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Difference between revisions of "Publications"
From GMOD
(Added about 20 new refs from PubMed and sorted existing refs by date. Added URL for GMOD article search on PubMed.) |
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* [http://www.aphidbase.com/ AphidBase]: a centralized bioinformatic resource for annotation of the pea aphid genome. <ref name=PMID:20482635/> | * [http://www.aphidbase.com/ AphidBase]: a centralized bioinformatic resource for annotation of the pea aphid genome. <ref name=PMID:20482635/> | ||
* Next generation transcriptomes for next generation genomes using est2assembly. <ref name=PMID:20034392/> | * Next generation transcriptomes for next generation genomes using est2assembly. <ref name=PMID:20034392/> | ||
+ | * Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:19957275/> | ||
* BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. <ref name=PMID:19820115/> | * BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. <ref name=PMID:19820115/> | ||
+ | * SNP@Evolution: a hierarchical database of positive selection on the human genome. <ref name=PMID:19732458/> ([[GBrowse]]-related) | ||
+ | * TBrowse: an integrative genomics map of Mycobacterium tuberculosis. <ref name=PMID:19683474/> ([[GBrowse]]-related) | ||
* [[CMap]] 1.01: a comparative mapping application for the Internet. <ref name=PMID:19648141/> | * [[CMap]] 1.01: a comparative mapping application for the Internet. <ref name=PMID:19648141/> | ||
* [[Apollo]]: a community resource for genome annotation editing. <ref name=PMID:19439563/> | * [[Apollo]]: a community resource for genome annotation editing. <ref name=PMID:19439563/> | ||
* [http://www.popgenie.org/ PopGenIE]: The Populus Genome Integrative Explorer. <ref name=PMID:19383103/> | * [http://www.popgenie.org/ PopGenIE]: The Populus Genome Integrative Explorer. <ref name=PMID:19383103/> | ||
* Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. <ref name=PMID:18845581/> | * Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. <ref name=PMID:18845581/> | ||
− | * | + | * [[GMODWeb]]: a web framework for the Generic Model Organism Database. <ref name=PMID:18570664/> |
+ | * FishMap: a community resource for zebrafish genomics. <ref name=PMID:18554176/> ([[GBrowse]]-related) | ||
+ | * Using the Generic Genome Browser ([[GBrowse]]). <ref name=PMID:18428797/> | ||
* [[MAKER]]: an easy-to-use annotation pipeline designed for emerging model organism genomes. <ref name=PMID:18025269/> | * [[MAKER]]: an easy-to-use annotation pipeline designed for emerging model organism genomes. <ref name=PMID:18025269/> | ||
* SmedGD: the Schmidtea mediterranea genome database. <ref name=PMID:17881371/> | * SmedGD: the Schmidtea mediterranea genome database. <ref name=PMID:17881371/> | ||
Line 43: | Line 48: | ||
* [[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/> | * [http://orygenesdb.cirad.fr/ OryGenesDB]: a database for rice reverse genetics. <ref name=PMID:16381969/> | ||
+ | * [http://dictybase.org dictyBase], the model organism database for Dictyostelium discoideum. <ref name=PMID:16381903/> | ||
* [[SynBrowse]]: a [[Synteny|synteny]] browser for comparative sequence analysis. <ref name=PMID:15994196/> [[Media:3461.pdf|PDF]] | * [[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/> | * [http://www.genome.arizona.edu/ FPC Web tools] for rice, maize, and distribution. <ref name=PMID:15888684/> |
Revision as of 22:59, 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.
An RSS feed is also available of new GMOD articles on PubMed.
Articles
Sorted by date, most recent first.
- AlliumMap-a comparative genomics resource for cultivated Allium vegetables. [1]
- SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss. [2]
- Tripal: a construction toolkit for online genome databases. [3]
- TparvaDB: a database to support Theileria parva vaccine development. [4]
- The GMOD Drupal bioinformatic server framework. [5]
- ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. [6]
- The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. [7]
- Choosing a genome browser for a Model Organism Database: surveying the Maize community. [8] PDF
- AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. [9]
- Next generation transcriptomes for next generation genomes using est2assembly. [10]
- Using the Generic Genome Browser (GBrowse). [11]
- BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. [12]
- SNP@Evolution: a hierarchical database of positive selection on the human genome. [13] (GBrowse-related)
- TBrowse: an integrative genomics map of Mycobacterium tuberculosis. [14] (GBrowse-related)
- CMap 1.01: a comparative mapping application for the Internet. [15]
- Apollo: a community resource for genome annotation editing. [16]
- PopGenIE: The Populus Genome Integrative Explorer. [17]
- Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. [18]
- GMODWeb: a web framework for the Generic Model Organism Database. [19]
- FishMap: a community resource for zebrafish genomics. [20] (GBrowse-related)
- Using the Generic Genome Browser (GBrowse). [21]
- MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. [22]
- SmedGD: the Schmidtea mediterranea genome database. [23]
- The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. [24]
- Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. [25]
- A Chado case study: an ontology-based modular schema for representing genome-associated biological information. [26]
- Celsius: a community resource for Affymetrix microarray data [27] PDF
- Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. [28] (See YSB.)
- The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. [29]
- AphidBase: a database for aphid genomic resources. [30]
- DroSpeGe: rapid access database for new Drosophila species genomes. [31] PDF
- T1DBase: integration and presentation of complex data for type 1 diabetes research. [32]
- Gbrowse Moby: a Web-based browser for BioMoby Services. [33]
- ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. [34] PDF
- Expanded protein information at SGD: new pages and proteome browser. [35]
- SwissRegulon: a database of genome-wide annotations of regulatory sites. [36]
- KISS: the kinetoplastid RNA editing sequence search tool. [37]
- BeetleBase: the model organism database for Tribolium castaneum. [38] PDF
- Xanthusbase: adapting wikipedia principles to a model organism database. [39]
- SynView: a GBrowse-compatible approach to visualizing comparative genome data. [40]
- OryGenesDB: a database for rice reverse genetics. [41]
- dictyBase, the model organism database for Dictyostelium discoideum. [42]
- SynBrowse: a synteny browser for comparative sequence analysis. [43] PDF
- FPC Web tools for rice, maize, and distribution. [44]
- 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. [45]
- wFleaBase: the Daphnia genome database. [46] PDF
- The Legume Information System (LIS): an integrated information resource for comparative legume biology. [47]
- Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. [48]
- Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. [49]
- Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. [50]
- ATIDB: Arabidopsis thaliana insertion database. [51] PDF
- Apollo: a sequence annotation editor. [52] PDF
- The generic genome browser (GBrowse): a building block for a model organism system database. [53] 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/>