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Bioinformatician & Big Data Scientist (Post-Doc Researcher)
Steve Kelly Lab, the Department of Plant Sciences

University of Oxford

Passionate about developing and applying bioinformatics to make sense of cross-data-type cross-species collections of big datasets in a way that makes sense!

BaselFlorence

Enormous amounts of biological data of various types have been and are increasingly being generated; yet, there is currently little or no development in methods that leverage datasets from multiple data-types collectively in biological research. For example, there is no mechanism to integrate RNA-seq data with imaging data, or to link phylogenetic data to metabolomics. My long term passion is to develop the next generation of bioinformatic tools to allow users to quickly and easily leverage data from multiple disparate experiments and datatypes to draw new conclusions about fundamental biological processes. This will not only lead to breakthroughs in the development of machine learning and statistical methods; it will also facilitate breakthroughs in biological applications such as gene-trait association networks, gene-gene interaction networks, drug target discoveries, trait signature identification, and many other timely applications.

My previous work can be classified into two main themes; development of bioinformatic methods, and biological applications.

Bioinformatic methods development: I developed and advanced a number of bioinformatic methods for gene expression clustering. My current state-of-the-art framework is called clust (Abu-Jamous & Kelly, Genome Biology, In Press). Clust extracts optimal and complete clusters automatically from one or more heterogeneous gene expression datasets collectively, it outperforms mainstream clustering algorithms with minimal manual intervention, and is available freely as an easy-to-use package on https://github.com/BaselAbujamous/clust. A web-based front-end will be released soon!

Applications in biology: I actively employ my bioinformatic methods and other methods to drive discoveries in biology. For instance, I identified a counter-intuitive transcriptomic signature in breast cancer cell-lines with a prognostic value in collaboration with Professor Adrian Harris and Dr Francesca Buffa (Department of Oncology, the University of Oxford). I also participated in defining the dynamics of distinct genetic programmes during human erythropoiesis (red blood production) in collaboration with Professor David Roberts and colleagues (Radcliffe Department of Medicine, University of Oxford). Moreover, I discovered a novel transcriptomic module that is consistently anti-correlated with growth in budding yeast, and elucidated the function of the CMR1 yeast gene in DNA metabolism. Additionally, I participated in identifying patterns of human brain activity during emotional stimuli in collaboration with Professor Elvira Brattico (Aarhus University, Denmark).

Currently, I work in Steve Kelly’s laboratory at the Department of Plant Sciences, the University of Oxford, within the C4 Rice Project. I have identified key engineering targets to improve photosynthesis in the rice crop. These targets have been validated and are in the process of being protected before progressing to engineering.

I published a research monograph book, a book chapter, and many journal articles, and I presented my work in various national and international conferences and research meetings.

My CV is available here.

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