulska (Bioinform., 2017)

Bio-knowledge-based filters improve residue-residue contact prediction accuracy. - Pawel P. Wozniak; J. Pelc; M. Skrzypecki; Gert Vriend; Malgorzata Kotulska (Bioinform., 2018)

Topological analysis as a tool for detection of abnormalities in protein-protein interaction data. - Alicja W. Nowakowska; Malgorzata Kotulska (Bioinform., 2022)

AmyloGraph: a comprehensive database of amyloid-amyloid interactions. - Michal Burdukiewicz; Dominik Rafacz; Agnieszka Barbach; Katarzyna Hubicka; Laura Bakala; Anna Lassota; Jakub Stecko; Natalia Szymanska; Jakub Wojciechowski; Dominika Kozakiewicz; Natalia Szulc; Jaroslaw Chilimoniuk; et al. (Nucleic Acids Res., 2023)