Global Summer Research Institute

VBI Faculty
Listed below are VBI faculty members that are looking for undergraduate participants to work in their labs & with their research groups for the Global Summer Research Institute.

Click on the links to find out more about the research faculty members at VBI are engaged in, and choose a group that is working on research that appeals to your interests!

• Christopher L. Barrett
Barrett in the 2010 VBI Scientific Annual Report
The NDSSL is pursuing an advanced research and development program for interaction-based modeling, simulation, and associated analysis, experimental design, and decision support tools for understanding large biological, information, social, and technological systems. Extremely detailed, multi-scale computer simulations allow formal and experimental investigation of these systems. The need for such simulations is derived from questions posed by scientists, policy makers, and planners involved with very large complex systems. The simulation applications are underwritten by a theoretical program in discrete mathematics and theoretical computer science that is sustained by more than a decade of experience with the interplay of research and application.

• Josep Bassaganya-Riera
Bassaganya-Riera in the 2010 VBI Scientific Annual Report
Josep Bassaganya-Riera is the Director of the Nutritional Immunology and Molecular Medicine Laboratory (NIMML, www.nimml.org) and a Professor of Immunology at VBI. He leads large-scale research programs on infectious diseases, gastrointestinal health, and obesity-related inflammatory complications. The central integrative theme of NIMML's active areas of research and discovery is to understand the inflammatory processes that underlie various human diseases. To fulfill its mission, NIMML has developed a fully integrated experimental, bioinformatics and computational environment that encompasses from immunological experimentation to modeling and simulation based on high-performance computing (www.modelingimmunity.org).

• Kristy Collins
Science and mathematics education is critical for our society’s future. The challenge of turning science and mathematics from an abstract concept into a personal experience for parents and children lies in making them encounter the subjects directly and interact with a professional scientist or mathematician. My science education research program includes investigating the interaction between scientists and the public and how children (and their parents) learn and excel within the Kids' Tech University (KTU; http://kidstechuniversity.org ) framework. I also facilitate research and education initiatives within VBI and have various other projects that would benefit from additional assistance including, VBI’s booth at the USA Science and Engineering Festival ( http://www.usasciencefestival.org/ ). Undergraduates interested in education initiatives in science, mathematics, technology, art/graphic art, computer science/programming should contact me.

• Allan W. Dickerman
Dickerman in the 2010 VBI Scientific Annual Report
Genomics is playing a greater role in understanding processes important for human health, ecology and economy. The increasingly important science of phylogenomics studies the relationship of a gene’s function to its evolution, thus providing greater insight into the mechanisms of both disease and health. In recent work, the Phylogenomics Research Group has been studying such societally important topics as agricultural pathogens, the commensal gut microbiome, and biofuels.

• Stephen Eubank
Stephen Eubank is a physicist in the NDSSL studying the effect of a network's structure on dynamical processes taking place on that network – for example how details in social contact networks affect the spread of disease in a community. The research is both theoretical, involving mathematical formalisms of dynamical systems, and experimental (computational, not wet lab), using NDSSL's disease outbreak simulation engines.

• Christopher Franck
The modern statistician is able to play a key role in science from the moment a research question is raised and data collection is planned to the point when final conclusions are articulated. Chris Franck’s research group collaborates with a number of VBI researchers, providing statistical solutions for experimental design, data collection, visualization, analysis, modeling, and technical writing for a variety of topics.

• Harold R. "Skip" Garner
Garner in the 2010 VBI Scientific Annual Report
The Medical Informatics research group develops technologies, tools, databases, and methods for biomedical research to make discoveries in genetics, genomics, medicine, and new research areas such as ethics. The work integrates bioinformatics and wet lab research and proceeds in two directions. Computational research allows scientists to initiate new projects, generate new hypotheses, and pursue promising research areas that involve the use of clinical samples. Bioinformatics permits follow-on analysis and interpretation of laboratory data to form new knowledge. A major emphasis of the lab now is the discovery of Biomarkers and drug targets for cancer and neurological diseases through the en masse analysis of the repeatitive (microsatellite) portion of the genome using microarrays and next generation DNA sequencing technologies. Very large data sets are generated and high performance computing is used to analyze and interpret the data.

• Ina Hoeschele
Hoeschele in the 2010 VBI Scientific Annual Report
The common theme of research in the Statistical Genetics Research Group is the statistical design and analysis of genome-wide linkage and association studies and experiments, and systems genetics experiments and studies. This set of strategies is used to further understand how the joint action and interaction of multiple genes and pathways determine complex diseases and biomedical phenotypes of humans, animals and plants.

• Raquel Hontecillas
Raquel Hontecillas is an Assistant Professor in the Nutritional Immunology and Molecular Medicine Laboratory at VBI and the Immunology Lead for the Center for Modeling Immunity to Enteric Pathogens (www.modelingimmunity.org). She studies the induction of mucosal immune responses following infection by viral or bacterial pathogens. She is currently working in the development of experimental models of infectious diseases in parallel to computational models for calibration or prediction testing. She is also involved in the design of novel vaccines and broad-based immune therapeutics against respiratory and gastroenteric infectious diseases.

• Shiv Kale
Eukaryotic pathogens of both plant and animals utilize a diverse array of tools to facilitate pathogenesis and disease. Many of these microbes devastate economically important crops, and several cause mortality and disease in humans. Dr. Kale’s research group centers on three fungal pathogens of humans: Aspergillus fumigatus, Coccidioides immitis, and Cryptococcus neoformans. The group focuses on the translocation and function of small-secreted proteins that are involved in pathogenesis. Through the characterization of these small-secreted proteins the Kale Group is currently developing novel therapeutics against fungal pathogens.

• Reinhard Laubenbacher
Laubenbacher in the 2010 VBI Scientific Annual Report
Systems biology brings together mathematical modeling, simulations, and quantitative experiments, allowing researchers to use the data of one of the approaches to repeatedly define the framework of the other approaches. Mathematical models are increasingly being used in systems biology to model a variety of biochemical networks. The Laubenbacher Research Group is focusing on the use of systems biology as an innovative approach to research, through both theoretical and applied projects.

• Christopher B. Lawrence
Lawrence in the 2010 VBI Scientific Annual Report
Alternaria and Aspergillus are some of the most ubiquitous molds found in the environment. These generally include many important plant pathogenic species. Additionally, these fungi are clinically linked to human airway disorders such as severe allergic asthma, chronic rhinosinusitis, and invasive Aspergillosis. The Lawrence Research Group studies the ways in which fungi cause diseases of plants and humans.

• Achla Marathe
Achla Marathe is the lead economist and social scientist at NDSSL. She has been working on issues that are at the interface of public health, economics and behavior, e.g. the spread of person to person infectious diseases and viable ways to mitigate them. She has been analyzing friendship networks to assess the influence of peers on initiation of smoking and the spread of obesity. Her other areas of research involve simulation and modeling of networked infrastructures such as communication and energy systems.

• Madhav Marathe
Madhav Marathe is a computer scientist in NDSSL and studies the problems of modeling and analysis of large urban social and infrastructure networks and analysis of graphs and graph dynamical systems in different applications. We develop methods from theoretical computer science as well as high performance computing for studying such systems, and have developed a large suite of simulation tools for studying dynamical processes on very large graphs.

• Pawel Michalak
Research in the Michalak lab focuses on subtle changes in genomes that drive both evolution and human disease. Recent advances in genomic based technologies such as “next-gen” sequencing of whole genomes and transcriptomes, provide a unique opportunity to investigate how genomic changes effect cellular function and species diversification. Current studies in the lab include whole genomic screening for mutations leading to cancer in people who have been exposed to radiation for prolonged periods. We are also interested in the control and segregation of chromosomes in polypoid species (species that have more than 2 copies of their chromosomes). This research is of special interest for Down syndrome, a condition cause by 3, rather than 2, copies of chromosome 21. These studies employ a variety of approaches including molecular biology, genetics and computational techniques. The lab is currently in search of motivated students in biology, computational sciences or statistics.

• David Mittelman
Briefly, my lab dissects the mutational pathways that induce genome changes over time. We also develop assays and technologies that exploit these processes of change for basic research, commerical, and therapeutic benefit. We are a multidisciplinary team with an experimental approach that combines traditional biochemistry, cell biology, and genetic techniques; coupled with population genetics simulations, genomics, and other computational methods. We actively recruit students from all disciplines of science, mathematics, engineering, and the arts. Examples of recent projects include (1) development of molecules synthetic and natural that can be used to disrupt/repair/alter gene function, (2) methods to track cells and organisms, and (3) methods to analyze whole genome data for persona genomics.

• Henning Mortveit
Henning Mortveit is a mathematician in NDSSL and works with dynamical processes that take place on networks. A central part of this work is to determine their characteristics without resorting to exhaustive computations. Using the structure of the network, the behavioral properties of the vertices in the network, and so on, one seeks insight about e.g. limit sets and stability. This work supports for example modeling and model validation.

• Biswarup Mukhopadhyay
Mukhopadhyay in the 2010 VBI Scientific Annual Report
Dr. Biswarup Mukhopadhyay's research group studies the biochemical mechanisms used by microorganisms to survive under extreme conditions. Research in the laboratory focuses on the physiology, enzymology and evolutionary biology of methanogenic archaea, mycobacterial metabolism and tuberculosis, and microbiological conversion of coal to methane in deep subsurface coalbeds.

• Jean Peccoud
Peccoud in the 2010 VBI Scientific Annual Report
The Synthetic Biology group at VBI is developing a design automation framework for engineering synthetic biological systems. The successful combination of experimental and computational methods within this framework will unleash the enormous potential of the rapidly emerging field of synthetic biology.

• Andy Pereira
Pereira in the 2010 VBI Scientific Annual Report
Plants have complex mechanisms for responding to and surviving environmental stresses such as drought, heat, cold, and disease. Analysis of the plant stress responses can provide valuable insight into protective mechanisms and resistance to the plant stresses. The goal of the Pereira research group is to develop a systems-level view of these complex biological processes through the development of probabilistic functional gene networks.

• Robert Settlage
Are you considering a career in Bioinformatics? Let’s get your feet wet. In this project, we will develop and build a visual tool for assembling genomes from vast amounts of DNA (or RNA) sequence data. The problem is this: a) the NextGen sequencing machines are producing vast amounts of data (>25Gbases per day) which are outpacing our ability to analyze the data and b) current algorithms all have manual steps where human interaction is the key to completing the project and yet the tools for performing the manual analysis are not optimized for the scope of the problem. Here we are looking for an individual(s) with knowledge in perl, relational databases, Java, and a drive to produce a usable product to help in creating an interface for genome sequence assembly.

• João Carlos Setubal
Setubal in the 2010 VBI Scientific Annual Report
Gene annotation, the process whereby evidence is inferred about the function of genes, is a key step in understanding the genome. Dr. João C. Setubal’s research group works primarily on bioinformatics for microbial genome annotation and sequence analysis, with a focus on facilitating the comparison of genomes.

• Bruno Sobral
Sobral in the 2010 VBI Scientific Annual Report
Discovering, developing, and deploying informatics-based methods, infrastructure, and resources to integrate and analyze infectious disease data; translational systems informatics to support clinical outcomes, research, and scientific discovery; and wet lab validation of computational analyses.

• Brett Tyler
Tyler in the 2010 VBI Scientific Annual Report
Interconnected genetic regulatory networks govern the interactions of hosts and pathogens due to an ongoing co-evolutionary battle between the organisms. Understanding the components and structure of these networks will help researchers develop more sophisticated approaches to disease prevention and control. Dr. Brett Tyler’s research group is building data collections and tool sets to dissect in detail host-pathogen genetic networks, with a particular focus on oomycete plant pathogens.

• Anil Vullikanti
Anil Vullikanti is a computer scientist in NDSSL and studies on the computational aspects of problems involving graphs and their dynamics arising in applications such as diffusion on social contact networks, mobile social networks and electrical power grids. Computing properties of such systems is challenging, and we focus on developing efficient algorithms and simulation based analysis techniques that scale to very large systems.

Additional information on faculty research can also be found in the VBI Annual and Scientific Reports.