Search

Project

VIGOR

VIGOR (VIral Genome ORF Reader) is a homology-driven viral gene finder capable of predicting proteins, polyproteins and mature peptides. VIGOR is able to identify and properly handle typical viral transcriptional and translational exceptions, like ribosomal slippage, RNA editing, stop codon readthrough, etc. The package consists of the software and a collection of highly-curated reference databases, one for each type of virus VIGOR is capable to annotate. Enabling VIGOR to annotate a...

Informatics

Informatics plays a critical role in transforming the deluge of genomics data into scientific discoveries. JCVI Informatics has been at the forefront of these advancements with informatics tools including whole genome assemblers and TIGRFAMS. As datasets grow in both volume and complexity, we are building tools to address pan genomes, microbiomes, single-cell genomes, genome visualization, haplotyping, and biomarker discovery. The Informatics group is leveraging new databasing...

Project

Genome Properties

The Genome Properties system consists of a suite of "Properties" which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. The Genome Properties database, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome....

Project

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)...

Human Microbiome

Both inside and out, our bodies harbor a huge array of bacteria and other microorganisms collectively known as the human microbiome. Although bacteria are often thought to be dangerous, many of those that comprise the microbiome are essential for life. Our researchers are focused on understanding the delicate bacterial balance in the human body and how slight changes in that balance can either improve health or lead to diseases. JCVI Human Microbiome Research Impact Since the...

Project

Global Ocean Sampling Expedition (GOS)

Overview In 2004, after a successful pilot project of shotgun metagenomics sequencing at the Bermuda Atlantic Time Series site, J. Craig Venter, PhD, and a Venter Institute team launched the Sorcerer II Global Ocean Sampling (GOS) Expedition. Inspired by 19th Century sea voyages like Darwin's on the H.M.S. Beagle and Captain George Nares on the H.M.S. Challenger, The Sorcerer II circumnavigated the globe for more than two years, covering a staggering 32,000 nautical miles, visiting 23...

Project

Sequencing of Human Adenovirus Clinical Isolates From Recent and Reference Genomes

Human adenoviruses (HAdV) are pathogens causing a range of human infectious diseases, including respiratory, ocular, gastrointestinal, renal and metabolic. HAdV infections can be highly contagious, causing high morbidity rate and mortality rates and result in outbreaks. They are also a model organism in the research laboratory for cell and molecular biology. The goal of this project is to understand HAdV biology, especially the evolution and emergence of new and highly pathogenic...

Project

DNA Synthesis and Biosecurity:
Lessons Learned and Options for the Future

Synthetic biology promises great scientific advances, but it also has the potential to pose unique biosecurity threats. It now is easier than ever to synthesize very long pieces of DNA from chemicals, potentially enabling a bioterrorist to build a toxin gene or an entire pathogenic virus. In 2007, the JCVI Policy Team released a report titled, “Synthetic Genomics: Options for Governance,” in which we proposed and evaluated a variety of options to address this biosecurity threat. A...

Project

First Minimal Synthetic Bacterial Cell

Researchers from the J. Craig Venter Institute (JCVI) and Synthetic Genomics, Inc. (SGI) have accomplished the next feat in synthetic biology research—the design and construction of the first minimal synthetic bacterial cell, JCVI-syn3.0. Using the first synthetic cell, Mycoplasma mycoides JCVI-syn1.0 (built by this same team in 2010), JCVI-syn3.0 was developed through a design, build, and test (DBT) process using genes from JCVI-syn1.0. The new minimal synthetic cell contains only...

Pages