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The Virginia Bioinformatics Institute (VBI) is a research institute dedicated to the study of the biological sciences. By using bioinformatics, which combines transdisciplinary approaches to information technology and biology, researchers at VBI interpret and apply vast amounts of biological data generated from basic research to some of today’s key challenges in the biomedical, environmental and agricultural sciences. Work at VBI involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics and synthetic biology. Transdisciplinary research at the institute encompasses scientific program areas that include bioinformatics, cellular networks, complex systems and genomes. Research at VBI is supported by state-of-the-art resources that include core laboratory and core computational facilities. The institute develops genomic, proteomic and bioinformatic tools that can be applied to the study of infectious diseases as well as the discovery of new vaccine, drug and diagnostic targets.
Advanced Computing and Decision Informatics Laboratory (ACDIL)
Constructing large simulations of co-evolving networks representing real world complex systems is challenging and novel. These systems are affected by physical, bio-physical laws and also human behavior, regulatory agencies, courts, government agencies, and private enterprises. Our application focus is in the following areas: infrastructure and economics, immunology, public health epidemiology, infectious and non-communicable diseases, social and behavioral modeling systems, and national security policy and decision informatics.
Programs include:
 The Network Dynamics & Simulation Science Laboratory (NDSSL) research and development program at VBI advances the science and engineering of co-evolving complex networks and develops innovative computational tools based on these advances to support the emerging field of policy informatics. Further information is available at the NDSSL web site http://ndssl.vbi.vt.edu/index.php.
Nutritional Immunology & Molecular Medicine Laboratory (NIMML) aims to elucidate the cellular and molecular mechanism(s) by which novel immune therapeutics modulate chronic inflammatory and infectious diseases. Our four principal lines of research are: 1) nutritional immunology, 2) gastrointestinal health, 3) obesity and its comorbidities (i.e., type 2 diabetes and cardiovascular disease) and 4) modeling immune responses. Modulation of inflammation and immunity are common integrative themes. For more information, see the NIMML site at http://www.nimml.org .
Social and Decision Informatics Laboratory (SDIL) focuses on the use and development of analytical technology in the areas of public health policy, national and international security policy & public and social policy. SDIL will be central to the practical transition of NDSSL-developed science and technology.
Cyberinfrastructure
 The Cyberinfrastructure (CID) research program at VBI engages in cyberinfrastructure systems development, deployment and integration in support of health sciences activities (“bench-to-bedside”). CID is an informatics-based group that can develop and deploy large-scale information systems, with substantial wet lab capability and experience to support validation of informatics-based hypotheses. The group applies the principles of cyberinfrastructure to integrate data, computational infrastructure, and people. CID has developed many public resources for curated, diverse molecular and literature data from various infectious disease systems, and implemented the processes, systems, and databases required to support them. It also conducts research by applying its methods and data to make new discoveries.
In September 2009, the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), awarded a 5-year, $27,670,448 contract to CID to support the biomedical research community’s work on infectious diseases. The funding is being used to integrate vital information on pathogens, provide key resources and tools to scientists, and help researchers to analyze genomic, proteomic and other data arising from infectious disease research. The new contract covers the development of two web-based resources for biomedical research. The first part of the project supports the development of the Pathogen Portal for the entire Bioinformatics Resource Center (BRC) program, which serves as an informatics coordinating center and gateway for four newly established BRCs. The second part of the project supports the development of the PATRIC 2.0 BRC for all bacterial species in the selected NIAID category A-C priority pathogens list.
Further information on the Pathogen Portal is available at http://pathogenportal.org
Further information on PATRIC 2.0 is available at http://patricbrc.vbi.vt.edu/portal/portal/patric/Home
Biosystems
 The Biosystems research division at VBI focuses on host-pathogen-environment interactions and inflammation. Scientific expertise in Biosystems includes genomics and proteomics technologies, human physiology, plant sciences, mathematical modeling, molecular and cellular biology, bacteriology, and biochemistry. This diversity promotes a transdisciplinary approach to science and bridges both plant and human health research.
In the years ahead, BioSystems is poised to advance knowledge of how pathogens of humans and plants cause disease through a combination of cutting-edge computational and experimental biology approaches.
Medical Informatics and Systems
The Medical Informatics and Systems (MIS) division works at the interface of medicine, molecular biology and informatics. Its research focuses on the study of human disease from an ‘-omics' perspective, specifically the analysis, integration and exploitation of very large ‘-omics' data sets, and the analysis of clinical operations to create health information technology (Health IT) solutions. Research in MIS is inherently transdisciplinary, with research oscillating between the laboratory and informatics analysis, where informatics can inspire a laboratory validation experiment or be used to analyze and interpret contemporary large data sets that are generated by laboratory experimentation to create new actionable knowledge. This ultimately yields new discoveries and work to translate them into clinical practice through a variety of mechanisms, including commercialization.
A sampling of the major projects in the division include:
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Developing health informatics tools to data mine text from electronic medical records (EMRs) to subsequently provide decision support and hypothesis generation for clinicians who face complex patient cases or who initiate research ideas inspired by the software analyzing their individual patients and populations;
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Using health informatics text analytics tools to improve patient care by matching data in a patient's EMR to pro-actively identify patients in need of some type of intervention (pain management, financial or travel assistance, etc.), who are candidates for clinical trials and other actionable observations;
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Using clinical observables and deep phenotypes of patients with cancer and neurological disorders that are correlated with deep genotyping, especially in less studied genomic regions such as those that may contain hypervariable microsatellite (repetitive) loci with hopes of discovering new diagnostic and prognostic markers, drug targets and other intervention strategies;
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Exploiting uniquely created model systems or new analytical methods to identify new mechanisms to analyze or explain human disease, susceptibility or variable response to therapy; and
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Integrating bioinformatics into clinical settings or into medical student training and research experiences, thus capitalizing on the recently established Virginia Tech Carilion School of Medicine and Research Institute.
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