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Forensics Microbiome Database
The Forensic Microbiome Database (FMD) is a unique resource that enables the visualization and comparison of 16S rRNA human microbiome data obtained from multiple body sites with metadata as it relates to forensics. The goal of the FMD is to predict the geographical location of subjects using human microbiome data. As part of this award, we actively continue to update the database with publicly available 16S rRNA microbiome data and we are expanding the dataset through the...
Influenza Research Database (IRD)
Influenza Research Database (IRD) is a US NIH/NIAID-funded, freely-available online bioinformatics resource for influenza virus data search, analysis and visualization. IRD is accessed ~1484 sessions per week (Google Analytics - 2016 average) and has been cited in more that 568 scientific publications. Recently, several new influenza virus sequence annotation tools have been added to IRD, including: (1) a sequence auto-curation pipeline that checks for potential sequencing artifacts, (2)...
Medicago truncatula Genome Database
Medicago truncatula, a close relative of alfalfa, is a preeminent model for the study of the processes of nitrogen fixation, symbiosis, and legume genomics. The genome was initially sequenced in a collaboration between the University of Oklahoma, TIGR (now JCVI), the Sanger Institute in the UK and Genoscope in France with funding from Samuel Roberts Noble Foundation, the National Science Foundation and the European Union's Sixth Framework Programme INRA (France) , and the BBSRC...
Saliva Proteome Database
Saliva is an important body fluid biofluid that helps in mastication, protection of oral and esophageal tissues, as well as provide immune functions against pathogens. Saliva has also systemic functions as it provides mucosal immunity and production of antibodies and antimicrobial proteins. Because of these functions, saliva has long been investigated known for its biological potential and as a diagnostic medium for both oral and systemic diseases. Compared to blood and other body fluids,...
Global H1 Influenza Nomenclature
The H1 subtype of influenza A viruses (IAV) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from non-swine hosts, swine H1 have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this project, we have developed rigorous phylogenetic criteria to establish a globally...
Genetic Diversity and Evolutionary Dynamics of West Nile Viruses
Arthropod-borne viruses (arboviruses) are those viruses that are transmitted to humans primarily through infected mosquitoes and ticks bites. West Nile virus (WNV) is the leading cause of domestically acquired arboviral disease in the United States which belongs to the genus Flavivirus in the family Flaviviridae with a positive single standard RNA genome. It was first identified in the West Nile subregion in the East African nation of Uganda in 1937. Its natural cycle is between...
Genetic Diversity and Evolutionary Dynamics of Eastern Equine Encephalitis Viruses (EEEV)
Eastern equine encephalitis virus (EEEV) and Madariaga virus (MADV) are mosquito-borne alphavirus (family Togaviridae) of significant public and veterinary health importance throughout the Americas. It has a single-stranded positive sense RNA genome of about 11,700 nt in length. EEEV causes a very debilitating disease in humans with case-fatality rates ranging between 50 and 75%; and for equids, rates can be as high as 80%. It is currently classified as a select agent on the NIAID...
Genetic Diversity and Evolutionary Dynamics of Rotaviruses
Rotavirus is regarded as the worldwide leading cause of severe acute dehydrating diarrhoea in young children and majority of animal species. So far seven rotavirus groups (A to G) have been identified; each group can be divided further into subgroups and genotypes. Currently, there are 23 different G types encoded by the VP7 gene and 32 different P types encoded by the VP4 gene associated with group A rotavirus. Of these different G- and P-types, only four G-types (G1, G2, G3, G4) and...
Respiratory Syncytial Virus: Host-Virus-Microbiome Interactions
As the single most important cause of serious lower respiratory tract disease in infants and young children in the United States and globally, RSV is of considerable public health importance and a high priority for vaccine development. RSV causes lower respiratory tract illness and potentiates childhood wheezing and asthma. Infants at risk for RSV infection and subsequent asthma have been frequently found to have bacterial super-infections and there are high incidences of pulmonary...
Genetic Diversity and Evolutionary Dynamics of Respiratory Syncytial Viruses (RSV)
Human respiratory syncytial virus (RSV) causes acute lower respiratory tract infection (ALRI) in young children and certain adults groups, including the immunocompromised and elderly. Nearly all children are infected with RSV by 2 years of age. It has been estimated that for 2005 RSV caused 33.8 million new episodes of ALRI in young children worldwide, requiring hospitalization due to severe illness in 3.4 million cases. Rapid antigenic and genetic diversity has been found in RSV...