The Genome Portal of the Department of Energy Joint Genome Institute
By Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, A. Aerts, Michael Cantor, D. Goodstein, A. Kuo, Simon Minovitsky, Roman Nikitin, R. Ohm and 7 more. Nucleic Acids Res., 2011
989 citations recorded by the source corpus.
The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. We describe here the general organization of the Genome Portal and the most recent addition, MycoCosm (http://jgi.doe.gov/fungi), a new integrated fungal genomics resource.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/1008403db50906c525879cdd29f6ae1f93f4476d
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Ecology
- Alex Copeland
- Andrew J. Tritt
- Bernard Henrissat
- A. Kohler
- Francis Martin
- A. Zuccaro
- F. Buscot
- Steven L. Salzberg
In Molecular Biology
- Mathieu Seppey
- E. Zdobnov
- Felipe A. Simão
- David S. Roos
- Christian J. Stoeckert Jr.
- Francis Martin
- A. Kohler
- Heath E. O’Brien
Citations in the corpus
- Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life (2016, methodology): “Using the gene cluster browser on the JGI fungal genome portal Mycocosm for Agaricomycotina (http:// jgi.doe.gov/fungi; Grigoriev et al., 2012), all gene families with a single copy in each of the Agaricales genomes and two outgroup taxa [Boletus edulis Bull., Boletales; Plicaturopsis crispa (Pers.)”
- OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs (2016, positive): “Gene sets for the additional metazoan species were retrieved from the Joint Genome Institute (24).”
- OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs (2012, methodology): “Gene sets for an additional 13 basal animal species were retrieved from Ensembl Genomes (35) and the Joint Genome Institute (36) (as of July 2012).”
- FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes (2018, background): “FungiDB contains nearly 100 genomes obtained from GenBank [3], Ensembl [4], Joint Genome Institute (JGI) [5], Aspergillus Genome Database (AspGD) [6], Candida Genome Database (CGD) [7], Saccharomyces Genome Database (SGD) [8], PomBase [9], and The Broad Institute [10].”
- MycoCosm portal: gearing up for 1000 fungal genomes (2013, background): “Since our last report (3), MycoCosm has grown to host >250 publicly available fungal genomes (Figure 1), 80% of which were sequenced by JGI and 20% by other groups added for comparative purposes.”
- Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists (2015, background): “4 – 23 ).”