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GAANN Fellowship 2012 – Drexel Biomedical Engineering

Bioinformatics of Infectious Diseases

The GAANN (Graduate Assistance in Areas of National Need) Fellowship is a doctoral fellowship program funded by the U.S. Department of Education.

Currently, we have four doctoral fellows enrolled in the GAANN program, and we are recruiting two more fellows with full tuition and stipend funding among U.S. Citizens and permanent residents. Qualifications include background in life sciences, engineering and computer sciences in addition to other requirements satisfied by Drexel BIOMED doctoral students. For more information contact Dr. Tozeren at aydin.tozeren@drexel.edu

Synopsis

The primary aim of this proposal is to contribute to the development of a highly skilled workforce in bioengineering with the ability to make a significant impact on the prevention and treatment of infectious diseases. Our specific main objective is to train five GAANN Fellows who will pursue the Doctoral Degree (PhD) in Biomedical Engineering with focus on bioinformatics and computational genomics of viral and bacterial infections. The program will concentrate on the development of a system view of the crosstalk between host cells and bacterial cells and viruses, as learned from genome sequences, gene and microRNA expression profiles, and complementary targeted proteomics. The program will bring together the diverse research and education backgrounds of Drexel Biomedical Engineering, Microbiology and Immunology, along with GlaxoSmithKline Bioinformatics Experts and Drexel's Coulter Translational Research Initiative to make a significant impact in training Next Gen scientists and Engineers studying contagious diseases.



The Facebook social network (left) has a total of 800 million active users and 104 billion connections between these users [1]. The 2009 H1N1 worldwide outbreak caused more than 41,000 hospitalizations as shown in the figure on the right with the area of each bubble representing the number of hospitalizations (orange) and deaths (red) [2]. Merging large-scale datasets will allow for accurate predictions of future outbreaks.

Current BIOMED GAANN Fellows:

Latifa Jackson

picture of a latifa jacskon

PERSONAL: I earned my B.S. in Cell/Molecular Biology and Genetics and my B.A. in French Language and Literature from the University of Maryland in College Park, MD. After time spent working in academic research and in international development, I went back to school to earn my M.S. in Ecology and Evolutionary Biology at the University of Arizona in Tucson, AZ. I am currently working on my Ph.D. at Drexel University to understand the intersection of genetic variation, immunity and infectious disease. In my spare time I like to make jewelry, painting and traveling to distant corners of the world.

RESEARCH: My research interests have grown out of my experiences living and working abroad in East and West Africa. One cannot see the impact of infectious diseases on human populations without thinking about possible solutions. For me, this means understanding how immune adaptive genetic variation is partitioned across geographical scales and how this variation contributes to immune defense of infectious diseases in human populations. I am currently working on a project to examine the variation in key immune function pathways in a global distribution of human populations. This work is fundamental to understanding not only reasons that certain human populations are immune to specific diseases, but it also had predictive ability to look at how various ethnic populations respond to drugs targeting immune pathways.


Gregory W. Schwartz

picture of a gregory schwartz

PERSONAL: I earned my BA in Mathematics and Biology at Franklin & Marshall College in Lancaster, PA. I am now conducting my Ph.D. research at Drexel University. My research interests involve combining mathematical concepts to biological systems and properties in a computational setting. My immediate research involves computational analysis of the B cell repertoire, including detection and mutation analysis of heavy chain sequences. In my spare time I like to try haphazardly to cook from scratch, fiddle with technology, and entertain my cat traditionally with yarn.

RESEARCH: My field of study falls firmly under the rubric of the Quantitative Biology and Bioinformatics. For my Ph.D. I am studying systems biology and, more specifically, the complex system interactions by which immune repertoires generate adaptive immunity to pathogens. I will develop methods to relate nucleotide level diversity to amino acid and protein level diversity and functionality. It is generally acknowledged that medicine must move forward to being more preventative and personalized; more vaccines and less antibiotics. One of the fundamental impediments towards such advances is a lack of understanding as to the exact role of diversity in the immune repertoires that underlie adaptive immunity. A clear understanding of this diversity and its functional consequences would help us identify ahead of time risk of autoimmunity and leukemia and the potential efficacy of vaccines to induce protective immunity. High throughput methods of sequence analysis and cell – cell interactions give us hope that such studies can be done. However, at present we are missing basic conceptual and computational tools to asses such data. Therefore, I believe the first step towards true personalized medicine is to create a reasonable model of immune diversity and it functional consequences. I will attempt to do this through system biology analysis of sequence data from different immune responses and animal models. This analysis will be done in close collaboration with several experimental biology labs in Drexel University, the University of Pennsylvania, and beyond. In this fashion I hope to take basic principles from the study of fractal and dynamical (physical) systems and apply them to solve essential biotechnological problems relating to the manipulation of the adaptive immune system.


Maksim Shestov

picture of a maksim shestov

PERSONAL: I earned my B.S. in Biomedical Engineering with a focus in Tissue Engineering, Biomaterials and Regenerative Medicine from Drexel University in 2012. I jumped right back into school in a pursuit of a PhD also at Drexel University with a focus in Bioinformatics and Biocomputation. My research interests involve analysis of disease signatures, drug development and repositioning, biological pathway analysis and applying novel methodologies for the intersection of tissue engineering, regenerative medicine and computational biology. In my spare time I enjoy boxing, traveling and improving my skills playing guitar and piano.

RESEARCH: The focus of my research has grown out of my undergraduate exposure to engineering and biology. In my graduate studies I gained an in depth look at the power and potential of computational tools to bring engineering, biology and informatics together. This combination of tools can have a truly broad impact on the future of medicine, treatment options and pharmaceuticals. I currently have 2 projects; one involves the understanding of regenerative pathways and potentials of homo sapiens and several model organisms taking cues from developmental biology. The 2nd involves the cross talk analysis between microorganisms and vertebrates which has the potential for important results for evolutionary biology and drug targeting.


Alex Pestell

picture of a maksim shestov

PERSONAL: I earned my BA in Physics and Philosophy at Drew University.

RESEARCH: I am now conducting my Ph.D research at Drexel University. My research interests involve applying mathematical analysis to biological systems. My current research involves computational analysis of micro RNA in liver diseases involving hepatitis virus. When I can, I read fiction and experiment with different recipes.

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