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A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.
Effective countermeasures against the recent emergence and rapid expansion of the 2019 novel coronavirus (SARS-CoV-2) require the development of data and tools to understand and monitor its spread and immune responses to it. However, little information is available about the targets of immune responses to SARS-CoV-2. We used the Immune Epitope Database and Analysis Resource (IEDB) to catalog available data related to other coronaviruses. This includes SARS-CoV, which has high sequence...
A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis.
Enteroviruses are potentially linked to the emergence of Acute Flaccid Myelitis (AFM), a rare but very serious condition that affects the nervous system. AFM has been associated with coxsackievirus A16, enterovirus A71 (EVA71) and enterovirus D68 (EVD68). Little is known about host-pathogen interactions for these viruses, and whether immune responses may have a protective or immunopathological role in disease presentations. Towards addressing this issue, we used the Immune Epitope Database to...
ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank.
ccPDB 2.0 (http://webs.iiitd.edu.in/raghava/ccpdb) is an updated version of the manually curated database ccPDB that maintains datasets required for developing methods to predict the structure and function of proteins. The number of datasets compiled from literature increased from 45 to 141 in ccPDB 2.0. Similarly, the number of protein structures used for creating datasets also increased from ~74 000 to ~137 000 (PDB March 2018 release). ccPDB 2.0 provides the same web services and flexible...
Coronavirus Pandemic: Putting Comprehensive Genomic Data in the Hands of Frontline Researchers Worldwide is Paramount
According to the CDC, SARS-CoV-2, the virus causing COVID-19, has now been detected in more than 150 countries/locations internationally. The World Health Organization (WHO) has declared COVID-19 a pandemic, and in the United States it has been declared it a national emergency. As governments and health organizations race to contain the disease, JCVI has released, in conjunction with the National Institutes of Health and the U.S. Department of Health and Human Services, a “Feature Virus”...
LJI Scientists Identify Potential Targets for Immune Responses to Novel Coronavirus
LA JOLLA, CA—Within two months, SARS-CoV-2, a previously unknown coronavirus, has raced around globe, infecting over a 100,000 people with numbers continuing to rise quickly. Effective countermeasures require helpful tools to monitor viral spread and understand how the immune system responds to the virus. Publishing in the March 16, 2020, online issue of Host, Cell and Microbe, a team of researchers at La Jolla Institute for Immunology, in collaboration with researchers at the J....
Scientists Identify Genome-Wide Traits Associated with Microbial Growth Strategy and Ecosystem Nutrient Status
(La Jolla, California)—February 18, 2020—Scientists from the J. Craig Venter Institute (JCVI), Arizona State University (ASU), Flathead Lake Biological Station, United States Department of Agriculture (USDA), and Universidad Nacional Autónoma de México, Mexico published results in the journal eLife, identifying key genomic traits indicative of an ecosystem’s nutrient status with respect to nitrogen and phosphorus, key ingredients in fertilizer. The study, focused on a...
A host subtraction database for virus discovery in human cell line sequencing data.
The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number...
Southern African Genome Diversity Study
Overview Scientists at the J. Craig Venter Institute have a long history of leadership in human genomic research. Since the work in the early 1990's by Dr. Venter and colleagues at the National Institutes of Health in describing expressed sequence tags (ESTs) to rapidly discover human genes, to the sequence and analysis of the first draft human genome published in 2001, to the first complete diploid human genome published in 2007, JCVI scientists remain committed to research into the human...
An 'eFP-Seq Browser' for visualizing and exploring RNA sequencing data.
Improvements in next-generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of '-seq'-based methods, of which RNA sequencing (RNA-seq) for generating transcriptomic data is the most popular. By analysing global patterns of gene expression in organs/tissues/cells of interest or in response to chemical or environmental perturbations, researchers can better understand an organism's biology. Tools designed to work with large RNA-seq...
Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR).
The Virus Pathogen Resource (ViPR; www.viprbrc.org ) is a US National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center providing bioinformatics support for major human viral pathogens. The hepatitis C virus (HCV) portal of ViPR facilitates basic research and development of diagnostics and therapeutics for HCV, by providing a comprehensive collection of HCV-related data integrated from various sources, a growing suite of analysis and visualization...