VBI Faculty
Faculty from VBI who are looking for undergraduate students to work in their labs & with their research groups.

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
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
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).

• Daniel Capelluto
Our current research centers on the molecular structure and biochemical functions of signaling transduction systems involved in membrane trafficking and cell signaling. Our goal is to understand how protein domains transduce signals from biological membranes. Our laboratory employs biophysical approaches including high field nuclear magnetic resonance spectroscopy, circular dichroism, computer modeling, fluorescence spectroscopy, and surface plasmon resonance spectroscopy. With these tools, we can determine protein:lipid interfaces, ligand binding pockets and membrane insertion of protein domains from the molecular to the atomic resolution.

• Daniela Cimini
Our lab is primarily interested in the cellular mechanisms responsible for inducing aneuploidy in somatic cells. Aneuploidy, the condition of a cell possessing an incorrect chromosome number, is well known for inducing severe pathological genetic syndromes (e.g., Down syndrome) and is a hallmark of cancer.

Somatic cell aneuploidy arises as a consequence of inaccurate chromosome segregation during mitosis. Whereas many possible mitotic errors can cause inaccurate chromosome segregation, we believe that not all of them are equally likely to occur in the leaving organism, and that some of them represent a more severe threat than others to chromosome stability.

By using a combination of live-cell imaging, quantitative light microscopy, protein inhibition, and mathematical modeling (performed in collaboration with Dr. Alex Mogilner and Dr. Gul Civelekoglu-Scholey) we aim at identifying and characterizing the cellular mechanisms responsible for chromosome mis-segregation in both normal and cancer cells.

• 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.

• Carla Finkielstein
The overall goal of our research program is to dissect the molecular mechanism by which the circadian clock modulates the cell’s response to genotoxic stress. This work involves laboratory-based cell and molecular biology research, mathematical modeling, and basic in vitro studies using both isolated cells and complex in vitro vascularized 3D environments to answer fundamental questions about the relevance of circadian factors in the response of the cell to DNA damage.

• Harold R. "Skip" Garner
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.

• Silke Hauf
Cell division is a highly orchestrated process. Thousands of proteins are involved with hundreds being important regulators. We want to understand how such a complex event can be reliably executed, despite fluctuations in cellular composition ('noise') and variation in the cell environment. We want to know whether cellular design principles resemble or differ from the principles that are implemented in man-made systems to achieve reliability. Because cell division is so central to life, much of the regulation is preserved throughout evolution. We use the unicellular eukaryote Schizosaccharomyces pombe (fission yeast) as a model organism and combine genetic techniques, advanced fluorescence microscopy, proteomics and computational modeling to explore the mechanisms of reliable cell division.

• Ina Hoeschele
Dr. Hoeschele is a statistical geneticist and applied statistician with vast experience in the statistical design and analysis of large-scale omics experiments including linkage analysis in model organisms and human pedigrees, genome-wide association studies, transcriptomics, methylomics, and comparative genomics. Main applications are cardiovascular disease, diabetes and cancer in collaboration with Wake Forest Medical School and the VA-MD Regional College of Veterinary Medicine.

• 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.

• Sallie Keller
The Social and Decision Analytics Laboratory (SDAL) brings together computational social scientists and statisticians to embrace "big data,” building methods to provide evidenced based social and behavioral analyses for policy decision-making. SDAL addresses social science issues in new ways that will transform the way we understand the world, such as understanding the creation of smart and resilient cities, what influences the spread of disease and constitutes an effective pubic health response, homelessness, the demand for science, technology, engineering, and math educated graduates, and drivers for innovation. In answering applied social science questions, the goal is to advance research methods and tools to access, use, and analyze new sources of structured and unstructured data.

Dr. Keller is located in the National Capital Region (NCR) campus in Arlington, Virginia.

• Christopher B. Lawrence
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 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, stress resistance and species diversification. Current studies in the lab include whole genomic screening for evolutionary novelties and "genomic parasites" such as mobile elements. This research has special implications for cancer and 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 computational sciences, statistics, and biology.

• 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.

• Jean Peccoud
Synthetic biology (SynBio) can be broadly defined as the integration of engineering and biology to modify or generate new biological systems that are purpose-built for desired functions. These functions can be anything from industrial chemical synthesis to treatments for human diseases. The Peccoud group has two main complementary research programs – the development of tools to streamline SynBio cellular engineering, and the application of these tools to experimental systems (http://www.genocad.com). SynBio tool development in our lab includes a computer-assisted design (CAD) system for design and synthesis of gene expression systems (GenoCAD) and a gene expression verification platform that utilizes an automated environmentally controlled microscope system (GenoSIGHT). We are using these tools to engineer cell cycle mutants in yeast and examine their mutant phenotypes. Cell cycle control is central to life and defects in the cell cycle can result in human disease such as cancer. The cell cycle is a complex system of gene expression programs that ensure coordinated cell growth, chromosome duplication and segregation, and cytokinesis. We are performing experimental verification of computational models of cell cycle regulation. This project utilizes molecular genetic techniques to generate cell cycle mutants and microscopy to quantify the phenotypes of the mutants. We are looking for dedicated students with interests in molecular biology, genetics or cell imaging.

• Robert Settlage
Are you considering a career in Bioinformatics? Let’s get your feet wet. Here we are looking for an individual(s) with a familiarity with iOS app development and a drive to produce a usable product to help in creating an interface for genome sequence analysis. 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.

• Stephanie Shipp
Detecting patterns in data and creating outputs that can be used quickly and without ambiguity becomes increasingly difficult as the size of the data grow. The research involves retrieving and analyzing increasingly massive amounts of data to inform social and economic policy decision-making. Focusing on societal challenges, such as the creation of smart cities or enhancing social well being, provides hands-on research that seeks out creative use of new sources of data to address the research questions. The methodological work includes creating a digital library of SDAL datasets, accessing and using structured and unstructured big data in our analyses, presenting results using state-of-the art visualization tools, and developing inferential quantitative techniques and tools to solve infrastructural and methodological challenges.

Dr. Shipp is located in the National Capital Region (NCR) campus in Arlington, Virginia.

• 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.

• David Xie
The primary interest of Epigenomics and Computational Biology Lab is to understand the molecular mechanisms underlying epigenetic transitions during important biological processes associated with human complex diseases. Toward this goal, we emphasize on the development of high-throughput sequencing approaches for data generation and the implementation of computational tools for “omics” data analysis. In particularly, we are interested in the strategies to monitor the fidelity of DNA methylation inheritance, assess methylation variation within and between cell populations, identify true epimutations, and eventually, discover novel therapeutic ways.

We offer training opportunities to students with background in mathematics/statistics, computer science or biological science.

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