xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures. - Marco Pasi; Matteo Tiberti; Alberto Arrigoni; Elena Papaleo (J. Chem. Inf. Model., 2012)

PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins. - Matteo Tiberti; Gaetano Invernizzi; Matteo Lambrughi; Yuval Inbar; Gideon Schreiber; Elena Papaleo (J. Chem. Inf. Model., 2014)

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops. - Gaetano Invernizzi; Matteo Tiberti; Matteo Lambrughi; Kresten Lindorff-Larsen; Elena Papaleo (PLoS Comput. Biol., 2014)

ENCORE: Software for Quantitative Ensemble Comparison. - Matteo Tiberti; Elena Papaleo; Tone Bengtsen; Wouter Boomsma; Kresten Lindorff-Larsen (PLoS Comput. Biol., 2015)

Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil. - Shaima Hashem; Matteo Tiberti; Arianna Fornili (PLoS Comput. Biol., 2017)

In silico identification of rescue sites by double force scanning. - Matteo Tiberti; Alessandro Pandini; Franca Fraternali; Arianna Fornili (Bioinform., 2018)

MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles. - Matteo Tiberti; Thilde Terkelsen; Kristine Degn; Ludovica Beltrame; Tycho Canter Cremers; Isabelle da Piedade; Miriam Di Marco; Emiliano Maiani; Elena Papaleo (Briefings Bioinform., 2022)

PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles. - Valentina Sora; Matteo Tiberti; Ludovica Beltrame; Deniz Dogan; Shahriyar Mahdi Robbani; Joshua Rubin; Elena Papaleo (J. Chem. Inf. Model., 2023)

A workflow to study mechanistic indicators for driver gene prediction with Moonlight. - Mona Nourbakhsh; Astrid Saksager; Nikola Tom; Xi Steven Chen; Antonio Colaprico; Catharina Olsen; Matteo Tiberti; Elena Papaleo (Briefings Bioinform., 2023)

PDBminer to Find and Annotate Protein Structures for Computational Analysis. - Kristine Degn; Ludovica Beltrame; Matteo Tiberti; Elena Papaleo (J. Chem. Inf. Model., 2023)

Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks. - Mona Nourbakhsh; Kristine Degn; Astrid Saksager; Matteo Tiberti; Elena Papaleo (Briefings Bioinform., 2024)

Revealing cancer driver genes through integrative transcriptomic and epigenomic analyses with Moonlight. - Mona Nourbakhsh; Yuanning Zheng; Humaira Noor; Hongjin Chen; Subhayan Akhuli; Matteo Tiberti; Olivier Gevaert; Elena Papaleo (PLoS Comput. Biol., 2025)