About the lab
My group performs research in computational and mathematical immunology. We use mathematical models, computer simulations and bioinformatical analyses, in order to understand the dynamics of lymphocyte repertoires in the immune system. The immune response involves cells of various types, including B, T and NK lymphocytes expressing a large diversity of receptors which recognize foreign antigens and self-molecules. The various cell types interact through a complicated network of communication, regulation and control mechanisms. This is what enables the immune system to perform the functions of danger recognition, decision, action, memory and learning. The dynamics of immune cell repertoires are, as a result, highly complex and non-linear.
My lab members develop various theoretical tools - mathematical models, computer simulations and novel bioinformatical methods - in order to analyze the dynamics of the immune system in various situations and predict the results of experimental and medical interventions.
Examples of past and current research topics include:
Vision for the future:
The more we learn about lymphocyte repertoires, the more we appreciate the staggering complexity that underlies their generation, selection, and function. When I started working in this area in the beginning of 1991, molecular markers and methods for investigating lymphocyte development and behavior were just being developed, and the human genome project was in its infancy - it has just presented as a possible plan to the US congress. During the years of my work in the field of theoretical immunology, I have seen it grow from a small group of interested individuals to a rich, active and challenging research field, whose members are becoming better integrated within the general immunology community. Theoretical immunology is still growing and has not yet fulfilled its potential, however. Thus, one of my career goals - aside from research - is to continue helping integrate theoretical work within all subfields of immunology. My choices of activities in professional society boards, conference and workshop organization, review and consulting boards reflect this career goal.           
The theoretical immunology community has by now internalized the lesson expressed, among other places, in my earliest reviews (1-3), that the immune system - or even any given part of it - are too complex to enable system behavior prediction out of highly simplified models. Hence the rising popularity of multi-scale modeling in this community. In my group, I plan to deepen research into the development and function of lymphocyte repertoires, and combine (in computer simulations) models that will unify the genetic, molecular, and multi-cellular aspects of lymphocyte repertoire dynamics.
One of the least-explored potential benefits of the human genome project is the emerging ability to characterize samples of lymphocyte repertoires by high-throughput sequencing. This has a huge potential for identification of subtle defects or changes in immune function, and developing between vaccines, better interventions in autoimmune diseases and malignancies, and better ways to rejuvenate the immune systems of elderly people. In spite of the potential, this area has been hardly touched so far - there are only a few papers presenting such data, and only since 2009 - because it is orders of magnitude more difficult than standard sequencing and genomic analysis. First, there is the repertoire complexity itself, which means that one cannot use "reference genes" in the analysis, and the available computational tools are of no use for theoretical immunologists; research groups must struggle to create the correct experimental controls and computational tools, as exemplified by e.g. Warren et al.'s recent paper on exhaustive T-cell repertoire sequencing (published online February 2011).
Second, analysis of B cell repertoires is even more complex than that of T cell repertoires - because of the additional diversifying processes that B cells undergo, i.e. somatic hypermutation and isotype switch. My group is one of only 5-6 groups in the world that are even trying - and, while all the other groups perform repertoire analyses based on the data generated, they all come to us for analysis of the mutations, because we have already developed methods and softwares for such analyses. Thus, a central theme in my research plans is to keep developing these methods, and collaborating with leading groups, in order to remain in the cutting edge of Ig gene research.  

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Ramit Mehr's CV