Dr Mohamed El-Hadidi

Department of Cancer and Genomic Sciences
Associate Professor in Bioinformatics
Programme Director MSc Bioinformatics

Contact details

Telephone: +97 14 4280737
Email: m.el-hadidi@bham.ac.uk

Address: University of Birmingham Dubai
Dubai International Academic City
PO Box 341799
Dubai

Dr Mohamed El-Hadidi, an Associate Professor and Programme Director for the Bioinformatics MSc programme at the Department of Cancer and Genomic Sciences, University of Birmingham, brings extensive experience to his role. With a strong focus on the insightful analysis of diverse OMICS data, including microbiome and human datasets, his contributions have been highly impactful.

Dr El-Hadidi's expertise extends to his involvement in human genome projects, proving invaluable for a deeper understanding of complex biological systems. Furthermore, he has a keen interest in multi-OMICS data integration, with a specific emphasis on microbiome-host Multi-OMICS data integration.

Notably, Dr El-Hadidi is based at the University of Birmingham's Dubai Campus, where his diverse background in academia, research, and the bioinformatics industry enriches the educational and research landscape. This unique blend of experience aligns closely with the University of Birmingham's mission to advance knowledge in bioinformatics and genomics.

ORCID iD

Google Scholar

ResearchGate

Qualifications

2016 PhD in Bioinformatics, Department of Computer Science, Faculty of Science, Eberhard Karls Universität Tübingen, Germany.
2012 MSc in Biotechnology, Department of Bioengineering, Instituto Superior Técnico (IST), Technical University of Lisbon, Portugal.
2011 MSc in Computational and Systems Biology, Department of Computer Science, School of Science and Technology, Aalto University, Finland.
2011 Postgraduate Diploma in Bioinformatics, Department of Biomedical Engineering, Information Technology Institute (ITI), Egypt.
2006 Bachelor of Science (BSc) in Biotechnology, Cairo University, Giza, Egypt.

Biography

Dr Mohamed El-Hadidi is a distinguished professional in the field of bioinformatics, currently serving as an Associate Professor and the Director of the Bioinformatics MSc Program at the College of Medical and Dental Sciences, The University of Birmingham - Dubai Campus. Before relocating to Dubai, he held the position of Assistant Professor and led the Bioinformatics Research Group at the Center for Informatics Sciences (CIS) within Nile University's School of Information Technology and Computer Science (ITCS) in Egypt, commencing in January 2017. He is also a dedicated member of the Scientific Committee of the Egyptian Genome Project.

Dr El-Hadidi's academic journey has been shaped by a multidisciplinary, international education, and a wealth of experience spanning over six years in biotechnology, coupled with 14 years dedicated to computational biology and bioinformatics. His academic journey culminated in the achievement of a PhD in Bioinformatics from the Department of Computer Science, Faculty of Science, at Eberhard Karls Universität Tübingen in Germany in 2016. Furthermore, he holds dual MSc degrees, one in Biotechnology from the Department of Bioengineering at Instituto Superior Técnico (IST) in Lisbon, Portugal, and another in Computational and Systems Biology from the Department of Computer Science, School of Science and Technology at Aalto University in Finland.

Dr El-Hadidi has been instrumental in shaping academic programs at Nile University, having initiated the bioinformatics postgraduate diploma program and currently overseeing the Biomedical Informatics undergraduate program. His research expertise is centered on applied bioinformatics, with a primary focus on Next Generation Sequencing (NGS) data analysis, metagenomics, and a specialization in microbiome data analysis for various medical and environmental applications. Through his involvement in the Egyptian Human Genome Project, he has gained valuable experience in the analysis of extensive genomic data, exploring the genetic underpinnings of diseases, thereby paving the way for precision medicine. His contributions are well-documented in several publications in esteemed international journals and conferences.

In addition to his distinguished academic career, Dr El-Hadidi has accumulated substantial experience in the bioinformatics industry through consulting roles in various companies. The blend of his academic and industry experience, alongside his profound expertise in bioinformatics and research, positions him as a valuable asset to the field.

Teaching

Module Lead for the following modules:

Introduction to Biology and Programming
Genomics & Next Generation Sequencing
Individual Project

Research

Research interests

Next Generation Sequencing (NGS) Data Analysis.
Multi-OMICS Data Integration.
Host-Microbiome OMICS Data Integration.
Human Genome Project and Variants Annotation.
Ancient DNA Data Analysis.

Current projects

Defining variants associated with diseases among Egyptian population.
Diagnosis of neurodegenerative diseases based on microbiome data analysis coupled by artificial intelligence.
Benchmarking of microbiome data analysis pipelines.

Other activities

National Appointments:

Vice President of the National Egyptian Bioinformatics Network, ASRT, Egypt.
Member of the Scientific Committee of the Egyptian Reference Genome Project Council, ASRT, Egypt.

Publications

Published Journal Articles

Manal Abouelwafa, Mohamed El-Hadidi, Amany Mostafa, Georrge John J (2023): Using CADD tools to inhibit the overexpressed genes FAP, FN1, and MMP1 by repurposing ginsenoside C and Rg1 as a treatment for oral cancer, Frontiers in Molecular Biosciences.

Ahmed Abdelkader, Amal A. Elzemrany, Mennatullah El-Nadi, Sherif A. Elsabbagh, Moustafa A. Shehata, Wagdy M. Eldehna, Mohamed El-Hadidi and Tamer M. Ibrahim (2022): In-Silico targeting of SARS-CoV-2 NSP6 for drug and natural products repurposing, Virology.

Mohamed R Abdelfadil, Manar H Taha, Mohamed El-Hadidi, Mervat A Hamza, Hanan H Youssef, Mohab Khalil, Ahmed R Henawy, Rahma A Nemr, Hend Elsawey, Gylaine Vanissa Tchuisseu Tchakounte, Mohamed Abbas, Gehan H Youssef, Katja Witzel, Mohamed Essam Shawky, Mohamed Fayez, Steffen Kolb, Nabil A Hegazi, Silke Ruppel (2022): Clay chips and beads capture in situ barley root microbiota and facilitate in vitro long-term preservation of microbial strains, FEMS Microbiology Ecology.

A. M. Serag, M. S. Abd El-Sabour, Rashed M. A, El-Hadidi Mohamed, Mohamad Maged, M. Magdy, Refaat, M. H.: Comparing the gut bacteria from Nile tilapia fish inhabiting some Egyptian northern lakes using high-throughput sequencing of the 16S rRNA gene (2022), Applied Biochemistry and Biotechnology, IFP 2.78.

Mohamed Emam, Mariam Oweda, Agostinho Antunes and Mohamed El-Hadidi (2021): Positive selection as a key player for SARS-CoV-2 pathogenicity: Insights into ORF1ab, S and E genes, Virus Research.

Reem Hassan, Marwa Tantawy, Nouran Gouda, Mariam Elzayat, Sara Gabra, Amena Nabih, Aya Diab, Mohamed El-Hadidi, Usama Bakry, Mohamed Refaat, Mervat El-Annany, Lobna Shalaby and Ahmed Sayed, (2020): Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt, Scientific Reports.

Yogesh Singh, Mohamed El Hadidi, Jakob Matthes, Zinah Wassouf, Julia M Schulze-Hentrich, Ursula Kohlhofer, Leticia Quintanilla-Martinez de Fend, Daniel Huson, Olaf Riess, Nicolas Casadei (2019): Enriched environmental conditions modify the gut microbiome composition and fecal markers of inflammation in Parkinson's disease, Frontiers in Neuroscience.

ME El-Houseini, A Ismail, AA Abdelaal, AH El-Habashy, ZF Abdallah, MZ Mohamed, M El-Hadidi, WCS Cho, H Ahmed, TA Al-Shafie (2019): Role of TGF-β1 and C-Kit Mutations in the Development of Hepatocellular Carcinoma in Hepatitis C Virus-Infected Patients: in vitro study, Journal of Biochemistry (Moscow).

Angela C Poole, Julia K Goodrich, Nicholas D Youngblut, Guillermo G Luque, Albane Ruaud, Jessica L Sutter, Jillian L Waters, Qiaojuan Shi, Mohamed El-Hadidi, Lynn M Johnson, Haim Y Bar, Daniel H Huson, James G Booth, Ruth E Ley (2019): Human salivary amylase gene copy number impacts oral and gut microbiomes, Cell host & microbe.

Hans-Martin Krause, Roman Hüppi, Jens Leifeld, Mohamed El-Hadidi, Johannes Harter, Andreas Kappler, Martin Hartmann, Paul Mäder, Andreas Gattinger (2018): Biochar affects community composition of nitrous oxide reducers in a field experiment, Soil Biology and Biochemistry.

Johannes Harter, Mohamed El-Hadidi, Daniel H. Huson, Andreas Kappler and Sebastian Behrens (2017): Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N2O formation, Scientific Reports.

Daniel H. Huson, Mike Steel, Mohamed El-Hadidi, Silke Peter, Matthias Willmann (2016): A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples, Journal of Biotechnology.

Johannes Harter, Pascal Weigold, Mohamed El-Hadidi, Daniel Huson, Andreas Kappler, and Sebastian Behrens (2016): Soil biochar amendment shapes the composition of N2O-reducing microbial communities, Science of The Total Environment.

Pascal Weigold, Mohamed El-Hadidi, Alexander Ruecker, Daniel H. Huson, Thomas Scholten, Maik Jochmann, Andreas Kappler, Sebastian Behrens (2016): A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil, Scientific Reports.

Daniel H. Huson, Sina Beier, Isabell Flade, Anna Gorska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh and Rewati Tappu (2016): MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data, PLOS Computational Biology.

Matthias Willmann, Mohamed El-Hadidi, Daniel Huson, Monika Schütz, Christopher Weidenmaier, Ingo Autenrieth, and Silke Peter (2015): Antibiotic selection pressure determination through sequence-based metagenomics, Antimicrobial Agents and Chemotherapy.

Published Conference Articles

Hagar Elshora and Mohamed El-Hadidi: Identification of Biomarkers Affecting The Response to ICBs in Melanoma patients with Supervised Machine Learning (2022), IEEE Novel Intelligent and Leading Emerging Sciences conference.

Manar Rashad, Mohamed Hamed and Mohamed El-Hadidi: Unravelling Diabetes-related Pathways Using 16S rRNA Microbiome Data from Human Gut and Nasal Cavity (2022), IEEE Novel Intelligent and Leading Emerging Sciences conference.

Nourelislam Awad and Mohamed El Hadidi: A Framework for Alternative Splicing Isoforms Detection in Lung Cancer (2021), 10th International Conference on Intelligent Computing and Information Systems (ICICIS).

Mariam Oweda, Joseph N. Tanyous and Mohamed Hamed and Mohamed Hadidi: Potential Probiotics for Viral Triggered Type 2 Diabetes (2021), IEEE Novel Intelligent and Leading Emerging Sciences conference.

Eman Abdelrazik, Mariam Oweda and Mohamed El-Hadidi: Benchmarking of Antimicrobial Resistance Gene Detection Tools in Assembled Bacterial Whole Genomes (2021), IEEE Novel Intelligent and Leading Emerging Sciences conference.

Mohamed Emam, Amna Ali, Eman Abdelrazik, Mustafa Elattar and Mohamed El-Hadidi: Detection of Mammalian Coding Sequences Using a Hybrid Approach of Chaos Game Representation and Machine Learning (2020): 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Ghadir Ali, Ahmed Shahin, Mohamed El-Hadidi and Mustafa Elattar: Convolutional Neural Network with Attention Modules for Pneumonia Detection (2020): International Conference on Innovation and Intelligence for Informatics, Computing and Technologies (3ICT).

Mohamed Abuelanin, Mohamed Fares and Mohamed El-Hadidi: Insilico Codon Bias Correction for Transgenic Biological Protein Sequences for Vaccine Production: (2020): IEEE Novel Intelligent and Leading Emerging Sciences conference.

Lamis Sharawy, Maha Tantawy, Yara Ahmed, Ahmed Taha, Tamer M Ibrahim, Omar Soliman and Mohamed El-Hadidi: In-Silico Comparative Analysis of Egyptian SARS CoV-2 with Other Populations: a Phylogeny and Mutation Analysis (2020): IEEE Novel Intelligent and Leading Emerging Sciences conference.

Amira Yousef, Ali Kishk, Mohamed El-Hadidi, Abdelrahman Zekri: Profiling of BRCA1 & BRCA2 mutations in Egyptian Colorectal Cancer Patients via Next Generation Sequencing (2020), American Association for Cancer Research, San Diego, CA, USA.

Ali Kishk and Mohamed El-Hadidi: AmpliconNet: Sequence Based Multi-layer Perceptron for Amplicon Read Classification Using Real-time Data Augmentation (2019): IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain.

Ali Kishk, Asmaa Elzizy, Dina Galal, Elham Abdel Razek, Esraa Fawzy, Gehad Ahmed, Mohamed Gawish, Safwat Hamad, Mohamed El-Hadidi (2018): A Hybrid Machine Learning Approach for the Phenotypic Classification of Metagenomic Colon Cancer Reads Based on Kmer Frequency and Biomarker Profiling, 9th Cairo International Biomedical Engineering Conference (CIBEC 2018).

Usama Bakry, Mohamed Fares, Ali Kishk, and Mohamed El-Hadidi (2018): MetaFlow: an interactive user-friendly workflow for automated analysis of whole genome shotgun sequencing metagenomic data, The IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2019, Spain.

Published Book Chapters

Nehal Abdelsalam, Hagar Elshoura and Mohamed El-Hadidi (2023): Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons, Metagenomic Data Analysis, Springer Nature.

Mariam Oweda, Joseph Boctor and Mohamed El Hadidi (2023): Comprehensive Guideline for Microbiome Analysis Using R, Metagenomic Data Analysis, Springer Nature.

Eman Abdelrazik and Mohamed El-Hadidi (2023): Tracking Antibiotic Resistance from the Environment to Human Health, Metagenomic Data Analysis, Springer Nature.