3DGenBench: a web-server to benchmark computational models for 3D Genomics. - Polina Belokopytova; Emil Viesná; Mateusz Chilinski; Yifeng Qi; Hossein Salari; Marco Di Stefano; Andrea Esposito 001; Mattia Conte; Andrea Maria Chiariello; Vladimir B. Teif; Dariusz Plewczynski; Bin Zhang; et al. (Nucleic Acids Res., 2022)

ConsensuSV - from the whole-genome sequencing data to the complete variant list. - Mateusz Chilinski; Dariusz Plewczynski (Bioinform., 2022)

Prediction of chromatin looping using deep hybrid learning (DHL). - Mateusz Chilinski; Anup Kumar Halder; Dariusz Plewczynski (Quant. Biol., 2023)

Unchecked and Overlooked: Addressing the Checkbox Blind Spot in Large Language Models with CheckboxQA. - Michal Turski; Mateusz Chilinski; Lukasz Borchmann (CoRR, 2025)