Dr. Mohamed El Hadidi

short bio

Dr. Mohamed El Hadidi is an Assistant Professor of Bioinformatics and Head of the Bioinformatics research group at the center for informatics sciences (CIS), the School of Information Technology, and Computer Science (ITCS) at Nile University since January 2017. El-Hadidi received interdisciplinary, international education and has over six years of experience in biotechnology fields, followed by ten years of experience in computational biology and bioinformatics fields. El-Hadidi received his PhD. Degree in Bioinformatics in 2016 from the Department of Computer Science, Faculty of Science, Eberhard Karls Universität Tübingen, Germany. Besides doctoral studies, From 2012-2016, he has worked as an assistant lecturer at the same University in Germany. El Hadidi was awarded an Erasmus Mundus Scholarship to finish his MSc’s degree in Europe. He had a dual master degree, First in Biotechnology from the Department of Bioengineering, Instituto Superior Técnico (IST), Technical University of Lisbon, Portugal, and 2nd MSc. in Computational and Systems Biology from the Department of Computer Science, School of Science and Technology, Aalto University, Finland. El-Hadidi has contributed towards the development of academic programs at Nile University, In 2018, he initiated the bioinformatics postgraduate diploma in Bioinformatics, and he is currently the director of the Biomedical Informatics undergraduate program. His research expertise falls in the area of applied bioinformatics, with a focus on Next Generation Sequencing (NGS) data analysis and metagenomics.  El Hadidi is an expert microbiome data analysis for various medical and environmental applications. He has several publications in prestigious international journals and conferences. Besides his academic career, El-Hadidi has gained significant experience in the bioinformatics industry during his role as the head of the Bioinformatics Unit of Colors Medical Laboratories in Egypt. 

research tracks

Co-authors

1)  Daniel H. Huson: Professor of Algorithms in Bioinformatics, University of Tuebingen

2) Hans-Joachim Ruscheweyh: Bioinformatician, D-BIOL, ETH Zurich

3) Suparna Mitra: University Academic Fellow

4) Sina Beier: PostDoc in Bioinformatics, Wellcome Sanger Institute

5) Andreas Kappler: Professor for Geomicrobiology, University of Tübingen, Germany

awards

Publications

Hassan R., Tantawy M., Gouda N.A., Elzayat M.G., Gabra S., Nabih A., Diab A.A., El-Hadidi M., Bakry U., Shoeb M.R., Elanany M., Shalaby L., Sayed A.A., “Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt”, Scientific Reports, Vol. 10, 2020, Doi:10.1038/s41598-020-61159-z2020Article
Emam M., Ali A., Abdelrazik E., Elattar M., El-Hadidi M., “Detection of Mammalian Coding Sequences Using a Hybrid Approach of Chaos Game Representation and Machine Learning”, Proceedings – 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020, 2020, Doi:10.1109/BIBM49941.2020.93134972020Conference Paper
Abuelanin M., Fares M., El-Hadidi M., “Insilico Codon Bias Correction for Transgenic Biological Protein Sequences for Vaccine Production”, 2nd Novel Intelligent and Leading Emerging Sciences Conference, NILES 2020, 2020, Doi:10.1109/NILES50944.2020.92578812020Conference Paper
Sharawy L., Tantawy M., Ahmed Y., Taha A., Soliman O., Ibrahim T.M., El-Hadidi M., “In-Silico Comparative Analysis of Egyptian SARS CoV-2 with Other Populations: A Phylogeny and Mutation Analysis”, 2nd Novel Intelligent and Leading Emerging Sciences Conference, NILES 2020, 2020, Doi:10.1109/NILES50944.2020.92579182020Conference Paper
Hassan R., Tantawy M., Gouda N.A., Elzayat M.G., Gabra S., Nabih A., Diab A.A., El-Hadidi M., Bakry U., Shoeb M.R., Elanany M., Shalaby L., Sayed A.A., “Author Correction: Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt (Scientific Reports, (2020), 10, 1, (4165), 10.1038/s41598-020-61159-z)”, Scientific Reports, 2020, Doi:10.1038/s41598-020-64153-72020Erratum
El-Houseini M.E., Ismail A., Abdelaal A.A., El-Habashy A.H., Abdallah Z.F., Mohamed M.Z., El-Hadidi M., Cho W.C.S., Ahmed H., Al-Shafie T.A., “Role of TGF-β1 and C-Kit Mutations in the Development of Hepatocellular Carcinoma in Hepatitis C Virus-Infected Patients: in vitro Study”, Biochemistry (Moscow), Vol. 84, pp 941 to 953, 2019, Doi:10.1134/S00062979190801082019Article
Poole A.C., Goodrich J.K., Youngblut N.D., Luque G.G., Ruaud A., Sutter J.L., Waters J.L., Shi Q., El-Hadidi M., Johnson L.M., Bar H.Y., Huson D.H., Booth J.G., Ley R.E., “Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes”, Cell Host and Microbe, Vol. 25, pp 553 to 5640000000, 2019, Doi:10.1016/j.chom.2019.03.0012019Article
Singh Y., El-Hadidi M., Admard J., Wassouf Z., Schulze-Hentrich J.M., Kohlhofer U., Quintanilla-Martinez L., Huson D., Riess O., Casadei N., “Enriched environmental conditions modify the gut microbiome composition and fecal markers of inflammation in parkinson’s disease”, Frontiers in Neuroscience, Vol. 13, 2019, Doi:10.3389/fnins.2019.010322019Article
Kishk A., Elzizy A., Galal D., Razek E.A., Fawzy E., Ahmed G., Gawish M., Hamad S., El-Hadidi M., “A Hybrid Machine Learning Approach for the Phenotypic Classification of Metagenomic Colon Cancer Reads Based on Kmer Frequency and Biomarker Profiling”, 2018 9th Cairo International Biomedical Engineering Conference, CIBEC 2018 – Proceedings, 2019, Doi:10.1109/CIBEC.2018.86418052019Conference Paper
Kishk A., El-Hadidi M., “AmpliconNet: Sequence Based Multi-layer Perceptron for Amplicon Read Classification Using Real-time Data Augmentation”, Proceedings – 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, 2019, Doi:10.1109/BIBM.2018.86212872019Conference Paper
Bakry U., Fares M., Kishk A., El-Hadidi M., “MetaFlow: An interactive user-friendly workflow for automated analysis of whole genome shotgun sequencing metagenomic data”, Proceedings – 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, 2019, Doi:10.1109/BIBM.2018.86211712019Conference Paper
Krause H.-M., Hüppi R., Leifeld J., El-Hadidi M., Harter J., Kappler A., Hartmann M., Behrens S., Mäder P., Gattinger A., “Biochar affects community composition of nitrous oxide reducers in a field experiment”, Soil Biology and Biochemistry, Vol. 119, pp 143 to 151, 2018, Doi:10.1016/j.soilbio.2018.01.0182018Article
Harter J., El-Hadidi M., Huson D.H., Kappler A., Behrens S., “Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N2O formation”, Scientific Reports, Vol. 7, 2017, Doi:10.1038/s41598-017-03282-y2017Article
Huson D.H., Steel M., El-Hadidi M., Mitra S., Peter S., Willmann M., “A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples”, Journal of Biotechnology, Vol. 250, pp 45 to 50, 2017, Doi:10.1016/j.jbiotec.2016.10.0202017Article
Harter J., Weigold P., El-Hadidi M., Huson D.H., Kappler A., Behrens S., “Soil biochar amendment shapes the composition of N2O-reducing microbial communities”, Science of the Total Environment, Vol. 562, pp 379 to 390, 2016, Doi:10.1016/j.scitotenv.2016.03.2202016Article
Weigold P., El-Hadidi M., Ruecker A., Huson D.H., Scholten T., Jochmann M., Kappler A., Behrens S., “A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil”, Scientific Reports, Vol. 6, 2016, Doi:10.1038/srep289582016Article
Huson D.H., Beier S., Flade I., Górska A., El-Hadidi M., Mitra S., Ruscheweyh H.-J., Tappu R., “MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data”, PLoS Computational Biology, Vol. 12, 2016, Doi:10.1371/journal.pcbi.10049572016Article
Willmann M., El-Hadidi M., Huson D.H., Schütz M., Weidenmaier C., Autenrieth I.B., Peter S., “Antibiotic selection pressure determination through sequence-based metagenomics”, Antimicrobial Agents and Chemotherapy, Vol. 59, pp 7335 to 7345, 2015, Doi:10.1128/AAC.01504-152015Article