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TOPSAN: a dynamic web database for structural genomics.
The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically...
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.
BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and...
Virus Pathogen Resource (ViPR)
In order to support research focused on newly emerging pathogens, the Division of Microbiology and Infectious Diseases (DMID) of the National Institute of Allergy and Infectious Diseases (NIAID), at the US National Institutes of Health (NIH), is supporting a variety of resources for researchers including: the Genomic Sequencing Centers for Infectious Diseases, Structural Genomics Centers for Infectious Diseases, Systems Biology for Infectious Diseases Research, and BEI Resources Repository...
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population.
A major concern about the ongoing swine-origin H1N1 influenza virus (S-OIV) outbreak is that the virus may be so different from seasonal H1N1 that little immune protection exists in the human population. In this study, we examined the molecular basis for pre-existing immunity against S-OIV, namely the recognition of viral immune epitopes by T cells or B cells/antibodies that have been previously primed by circulating influenza strains. Using data from the Immune Epitope Database, we found that...
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) an...
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 consistent...
Archaeopteryx.js: Web-based Visualization and Exploration of Annotated Phylogenetic Trees
As part of the Virus Pathogen Resource (ViPR) and the Influenza Research Database (IRD) bioinformatics resources we have developed Archaeopteryx.js for the web-based visualization and exploration of annotated phylogenetic trees. A unique advantage of Archaeopteryx.js is its user-driven metadata-based visualization abilities, which allow for visual pattern recognition in phylogenetic data. For example, data (such as virus clade and subtype, host species, temporal and geographic information) can...
A community effort to protect genomic data sharing, collaboration and outsourcing.
The human genome can reveal sensitive information and is potentially re-identifiable, which raises privacy and security concerns about sharing such data on wide scales. In 2016, we organized the third Critical Assessment of Data Privacy and Protection competition as a community effort to bring together biomedical informaticists, computer privacy and security researchers, and scholars in ethical, legal, and social implications (ELSI) to assess the latest advances on privacy-preserving techniques...
Profiling analysis of circulating microRNA in peripheral blood of patients with class IV lupus nephritis.
Renal involvement in Systemic Lupus Erythematous (SLE) patients is one of the leading causes of morbidity and a significant contributor to mortality. It's estimated that nearly 50% of SLE individuals develop kidney disease in the first year of the diagnosis. Class IV lupus nephritis (LN-IV) is the class of lupus nephritis most common in Colombian patients with SLE. Altered miRNAs expression levels have been reported in human autoimmune diseases including lupus. Variations in the expression...