Member of the Faculty of Pathology
Beth Israel Deaconess Medical Center
Beth Israel Deaconess Medical Center
330 Brookline Ave
Boston MA 02215
Oppenheimer trust award
My group performs computational biology using a systems approach to deliver interventions through understanding of processes underlying disease.
In Africa, we exploit what we find in analysis of genomcis into focused development of health research capacity
In USA we translate understanding of the underlying processes of disease into broadly applicable health interventions.
African Genomics and Disease
(Keywords: HIV, Leishmania, Sleeping sickness, Health internventions, BIoinformatics, African Genomics, Systems biology)
The applied global aspect of my work is capacity development using genomics to impact health in Africa. The approach exploits bringing together the availability of genomic information and the intellectual pool in African countries to provide disease targeted training and research development. This results in long term collaborations and access to diverse datasets from cohorts and genomes. Work we perform includes:
Sequencing and analysis of the tsetse fly genome,
Systems biology approaches to understanding the response of the host to infection with Leishmania
HIV diversity and evolution
Development of networks of laboratories for translation of genomic information.
My work has recently become focused by the offer of large scale funding by the Wellcome Trust and NIH to develop genomics analysis capacity for health in Africa. I am the bioinformatics lead on this project and am a member of the ‘H3 Africa’ steering committee - developing the strategy and funding rollout in 2011 of $ 37M to improve genomics capacity in Africa. My particular focus will be recruitment and training of Africans in Biostatistics and bioinformatics - bringing faculty and students here to the HSPH for funded collaborations and visits, and developing training within Africa by HSPH faculty.
Molecular profiling to understand disease
(Keywords: Stem Cells, Cancer Stem Cells, Systems Biology of stem cells, Induced pluripotent stem cells, computational biology, bioinformatics)
The fundamental research aspect of my work focuses upon development and deployment of systematic approaches to organizing molecular information. My group performs computational analysis of stem cells - in normal and diseased blood and importantly, in cancer stem cells. We are particularly interested in understanding the processes shared by cancer stem cells across different tissues and organs. We work together with leading researchers at the Harvard Stem Cell Institute to compare and discover stem cell processes between leukemia, glioma and colon cancer. Discovery of common stemlike processes in these systems can lead to development of powerful drugs that can target cancers so that there is no remission.
By systematic organization of molecular profiles my group performs integration across biological processes leading to discovery of key processes and targets involved in normal and diseased systems. Most molecular profiling exploits the availability of gene expression assays using arrays or next generation sequencing. I take this information and transform it onto molecular pathways and networks of interaction. By performing this transformation in a highly systematic manner, I am able to generate consistent functional profiles of cells, tissues and populations. I have been applying this ‘pathway fingerprinting’ approach to the understanding of the key processes of stem cell regulation. As a result, we have recently discovered a ‘pluripotent signature’ that links closely to the survival of cancer patients. We have used this signature to classify induced pluripotent cells (iPS - stem cells) and thus determine the true pluripotency of artificially induced stem cells. A characterization of iPS we have performed is now under submission as a brief communication to Nature.
Working closely with the Harvard Stem Cell Institute, my group is developing a system called the ‘Stem Cell Discovery Engine’. This system integrates molecular profiles and phenotypes from diverse kinds of stem cells and differentiated cells. Using this tool, we are discovering the key processes that contribute to cancer stem cell survival. As the importance of bioinformatics increases in biomedical research, it is becoming clear that the stem cell institute, the HSPH, and organizations such as Catalyst all require greater bioinformatics capacity. I am actively engaged in developing scalable approaches to provide bioinformatics expertise to impact health research across Harvard.
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