UofK - H3ABioNet - Pan African Bioinformatics Network

Building pan-African Bioinformatics Capacity

About the node

Member Node

Website: http://uofk.edu/
Node Accreditations: Exome Variant Calling RNA-Seq GWAS 16s rRNA Microbiome Variant Calling

University of Khartoum-H3ABioNet Sudan Node
Member Node

The history of the University of Khartoum (UofK) dates back to as far as 1898, when Lord Kitchener of Khartoum proposed establishing a college in memory of General Gordon who had been killed in Sudan. The college was officially opened in 1902 and later on, Henry Wellcome donated a fully equipped laboratory for bacteriological analysis. Then in January 1945, these schools were brought under the administration of a special arrangement with the University of London. The college was upgraded in 1951 as the University College of Khartoum. In 1956, when the country gained independence, it was converted to the University of Khartoum and is one of the oldest Universities in Africa. The University's vision is to participate, through its role in the field of higher education and scientific research, in the creation of a unified, developed and advanced Sudanese Nation. The Faculty of Science was founded in 1937 as one of the Higher Schools of Gordon Memorial College. In 1945 these schools came under a single independent administration. In 1947 the School of Science became the Faculty of Science and continued to maintain this name until the University College of Khartoum became the University of Khartoum in 1956.

Assoc. Prof Faisal M. Fadlelmola - Head & Founder of Centre for Bioinformatics & Systems Biology

Dr. Faisal Mohamed Fadlelmola is an Associate Professor who has extensive regional and International academic and research experiences in cancer genomics, bioinformatics and Information Technology. He is a Fellow of the British Computer Society and Chartered IT Professional (FBCS CITP, UK), and the Fellow of Institute of Biomedical Sciences in London (FIBMS, UK) and Certified Training and Development Professional (CTDP, Toronto, Canada). He has been awarded two masters from UK, the first M.Sc. in Medical Molecular Biology from the University of Westminster, London, UK (1999) and the second M.Sc. in Computer-based Information Systems from the University of Sunderland, Sunderland, UK (2000). Then, he had been awarded his PhD in Molecular Human Genetics and Bioinformatics from the Institute of Human Genetics, University of Wurzburg in Germany (2003). He received his postdoctoral fellowship training on Cancer Genomics and Bioinformatics at the Centre for Translational and Applied Genomics (CTAG), British Columbia Cancer Agency, British Columbia, Vancouver Canada (2004-2006). He also worked as a Senior Research Associate at CTAG (January 2007-December 2008). Then, he relocated to Botswana as a founding academic staff for the newly established School of Medicine at the University of Botswana (2009-2011) where he worked as a Biomedical Scientist/Assistant Professor and taught genetics/genomics, bioinformatics, health informatics and information technology to medical students. On August 2011 he joined the newly transferred Future University of Sudan in Khartoum (formerly ComputerMan College) as associate professor of cancer genomics, bioinformatics and information technology. Since August 2012, he works as the Principal Investigator for the USA NIH H3ABioNet Sudan Node. H3ABioNet, the NIH funded Pan African Bioinformatics Network for Human Heredity and Health in Africa, is being developed to support H3Africa research projects through the development of bioinformatics capacity on the continent. In October 2014, he started working as head and founder of the newly established Centre for Bioinformatics and Systems Biology (CBSB) at the Faculty of Science, University of Khartoum, Sudan. He was the chair of the H3ABioNet Research Working Group (January 2015-Present) as well as active member of Education and Training Working Group and the H3ABioNet Management Committee (January 2013-August2017) and some of the H3Africa Working Groups. In September 2017, the NIH H3ABioNet grant was renewed for another five years (September 2017-June 2022). Currently, he is the chair of the H3ABioNet Databases & Resources WorkPackage (January 2018-Present) as well as active member of Training WorkPackage and the H3ABioNet Management Committee (September 2017-Present) and some of the H3Africa Working Groups. Prof Fadlelmola is actively involved in training and education as well as curriculum development in Bioinformatics and Genomic Medicine in Africa (January 2013-Present). He has been involved in a variety of research projects on topics such as cancer genomics, bioinformatics, molecular epidemiology of cancer, translational and applied genomics, mobile health and mobile learning, among many others.

BioinformaticsTranslational MedicineGenomicsData MiningSystem Biology EpigenomicsRNA-SeqGenetic VariationGenotyping ExperimentGene Expression Human GeneticsGWAS StudyMedical InformaticsMetabolomicsMicroarray Experiment Molecular BiologyOncologyPharmacogenomicsSystems BiologySoftware Engineering Translational Medicine

Assoc. Prof Faisal M. Fadlelmola - Head & Founder of Centre for Bioinformatics & Systems Biology

Mrs Samah Ahmed - PhD Student

Mrs. Samah M. Ahmed graduated with B. Pharm (honors) first class from Faculty of Pharmacy, University of Khartoum in 2010. She has awarded her M. Sc. in molecular medicine from Institute of Endemic Diseases (IEND), University of Khartoum in 2014. Her M.Sc. partial fulfillment research project was entitled "Pomegranate as a treatment for Leishmania donovani infection; an invitro study. Currently Mrs. Ahmed is a PhD candidate at the Center of Bioinformatics and Systems Biology (CBSB) under supervision of Prof. Faisal M. Fadlelmola; her PhD is revolving around "ADME genes profiling in prostate cancer among Sudanese population: Towards personalized treatment" She is a lecturer at the Faculty of Clinical and Industrial Pharmacy, National University-Sudan. She has skills in cell-line culture, immuno-informatics, structural bioinformatics and drug design.

BioinformaticsMedicineGenomicsBiomedical ScienceDrug Metabolism Genetic VariationHuman GeneticsImmunologyMedical Biotechnology Medical InformaticsMolecular BiologyMolecular ModellingPersonalized Medicine PharmacogenomicsPopulation GeneticsStructure Prediction

Ms Nihad Alsayed - PhD Student

Ms. Nihad H. Alsayed graduated with B. Sc. (honours) First Class in Zoology (Biochemistry and Physiology) from Faculty of Science, University of Khartoum in 2012. She has been awarded Master of Science (MSc) in Genetics and Molecular Biology from University of Khartoum in 2016. Her M.Sc. partial fulfilment research project was entitled "Gene Expression Profiles of Hodgkin Lymphoma (HL) and Anaplastic Large Cell Lymphoma (ALCL) cell lines, Supervisor: Prof. Faisal M. Fadlelmola". Currently, Ms. Alsayed is a PhD Candidate at the Centre for Bioinformatics and Systems Biology (CBSB) under the supervision of Prof. Faisal M. Fadlelmola.; her PhD is revolving around "Genomic Profiling of Prostate Tumour Tissues in Sudanese Patients: Towards Better Therapeutic Targets and Biomarkers Approaches". She is a part-time lecturer at the Faculty of Medical Laboratory Science, Nile College-Sudan. She has skills in designing and implementing molecular biology techniques and experiments. Ms. Alsayed has also acquired skills in bioinformatics mainly in cDNA microarray data analysis techniques including: image processing, normalization, data mining, clustering and classification of the differentially expressed genes (DEGs), pathway analysis and protein-protein interaction, in addition to RNA-seq analysis.

BioinformaticsGenomicsData MiningExperimental Design and Studies Gene ExpressionGenetic VariationHuman GeneticsMolecular Biology RNA-SeqGWAS AnalysisMicrobiome AnalysisData Curation

Ms. Rania Sibira - PhD Student

Dr. Rania M. Sibira graduated from Faculty of Medicine, University of Khartoum in 2012. She has awarded a MSc. in molecular medicine from Institute of Endemic Diseases (IEND), University of Khartoum in 2014. Her MSc. partial fulfillment research project was entitled "The behavior of esophageal squamous cell carcinoma". Currently Dr. Sibira is a PhD candidate at the Center of Bioinformatics and Systems Biology (CBSB) under supervision of Prof. Faisal M. Fadlelmola; her PhD is revolving around "ADME genes profiling in brain cancer among Sudanese population; towards precision medicine". She is now a registrar of neurosurgery at Sudan Medical Specialization Board (SMSB). She also has technical skills in DNA extraction , PCR and bioinformatics.

MedicineBioinformaticsEpigenetics Exome Sequencing Gene ExpressionGWAS StudyHaematologyHuman Genetics ImmunologyInfectious DiseaseMicrobiologyMolecular Biology OncologyParasitologyPersonalized MedicineVirology

Dr. Sahar Siddig Gamil - Postdoc Fellow

Dr. Sahar has graduated from the faculty of Medicine - University of Khartoum with an MBBS degree in 2010. She got her Master degree in Medical Biochemistry from the Department of Biochemistry- Faculty of Medicine - University of Khartoum in 2012 by course and supplementary thesis with the title: "C-reactive protein levels in Sudanese Overweight and Obese Adults". Dr. Sahar got her PhD from the Department of Biochemistry-University of Khartoum by thesis with the title:" Endothelial Nitric Oxide Synthase Gene Polymorphisms and Serum levels of Asymmetric Dimethylarginine in Sudanese with Essential Hypertension". She won a German Academic Exchange Service (DAAD) scholarship to continue her PhD in Germany. Now she is a postdoc fellow in the NH3bioNet (University of Khartoum Node) under supervision of Prof. Faisal Fadlelmola. Her main project is analysis of whole exome sequencing of Sudanese genomics, in addition to projects in precision and genomic medicine. Dr. Sahar is currently an Assistant professor in the Department of Biochemistry-University of Khartoum and a Registrar of Clinical Immunology. Her main research interests are immunepathophysiology of cardiovascular diseases and genomic medicine.

Molecular BiologyDNA ExtractionPCRElectrophoresisTaqMan Genotyping Technique DNA BlottingDNA CloningSequencing TechniquesNGS Data AnalysisImmunology

Mr. Mohammed Sabry - Software Engineer/Developer

Mohammed Sabry is a self-motivated lifelong learner. He recently joined the Centre for Bioinformatics & Systems Biology and H3ABioNet Sudan node as a Software Engineer/Developer.

He worked as a freelance web developer for a year and a half (2016 - 2017), he then shifted his focus to data science and machine learning. He was on a mentorship program from 2018 to 2019 offered by one student of the first cohort of Africa Masters of Machine Intelligence (AMMI), ended by publishing a research paper on reducing the variance of deep Q-learning algorithms. Prior to that Mohammed was refining his skills in all aspects of the data science pipeline from designing datasets to analyzing and visualizing to communicating results by participating in competitions and working in personal projects. He is also currently enrolled as a fourth-year student at Faculty of Engineering at University of Khartoum, Sudan, and he specializes in Software Engineering.

His current interests include design data visualization tools, power efficient machine learning systems from training to deploying, interpretability of deep learning models, deep learning for life sciences, and topological data analysis

Python ProgrammingJava ProgrammingMySQLSpark Programming TDA Toolkits UsageDeepChemSklearn |Pandas |NumpyFlask

Mr. Mohammed Sabry - Software Engineer/Developer

Ms Alyaa Elbadawi - PhD Student

Ms. Alyaa Elbadawi graduated with B. Sc. (honours) First Class in Zoology (Parasitology) from Faculty of Science, University of Khartoum in 2012. She has been awarded Master of Science (MSc) in Genetics and Molecular Biology from University of Khartoum in 2016. Her M.Sc. partial fulfilment research project was entitled " Association of a common rs9939609 variant in the fat mass and obesity-associated (FTO) gene with obesity in Sudanese children, Supervisor: Prof. Faisal M. Fadlelmola". Currently, Ms. Elbadawi is a PhD Candidate at the Centre for Bioinformatics and Systems Biology (CBSB) under the supervision of Prof. Faisal M. Fadlelmola.; her PhD is revolving around "Genomic & proteomic profiling of cervical malignant tissues Among Sudanese women".

RNA-Seq analysis GWAS16S rRNA MicrobiomeDNA Extraction PCR and RFLP TechniquesGel ElectrophoresisMicroscopy

Ms. Maram Suliman - PhD candidate

Ms. Maram A. Suliman graduated from faculty of Science; University of Khartoum with B. Sc. in Zoology (honors) second upper class (2007). She awarded her M.Sc. in molecular biology by research from Institute of Endemic Diseases, University of Khartoum (2020). Her M.Sc. research was about telomere length as a predictor of breast cancer and hepatocellular carcinoma in Sudan. She is skillful in different molecular biology techniques. Ms. Suliman is a teaching staff at the department of biology, Ibn Sina University, Khartoum, Sudan. Ms. Suliman is a PhD candidate at CBSB, University of Khartoum under supervision of Professor Faisal M. Fadlelmola. Ms. Suliman PhD study is revolving around “Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Sudan”. In her spare time, Ms. Suliman likes charitable work, adventure seeking and amateur photography.

Molecular Biology TechniquesLinuxMicrobiome AnalysisVariant Calling Analysis

Ms. Eman Ahmed - PhD candidate

Ms. Eman S. Y. Ahmed graduated with B.Pharm (Honors) Second Class from the Faculty of Pharmacy, University of Khartoum, Sudan in 2012. She has awarded her M.Sc. in Pharmaceutical Technology from Faculty of Pharmacy, University of Medical Science and Technology (UMST), Sudan in 2018 with (Honors) Distinction.
On July 26th, 2018 she published her M.Sc. partial fulfillment research project in a scientific paper entitled “Extraction And Evaluation of Mangifera Indica Gum as a Sustain Release Polymer in Glibenclamide Matrix Tablets” (http://www.ukjpb.com/article_details.php?id=391). During the period from 14 - 15 October, 2019 she presented the findings of this paper Virtually at Global Conference on Nanomedicine, Nanobiology, Nanotechnology & Pharmacology (SciTech Nanosciences- Pharma 2019) at Hotel Sunroute Plaza Shinjuku, Tokyo, Japan, 2019. (https://www.youtube.com/watch?v=GaUgwKxZQv4).
By January 16th, 2020 Eman published the details of her MSc research in a Book entitled: Mangifera Indica Gum as Sustain Release Polymer “From Extraction To In Vitro Release Kinetics” which has been published in Lap Lambert Academic Publishing, (https://www.amazon.com/dp/6200431086).
Currently Ms. Ahmed is a PhD candidate at the Center of Bioinformatics and Systems Biology (CBSB) under the supervision of Prof. Faisal M. Fadlelmola; her PhD is revolving around “Characterization of SARS-COV-2 and COVID-19 in Sudan through utilizing epidemiological, genomics, bioinformatics, and pharmacogenomics approaches: Towards better Diagnostic and Therapeutic Targets” She is a Teaching Assistant (Part-Time) at Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum.

Pharmaceutical Analysis and ManufacturingDosage forms PreparationPolymer Research Bio-Pharmaceutics BiostatisticsResearch MethodologyStructural Bioinformatics