MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. - Daniel H. Huson; Sina Beier; Isabell Flade; Anna Górska; Mohamed El-Hadidi 001; Suparna Mitra; Hans-Joachim Ruscheweyh; Rewati Tappu (PLoS Comput. Biol., 2016)

MetaFlow: an interactive user-friendly workflow for automated analysis of whole genome shotgun sequencing metagenomic data. - Usama Bakry; Mohamed Fares; Ali Kishk; Mohamed El-Hadidi 001 (BIBM, 2018)

AmpliconNet: Sequence Based Multi-layer Perceptron for Amplicon Read Classification Using Real-time Data Augmentation. - Ali Kishk; Mohamed El-Hadidi 001 (BIBM, 2018)

Detection of Mammalian Coding Sequences Using a Hybrid Approach of Chaos Game Representation and Machine Learning. - Mohamed Emam; Amna Ali; Eman Abdelrazik; Mustafa Elattar; Mohamed El-Hadidi 001 (BIBM, 2020)

Insilico Codon Bias Correction for Transgenic Biological Protein Sequences for Vaccine Production. - Mohamed Abuelanin; Mohamed Fares; Mohamed El-Hadidi 001 (NILES, 2020)

In-Silico Comparative Analysis of Egyptian SARS CoV-2 with Other Populations: a Phylogeny and Mutation Analysis. - Lamis Sharawy; Maha Tantawy; Yara Ahmed; Ahmed Taha; Omar Soliman; Tamer M. Ibrahim; Mohamed El-Hadidi 001 (NILES, 2020)

Benchmarking of Antimicrobial Resistance Gene Detection Tools in Assembled Bacterial Whole Genomes. - Eman Abdelrazik; Mariam Oweda; Mohamed El-Hadidi 001 (NILES, 2021)

Potential probiotics for viral triggered type 2 diabetes. - Mariam Oweda; Joseph N. Tanyous; Mohamed Hamed; Mohamed El-Hadidi 001 (NILES, 2021)

Supervised ML for Identifiying Biomarkers Driving the Response to ICBs in Melanoma patients. - Hagar Elshora; Mohamed El-Hadidi 001 (NILES, 2022)

Unravelling Diabetes-related Pathways Using 16S rRNA Microbiome Data from Human Gut and Nasal Cavity. - Manar Rashad; Mohamed Hamed; Mohamed El-Hadidi 001 (NILES, 2022)

Integrated Analysis of Bulk and Single-Cell Transcriptomics in Cervical Cancer: Insights into BPGM, EGLN3, and SUN1. - Assem K. Elsherif; Mohamed Emam; Asmaa M. Abushady; Mariam Gamaleldin; Walid Al-Atabany; Mohamed El-Hadidi 001 (BIBE, 2023)

The Melody of Silent Mutations: Microbiome Adaptation Across the Subduction Zone. - Laila Abdel Samad; Mohamad Maged; Kohar Garo; Bahia Riad; Mohamed El-Hadidi 001 (NILES, 2023)

Deep Learning Applications in Single-Cell Multi-Omics Analysis: A Review. - Manar H. Taha; Mohamed El-Hadidi 001; Sahar Ali Fawzi (NILES, 2024)

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 001; Mohamed Mysara (BMC Bioinform., 2024)

Comparative evaluation of multiomics integration tools for the study of prediabetes: insights into the earliest stages of type 2 diabetes mellitus. - Mohamed Emam; Ahmed Tarek; Mohamed Soudy; Agostinho Antunes; Mohamed El-Hadidi 001; Mohamed Hamed (Netw. Model. Anal. Health Informatics 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 001; Tomasz Burzykowski; Mohamed Mysara (BMC Bioinform., 2025)

Generative deep learning in bioinformatics: a microservices-driven paradigm for big data environment. - Ahmed F. El-Sayed; Saad M. Darwish; Nevine M. Labib; Mohamed S. El-Hadidi (J. Big Data, 2026)