Institution
J. Craig Venter Institute
Nonprofit•La Jolla, California, United States•
About: J. Craig Venter Institute is a nonprofit organization based out in La Jolla, California, United States. It is known for research contribution in the topics: Genome & Gene. The organization has 1268 authors who have published 2300 publications receiving 304083 citations. The organization is also known as: JCVI & The Institute for Genomic Research.
Topics: Genome, Gene, Genomics, Population, Microbiome
Papers published on a yearly basis
Papers
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Oxford Brookes University1, University of Massachusetts Lowell2, University of Wisconsin-Madison3, J. Craig Venter Institute4, Washington and Lee University5, University of California, Riverside6, University of Cologne7, Osaka Medical College8, California Academy of Sciences9, Aarhus University10, Baylor College of Medicine11, University of Jena12, Harvard University13, National Museum of Natural History14, University of Manchester15, American Museum of Natural History16, Uppsala University17, Spanish National Research Council18, Federal University of Rio de Janeiro19, Queen Mary University of London20, Ghent University21, University of Rochester22, Humboldt University of Berlin23, University of Göttingen24, Osaka University25, Université libre de Bruxelles26
TL;DR: The results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA, and this study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes ofpolyploidization events across eukaryotes.
Abstract: Background: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence ...
362 citations
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TL;DR: Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species.
Abstract: The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are highly conserved among photosynthetic species. Many of these have no assigned function and may play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species.
362 citations
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TL;DR: The complete genome of Aeromonas hydrophila ATCC 7966(T) was sequenced and provides valuable insights into its ability to flourish in both aquatic and host environments.
Abstract: The complete genome of Aeromonas hydrophila ATCC 7966T was sequenced. Aeromonas, a ubiquitous waterborne bacterium, has been placed by the Environmental Protection Agency on the Contaminant Candidate List because of its potential to cause human disease. The 4.7-Mb genome of this emerging pathogen shows a physiologically adroit organism with broad metabolic capabilities and considerable virulence potential. A large array of virulence genes, including some identified in clinical isolates of Aeromonas spp. or Vibrio spp., may confer upon this organism the ability to infect a wide range of hosts. However, two recognized virulence markers, a type III secretion system and a lateral flagellum, that are reported in other A. hydrophila strains are not identified in the sequenced isolate, ATCC 7966T. Given the ubiquity and free-living lifestyle of this organism, there is relatively little evidence of fluidity in terms of mobile elements in the genome of this particular strain. Notable aspects of the metabolic repertoire of A. hydrophila include dissimilatory sulfate reduction and resistance mechanisms (such as thiopurine reductase, arsenate reductase, and phosphonate degradation enzymes) against toxic compounds encountered in polluted waters. These enzymes may have bioremediative as well as industrial potential. Thus, the A. hydrophila genome sequence provides valuable insights into its ability to flourish in both aquatic and host environments.
362 citations
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Agriculture and Agri-Food Canada1, National Research Council2, J. Craig Venter Institute3, Centre national de la recherche scientifique4, University of Queensland5, University of Missouri6, University of Warwick7, University of Western Australia8, Plant Genome Mapping Laboratory9, Southern Cross University10, University of York11
TL;DR: Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture, and epigenetic mechanisms play a role in the functional diversification of duplicate genes.
Abstract: Background: Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. Results: We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/ Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event. Conclusions: Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.
362 citations
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TL;DR: The CIP RES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway, is described.
Abstract: The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Discovery Environment (XSEDE) project. Here we describe the CIPRES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway. Software developers can use the CRA to extend their web or desktop applications to include the ability to run MrBayes, BEAST, RAxML, MAFFT, and other computationally intensive algorithms on XSEDE. The CRA also makes it possible for individuals with modest scripting skills to access the same tools from the command line using curl, or through any scripting language. This report describes the CRA and its use in three web applications (Influenza Research Database – www.fludb.org, Virus Pathogen Resource – www.viprbrc.org, and MorphoBank – www.morphobank.org). The CRA is freely accessible to registered users at https://cipresrest.sdsc.edu/cipresrest/v1; supporting documentation and registration tools are available at https://www.phylo.org/restusers.
360 citations
Authors
Showing all 1274 results
Name | H-index | Papers | Citations |
---|---|---|---|
John R. Yates | 177 | 1036 | 129029 |
Anders M. Dale | 156 | 823 | 133891 |
Ronald W. Davis | 155 | 644 | 151276 |
Steven L. Salzberg | 147 | 407 | 231756 |
Mark Raymond Adams | 147 | 1187 | 135038 |
Nicholas J. Schork | 125 | 587 | 62131 |
William R. Jacobs | 118 | 490 | 48638 |
Ian T. Paulsen | 112 | 354 | 69460 |
Michael B. Brenner | 111 | 393 | 44771 |
Kenneth H. Nealson | 108 | 483 | 51100 |
Claire M. Fraser | 108 | 352 | 76292 |
Stephen L. Hoffman | 104 | 458 | 38597 |
Michael J. Brownstein | 102 | 274 | 47929 |
Amalio Telenti | 102 | 421 | 40509 |
John Quackenbush | 99 | 427 | 67029 |