Difference between revisions of "Publications"
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* [http://database.oxfordjournals.org/cgi/content/abstract/baq007 Choosing a genome browser for a Model Organism Database: surveying the Maize community]. <ref name=PMID:20627860/> [[Media:ChoosingAGenomeBrowser.pdf|PDF]] | * [http://database.oxfordjournals.org/cgi/content/abstract/baq007 Choosing a genome browser for a Model Organism Database: surveying the Maize community]. <ref name=PMID:20627860/> [[Media:ChoosingAGenomeBrowser.pdf|PDF]] | ||
| − | + | * [http://www.popgenie.org/ PopGenIE]: The Populus Genome Integrative Explorer. <ref name=PMID:19383103/> | |
| − | + | * A [[Chado]] case study: an ontology-based modular schema for representing genome-associated biological information. <ref name=PMID:17646315/> | |
| − | * [http://www. | + | * [http://celsius.genomics.ctrl.ucla.edu/ Celsius]: a community resource for Affymetrix microarray data <ref name=PMID:17570842/> [[Media:Gb-2007-8-6-r112.pdf|PDF]] |
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* Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <ref name=PMID:17389913/> (See [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ YSB].) | * Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. <ref name=PMID:17389913/> (See [http://gbrowse.princeton.edu/cgi-bin/gbrowse/yeast_strains_snps/ YSB].) | ||
* The development of BAC-end sequence-based microsatellite markers and placement in the [http://soybeangenome.siu.edu/ physical and genetic maps of soybean]. <ref name=PMID:17287974/> | * The development of BAC-end sequence-based microsatellite markers and placement in the [http://soybeangenome.siu.edu/ physical and genetic maps of soybean]. <ref name=PMID:17287974/> | ||
| + | * [http://www.aphidbase.com/ AphidBase]: a database for aphid genomic resources. <ref name=PMID:17237053/> | ||
| + | * [http://insects.eugenes.org/DroSpeGe/ DroSpeGe]: rapid access database for new Drosophila species genomes. <ref name=PMID:17202166/> [[Media:D480.pdf|PDF]] | ||
* [http://t1dbase.org T1DBase]: integration and presentation of complex data for type 1 diabetes research. <ref name=PMID:17169983/> | * [http://t1dbase.org T1DBase]: integration and presentation of complex data for type 1 diabetes research. <ref name=PMID:17169983/> | ||
* Gbrowse Moby: a Web-based browser for [http://biomoby.open-bio.org/ BioMoby] Services. <ref name=PMID:17147784/> | * Gbrowse Moby: a Web-based browser for [http://biomoby.open-bio.org/ BioMoby] Services. <ref name=PMID:17147784/> | ||
| + | * [[ParameciumDB]]: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. <ref name=PMID:17142227/> [[Media:Gkl777.pdf|PDF]] | ||
* Expanded protein information at SGD: new pages and proteome browser. <ref name=PMID:17142221/> | * Expanded protein information at SGD: new pages and proteome browser. <ref name=PMID:17142221/> | ||
* [http://www.swissregulon.unibas.ch/ SwissRegulon]: a database of genome-wide annotations of regulatory sites. <ref name=PMID:17130146/> | * [http://www.swissregulon.unibas.ch/ SwissRegulon]: a database of genome-wide annotations of regulatory sites. <ref name=PMID:17130146/> | ||
| + | * [http://rna.bmb.uga.edu/kiss/ KISS]: the kinetoplastid RNA editing sequence search tool. <ref name=PMID:17123956/> | ||
| + | * [http://bioinformatics.ksu.edu/BeetleBase/ BeetleBase]: the model organism database for Tribolium castaneum. <ref name=PMID:17090595/> [[Media:Gkl776.pdf|PDF]] | ||
| + | * [http://xanthusbase.org/ Xanthusbase]: adapting wikipedia principles to a model organism database. <ref name=PMID:17090585/> | ||
* [[SynView]]: a [[GBrowse]]-compatible approach to visualizing comparative genome data. <ref name=PMID:16844709/> | * [[SynView]]: a [[GBrowse]]-compatible approach to visualizing comparative genome data. <ref name=PMID:16844709/> | ||
| + | * [http://orygenesdb.cirad.fr/ OryGenesDB]: a database for rice reverse genetics. <ref name=PMID:16381969/> | ||
| + | * [[SynBrowse]]: a [[Synteny|synteny]] browser for comparative sequence analysis. <ref name=PMID:15994196/> [[Media:3461.pdf|PDF]] | ||
| + | * [http://www.genome.arizona.edu/ FPC Web tools] for rice, maize, and distribution. <ref name=PMID:15888684/> | ||
| + | * Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. <ref name=PMID:15805491/> | ||
| + | * [http://wfleabase.org/ wFleaBase]: the Daphnia genome database. <ref name=PMID:15752432/> [[Media:1471-2105-6-45.pdf|PDF]] | ||
| + | * [http://www.comparative-legumes.org/ The Legume Information System (LIS)]: an integrated information resource for comparative legume biology. <ref name=PMID:15608283/> | ||
* [http://www.pseudomonas.com/ Pseudomonas aeruginosa Genome Database] and [http://www.cmdr.ubc.ca/bobh/PAAP.html PseudoCAP]: facilitating community-based, continually updated, genome annotation. <ref name=PMID:15608211/> | * [http://www.pseudomonas.com/ Pseudomonas aeruginosa Genome Database] and [http://www.cmdr.ubc.ca/bobh/PAAP.html PseudoCAP]: facilitating community-based, continually updated, genome annotation. <ref name=PMID:15608211/> | ||
* Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. <ref name=PMID:15601538/> | * Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. <ref name=PMID:15601538/> | ||
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* [[Caryoscope]]: an Open Source Java application for viewing microarray data in a genomic context. <ref name=PMID:15488149/> | * [[Caryoscope]]: an Open Source Java application for viewing microarray data in a genomic context. <ref name=PMID:15488149/> | ||
| − | * [http://www. | + | * [http://www.atidb.org/ ATIDB]: Arabidopsis thaliana insertion database. <ref name=PMID:12582244/> [[Media:Gkg222.pdf|PDF]] |
| + | * [[Apollo]]: a sequence annotation editor. <ref name=PMID:12537571/> [[Media:Gb-2002-3-12-research0082.pdf|PDF]] | ||
| + | * The [[GBrowse|generic genome browser (GBrowse)]]: a building block for a model organism system database. <ref name=PMID:12368253/> [[Media:1599-1.pdf|PDF]] | ||
==Bibliography== | ==Bibliography== | ||
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==Adding Citations== | ==Adding Citations== | ||
| − | Enter them into the '''Articles''' section. Example: | + | Enter them into the '''Articles''' section. References are ordered by PMID, most recent (highest) PMID first; please enter your reference in the appropriate place in the list. |
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| + | Example: | ||
| − | <nowiki><ref name=PMID:15752432/></nowiki> | + | <nowiki><ref name=PMID:15752432/></nowiki> |
[[Category:GMOD Community]] | [[Category:GMOD Community]] | ||
[[Category:Help]] | [[Category:Help]] | ||
[[Category:Publications]] | [[Category:Publications]] | ||
Revision as of 20:26, 10 July 2012
The following is a partial listing of publications/references describing GMOD components or databases and applications built using GMOD components. For a list of databases see GMOD Users.
Articles
- Choosing a genome browser for a Model Organism Database: surveying the Maize community. [1] PDF
- PopGenIE: The Populus Genome Integrative Explorer. [2]
- A Chado case study: an ontology-based modular schema for representing genome-associated biological information. [3]
- Celsius: a community resource for Affymetrix microarray data [4] PDF
- Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. [5] (See YSB.)
- The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. [6]
- AphidBase: a database for aphid genomic resources. [7]
- DroSpeGe: rapid access database for new Drosophila species genomes. [8] PDF
- T1DBase: integration and presentation of complex data for type 1 diabetes research. [9]
- Gbrowse Moby: a Web-based browser for BioMoby Services. [10]
- ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. [11] PDF
- Expanded protein information at SGD: new pages and proteome browser. [12]
- SwissRegulon: a database of genome-wide annotations of regulatory sites. [13]
- KISS: the kinetoplastid RNA editing sequence search tool. [14]
- BeetleBase: the model organism database for Tribolium castaneum. [15] PDF
- Xanthusbase: adapting wikipedia principles to a model organism database. [16]
- SynView: a GBrowse-compatible approach to visualizing comparative genome data. [17]
- OryGenesDB: a database for rice reverse genetics. [18]
- SynBrowse: a synteny browser for comparative sequence analysis. [19] PDF
- FPC Web tools for rice, maize, and distribution. [20]
- Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. [21]
- wFleaBase: the Daphnia genome database. [22] PDF
- The Legume Information System (LIS): an integrated information resource for comparative legume biology. [23]
- Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. [24]
- Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. [25]
- Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. [26]
- ATIDB: Arabidopsis thaliana insertion database. [27] PDF
- Apollo: a sequence annotation editor. [28] PDF
- The generic genome browser (GBrowse): a building block for a model organism system database. [29] PDF
Bibliography
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Adding Citations
Enter them into the Articles section. References are ordered by PMID, most recent (highest) PMID first; please enter your reference in the appropriate place in the list.
Example:
<ref name=PMID:15752432/>
