Building pan-African Bioinformatics Capacity
National Research Center, Egypt
Affiliate Node
National Research Center, Egypt
Affiliate Node
The National Research Centre (NRC) ss the largest multidisciplinary R&D centre in Egypt devoted to basic and applied research within the major fields of interest. NRC possesses an impressive scientific & technological infrastructure and man power resources of 4735 research staff. The centre has 14 divisions and 108 departments covering the major areas of industry, health, environment, agriculture, basic sciences and engineering. It is headed by a president with ministerial status, assisted by two vice presidents, one for research and the other for technical affairs. The minister of state for Scientific Research is the higher president of NRC. The NR Chas to correspond to the country’s key production and services sectors through the research conducted in different areas of science and technology, scientific consultation and training as well. The NRC mission is to conduct basic and applied research within the major fields of interest in order to develop production and services sectors.
Dr. Mahmoud ElHefnawi - Node PI
Dr. Mahmoud ElHefnawi is the Biomedical informatics and chemoinformatics group leader and professor at Informatics and Systems Department at National research centre. He was also a part time adjunct professor and senior scientist at Nile University. His H index is 11 and led many projects in bioinformatics, gene therapy in cancer, and drug discovery. He published more than fifty five International publications on topics including rational drug design, docking, and optimizing gene therapy for Influenza, Hepatitis C Virus (HCV), and different cancers, structural bioinformatics and motif predictions applications in virology,and applications of machine learning in bioinformatics as well as other bioinformatics and medical biotechnology applications. His interests span the computational as well as the medical and life sciences fields. From the informatics and engineering point, he worked on data mining and classification algorithms, reverse engineering of gene networks, HMM models, motif prediction algorithms, and other machine learning techniques. In the bioinformatics application side, he worked on: applications of the Bioinformatics methods and techniques to study viral evolution, progression stages, RNA motifs and secondary structures, protein 3D structure and domain prediction, prognosis drug resistance mechanisms and modeling, modeling viral immune system networks of interactions, rational drug design, small molecule inhibitors, and siRNA design as therapeutic agents for Hepatitis C virus, and Influenza. Also, he worked on NGS informatics, metagenomics, the human microbiome, and personalized genomics. Furthermore, he worked on gene therapy applications in cancer drug discovery using siRNAs and microRNAs. He has many national and international collaborations with other research groups. He has/ had in supervisions more than twenty five MSc and PhD thesis from different disciplines and faculties.
BioinformaticsGenomicsComparative GenomicsData Mining Drug DiscoveryEpigeneticsEpigenomicsEvolutionary Biology Exome SequencingFunctional GenomicsGene and Protein Families Genetic VariationGenotype and PhenotypeGWASImmunology Infectious DiseaseMachine LearningMedical BiotechnologyMedical Informatics MetabolomicsMetagenomicsMicroarray ExperimentMicrobial Ecology Molecular DynamicsMolecular Interactions, Pathways and Networks PharmacogenomicsPhenomicsPhylogenomicsPopulation Genetics Population GenomicsProtein Structure AnalysisProteinsProteomics Public Health and EpidemiologyQuantitative GeneticsRNA-SeqSequence Analysis Sequence AssemblyStatistics and ProbabilityStructure PredictionSystems Biology TranscriptomicsTranslational MedicineVirologyWhole Genome Sequencing Gene ExpressionMolecular ModellingPersonalised Medicine
Hanan Shaat - Research Assistant
Hanan Shaat Research assistant (National research center) Phone: 0020 1060135416 Hanan Shaat is qualified as a researcher in Chemistry and Bioinformatics, as she is enrolling in the bioinformatics diploma at Nile University in Egypt (2019). She had a BSc. of Microbiology and Chemistry, with total grade very good (2008), faculty of science Benha university (Egypt), and diploma of analytical biochemistry with excellent grade (2009, Menufiya University, Menufiya (Egypt)). She hold a master degree in Chemistry in 2016 Benha University entitled: Use of metallic nanoparticles for delivery of anti-liver cancer siRNA. Through this study, she could gain a valuable experience in bioinformatics, molecular biology and nanotechnology. The key aspects in her master thesis helped her to publish an article in international journal of pharmaceutics. She awarded the prize of the best article from Al-Najah National University in 2018. She won a qualifying program scholarship offered by Misr Elkheir foundation in Egypt that supported her with language courses and scientific research training program. She gained high experience in the medical analysis field through her work for more than 10 years in different laboratories in Egypt.
BioinformaticsGenomicsDrug MetabolismExperimental Design and Studies Drug DiscoveryGene ExpressionGene StructureInfectious Disease Molecular BiologyMolecular DynamicsGene and Protein Families Molecular Interactions, Pathways and NetworksVirologyFunctional Genomics
Mohammad Tarek - Research Assistant and Medical Student
Mohammad Tarek Mansour is a medical Student at Armed Forces College of Medicine (AFCM) in Cairo, Egypt and a Research Assistant at Dr. Mahmoud ElHefnawi Lab at National Research Center (NRC). He started the passion for bioinformatics early in preparatory school and participated in international science fairs in Jordan, California, Pennsylvania and Online science competitions presenting research that harness mathematics and bioinformatics for vaccine design and drug discovery against cancer, harnessing different research awards and scientific memberships since high school education. Along this early research career, he acquired different bioinformatics skills for dealing with different forms of biological data and designing meaningful bioinformatics tools for biologists and medical professionals. Furthermore, he acquired molecular biology skills by participating and winning awards at international synthetic biology competitions in which he focused on translating the bio-data into therapeutic tools by engineering therapies and harnessing the power of mathematics and bioinformatics to analyze, simulate, predict and validate these therapeutic designs. Collaborating with different research groups, he is applying bioinformatics to solve different biological and clinical questions that could provide translational research for more promising medical applications.
Exome SequencingStructural AnalysisGene and Protein FamiliesGenetic Variation Genotype and PhenotypeApplied MathematicsImmunologyChIP-seqMedicine Machine LearningComputational BiologyComputational ChemistryData Visualisation Drug MetabolismMicroarray ExperimentMolecular BiologyMolecular Dynamics Molecular Interactions, Pathways and NetworksPharmacogenomicsGene Expression Genotyping ExperimentGWASProtein Structure AnalysisProteins Proteomics HaematologyHuman GeneticsRNA-Seq Sequence AnalysisGene Structure Simulation ExperimentMolecular ModellingStructure Prediction Systems Biology TranscriptomicsTranslational MedicineVirologyBioinformaticsGenomics Whole Genome SequencingWorkflowsOncologyPersonalised Medicine Rare DiseasesSoftware EngineeringComputer ScienceMathematics Drug DiscoveryEpigeneticsEpigenomics
Mr. Mahmoud Warda - Computer Specialist
Single-cell transcriptomics to explore the immune system in health and diseases The immune system varies in cell types, states, and locations. The complex networks, interactions, and responses of immune cells produce diverse cellular ecosystems composed of multiple cell types, accompanied by genetic diversity in antigen receptors. Within this ecosystem, innate and adaptive immune cells maintain and protect tissue function, integrity, and homeostasis upon changes in functional demands and diverse insults. Characterizing this inherent complexity requires studies at single-cell resolution. Recent advances such as massively parallel single-cell RNA sequencing and sophisticated computational methods are catalyzing a revolution in our understanding of immunology. Along with the development of sequencing technologies, more and more information can be obtained simultaneously from the same single cell, including genome, epigenome, transcriptome, proteome, spatial and time dimension data. Therefore, predictive modeling of a single cell requires the integration of these or more data in an appropriate to avoid comprehension difficulties caused by superfluous information. One more piece to consider is that the integration method would maintain high-quality acquisition of multiple parameters, such as accuracy, sensitivity, coverage, throughput, and cost. In addition to the challenges posed by the analysis, the bottleneck of single-cell isolation technology also needs to be taken into consideration. The initial step in achieving single-cell characterization is the isolation of individual target cells from a complex biological population.
BioinformaticsGenomicsComputer ScienceBiobankMolecular Dynamics BiodiversityBiomedical SciencesEpigenomicsExome Sequencing Gene and Protein FamiliesGenetic VariationGenotype and PhenotypeImmunology Machine LearningComputational BiologyComparative genomicsData Visualisation Data Integration and WarehousingMicroarray ExperimentMolecular Biology Molecular Interactions, Pathways and NetworksPharmacogenomicsGene Expression Genotyping ExperimentGWASProtein Structure AnalysisProteins Proteomics HaematologyHuman GeneticsRNA-Seq Sequence AnalysisGene Structure Data MiningMolecular ModellingStructure PredictionSystems Biology Whole Genome SequencingWorkflowsOncologyData Management Evolutionary BiologySoftware EngineeringFunctional GenomicsInfectious Diseases MetabolomicsMetagenomicsMicrobial EcologyPhenomicsVirology Population GeneticsPhylogenomicsStatistics and ProbabilityPopulation Genomics Public Health and EpidemiologyQuantitative GeneticsSequence Assembly TranscriptomicsTranslational Medicine 
