H3ABioNet CUBRe Postgraduate workshop 2014 Trainers

Introduction to Linux and Python Programming

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Dr. Oyelade, Olanrewaju Jelili Received his Bachelor Degree in Computer Science with Mathematics (Combined Honour) and M.Sc. in Computer Science from Obafemi Awolowo University, Ile-Ife, Nigeria and Ph.D in Covenant University, Ota, Nigeria. He is a Faculty member in the Department of Computer and Information Sciences, Covenant University, Nigeria. His current research interests include Bioinformatics, clustering, Fuzzy logic and Algorithms. He is a member of International Society for Computational Biology (ISCB), Africa Society for Bioinformatics and Computational Biology (ASBCB), Nigeria Society of Bioinformatics and Computational Biology (NISBCB), the Nigerian Computer Society (NCS), and Computer Professional Registration Council of Nigeria (CPN).

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Mrs Itunuoluwa Isewon is a faculty in the Department of Computer and Information Sciences, Covenant University, Nigeria and a former Research Fellow at the German Cancer Research Center (aka DKFZ), Heidelberg, Germany under the DAAD fellowship.

Introduction to Bioinformatics and Proteomics Resources

Shaun Aron

Shaun Aron has been a member of Wits Bioinformatics since 2007 when he joined as an MSc student in Human Genetics/Bioinformatics. After completing an Honours degree in Human Genetics, he was intrigued by the computational approaches being developed to address complex biological questions and decided to hang up the pipette and pick up a computer instead. His MSc aimed to apply relevant bioinformatic techniques to characterise and possible identify the molecular cause for a rare genetic skin disorder called Keratolytic Winter Erythema. While completing his MSc he joined Wits Bioinformatics as an Associate Lecturer/Consultant in 2009 and has been involved in various teaching, training and consulting activities within the university. In 2013 he took up the position of H3ABioNet Bioinformatics Consultant/Trainer at the Wits Node of H3ABioNet. Shaun has a keen interest in the genetic basis of rare genetic disorders, population genetics and the practical application of bioinformatics for biologists. He is also actively involved in the education and training endeavours of the H3ABioNet and H3Africa AWIGEN project.

Introduction to Biostatistics

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After studying computer science, mathematics and signal processing at the École Normale Supérieure de Cachan (Rennes, France), Jean-Baka graduated with an MSc in computer science in 2006. I then traveled on a one-year sabbatical in 2006-2007 to lecture in Niamey, Niger and Yaouné, Cameroon, in a project aimed at developing capacity in mathematics and CS higher education and research in Africa. Back in France,  I started my PhD in Montpellier (at LIRMM, a CNRS lab) under the supervision of Prof. Olivier Gascuel, in the field of phylogenetics and statistical modeling. I defended my PhD thesis in December 2011, which is titled “Combination of phylogenetic and sequential models to analyze biological sequences: reconstructing ancestral profile HMMs.” I am now a postdoctoral fellow at SANBI, in the research group led by Dr. Nicki Tiffin. I am working for the H3Africa consortium, more specifically in the NIH-funded H3ABioNet project. Within this project, my first objective is to develop and make use of a new tool to assess capacity in bioinformatics in Africa and to report about the effectiveness of the H3ABioNet project, in terms of capacity building.

Introduction to NGS and GWAS

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Dr. Lawrence Heisler is a research associate working at the Ontario Institute of Cancer Research in Toronto Ontario. He received his PhD in neuroendocrine physiology in 1993 from Queen’s University in Kingston Ontario. After completion of his degree he moved toward biological computing and bioinformatics working with the analysis and development of microarrays then next-generation sequencing technologies.  He has worked extensively in human and yeast genomics.  Currently he works in the production core, developing analysis pipeline and working on a variety of research projects in support of investigators at OICR.

 

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Takafumi Yamaguchi, MSc. is a bioinformatician at Ontario Institute for Cancer Research (OICR). His current focus is next generation sequencing (NGS) data analysis and the development of NGS analysis pipeline including DNA reads quality control, alignment and mutation calling.
After obtaining the knowledge and experimental skills in genetics, molecular biology during undergraduate studies at the University of Manitoba, he learned systems biology, programming and NGS data analysis under the supervision of Dr. Fritz Roth at the University of Toronto. His project during the graduate studies was systematic analysis of suppressor mutations in yeast deletion strains using NGS technology.
He started working with Dr. Paul Boutros at OICR as a bioinformatician after receiving a Master of Science in 2013. He is currently involved in multiple projects including the Canadian Prostate Cancer Genome Network (CPC-GENE) Project, International Cancer Genome Consortium (ICGC) Cancer Genome Project, and The Cancer Genome Atlas(TCGA) DREAM Challenge.

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Dr. Segun Fatumo is a visiting research fellow with the International Health Research Group at the University of Cambridge, UK and at the Genetic Epidemiology Group at the Wellcome Trust Sanger Institute under the arrangement of H3ABionet capacity building. He holds MS and PhD from University of Cologne Germany and Covenant University Ota Nigeria and a postgraduate certificate in public health from University of Liverpool, UK. He worked as postdoctoral research associate at the Center for Tropical and Emerging Global Disease at the University of Georgia and at Institute of Structural and Molecular Biology, University College London.
His research explores genomic diversity and its impact on infectious and cardiometabolic risk factors among African populations. His current research focuses on association analysis of nearly 5,000 Uganda participants genotyped with the 2.5M Illumina chip array using mixed models. His work has largely centred on the genetic basis of cardiometabolic traits and diseases, particularly lipid metabolism, coronary artery and infectious disease, and the use of genetic tools for causal inference.

Databases, data mining and analysis pipelines

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Amel Ghouila is a bioinformatician at the Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Institut Pasteur de Tunis, working on the NIH-funded H3ABioNet project. Within this project, her first objective is to develop predictive data mining tools that are becoming an essential instrument in clinical medicine. She is also involved on education and training activities within this project. Amel has a background in Informatics and was teaching it for several years at the computer sciences department of the Faculty of Sciences of Bizerte, Tunisia. She then obtained a PhD in Bioinformatics jointly from University Montpellier 2, France and University Tunis El Manar, Tunisia during which she has been working on the development of new methods for pathogens annotation. Her main interests include functional annotation, data mining techniques and database conception and implementation.

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Kais Ghedira is a bioinformatician who is a member of the Laboratory of Medical Parasitology, Biotechnologies and Biomolecules (LR11IPT06) and member of the Group of Bioinformatics and Mathematical Modeling (GBM), in Institut Pasteur de Tunis (IPT). After his master he obtained a diploma from the Institut Pasteur of Paris for the course Informatics in Biology in 2007. He then started his PhD in Bioinformatics in 2007 and defended it in 2011 in the faculty of Sciences of Bizerte, Tunisia in which he worked on the analysis of gene expression and regulation in prokaryotic and eukaryotic cells. In 2013 he got a permanent position in IPT as an assistant professor. In the frame of his PhD, he worked for 5 months in Biobase GmbH company in Germany which is an international bioinformatics company focusing on the generation, maintenance and licensing of databases and tools in the field of molecular biology. He was involved in several international and national projects funded by EC and IPT and actually is a member of the H3ABioNet project funded by the NIH. His main work in the frame of this project consist of a meta-analysis of OMICS data, phenotypic data and identification of candidate genes related to disease and the remodeling of a clinical SCD database. He is also involved in education and training activities within this project and is being part of the bioinformatics curriculum development group. Kais is a bioinformatician with biological background who has been a lecturer in several international courses in IPT and actually is a bioinformatics lecturer in the Higher Institute of Biotechnology of Sidi Thabet (ISBST). He is mainly interested in the analysis of large scale OMICS data, data integration, functional analysis of gene expression, gene regulation and prediction of gene/protein interaction networks.

CUBRe LOCUM

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Professor Ezekiel Femi Adebiyi obtained the Ph.D degree in 2002 in Computer Science-Algorithms and Bioinformatics from the University of Tubingen, Germany on a German Academic Exchange Programme (DAAD) Scholarship. He had his basic and research training in Mathematics at the University of Ilorin, Nigeria with the B.Sc (Second Class Upper) and the M.Sc degrees. Starting as a Graduate Assistant at the University of Ilorin, Nigeria in 1992, Ezekiel Adebiyi rose rapidly to become a Professor at Covenant University in June 2010. In between this working track, he served as Research Fellow in several institutes in the US and also in Europe. He has also worked in World-Class organizations and therefore has a rich blend of academic and professional experience. He is the President, Nigeria Society of Bioinformatics and Computational Biology, formerly Vice-President and presently Secretary, African Society of Bioinformatics and Computational Biology. Prof. Ezekiel Adebiyi is the leader of the Covenant University Bioinformatics Research. He is industrious, with a passion to turning his theories to products. His main research interests are in computational complexity and computational molecular biology, with emphases on the bioinformatics of malaria research and recently human genetics.

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