MysiRNA: Improving siRNA efficacy prediction using a machine-learning model combining multi-tools and whole stacking energy (ΔG). - Mohamed Mysara; Mahmoud ElHefnawi; Jonathan M. Garibaldi (J. Biomed. Informatics, 2012)

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads. - Mohamed Mysara; Natalie Leys; Jeroen Raes; Pieter Monsieurs (BMC Bioinform., 2015)

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data. - Mohamed Mysara; Natalie Leys; Jeroen Raes; Pieter Monsieurs (BMC Bioinform., 2016)

PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing. - Gleb Goussarov; Ilse Cleenwerck; Mohamed Mysara; Natalie Leys; Pieter Monsieurs; Guillaume Tahon; Aurélien Carlier; Peter Vandamme; Rob Van Houdt (Bioinform., 2020)

Utilizing genomic signatures to gain insights into the dynamics of SARS-CoV-2 through Machine and Deep Learning techniques. - Ahmed M. A. Elsherbini; Amr Hassan Elkholy; Youssef M. Fadel; Gleb Goussarov; Ahmed Mohamed Elshal; Mohamed El-Hadidi; Mohamed Mysara (BMC Bioinform., 2024)

metaGEENOME: an integrated framework for differential abundance analysis of microbiome data in cross-sectional and longitudinal studies. - Ahmed Abdelkader; Nur A. Ferdous; Mohamed El-Hadidi; Tomasz Burzykowski; Mohamed Mysara (BMC Bioinform., 2025)