Publications
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.
GMOD on Mendeley
If you use Mendeley, please join the GMOD group and contribute GMOD
and GMOD-related papers to the pool there. The following feed shows
papers recently added to the GMOD Mendeley group.
Articles
Sorted by PubMed ID, highest (most recent) first. This listing is
compatible with the
Mendeley web importer and has embedded
COiNs bibliographic data.
- Canto: An online tool for community literature curation
DOI:10.1093/bioinformatics/btu103
[1]
- AlliumMap-a comparative genomics resource for cultivated Allium
vegetables. PMID:22559261
[2]
- SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus
mykiss. PMID:22120661
[3]
- Tripal: a construction toolkit for online genome
databases. PMID:21959868
[4]
- TparvaDB: a database to support Theileria parva vaccine development.
PMID:21546359
[5]
- The GMOD Drupal bioinformatic server framework. PMID:20971988
[6]
- ParameciumDB in 2011: new tools and new
data for functional and comparative genomics of the model ciliate
Paramecium tetraurelia. PMID:20952411
[7]
- The Sol Genomics Network (solgenomics.net): growing
tomatoes using Perl. PMID:20935049
[8]
- Using the Generic Synteny Browser
(GBrowse_syn) PMID:20836076
[9]
- Galaxy: a comprehensive approach for supporting
accessible, reproducible, and transparent computational research in
the life sciences. PMID:20738864
[10]
- Choosing a genome browser for a
Model Organism Database: surveying the Maize community.
PMID:20627860
[11]
PDF
- AphidBase: a centralized bioinformatic resource for
annotation of the pea aphid genome. PMID:20482635
[12]
- Galaxy: a web-based genome analysis tool for
experimentalists”. PMID:20069535
[13]
- Next generation transcriptomes for next generation genomes using
est2assembly. PMID:20034392
[14]
- Using the Generic Genome Browser (GBrowse).
PMID:19957275
[15]
- BeetleBase in 2010: revisions to provide comprehensive genomic
information for Tribolium castaneum. PMID:19820115
[16]
- SNP@Evolution: a hierarchical database of positive selection on the
human genome. PMID:19732458
[17]
(GBrowse-related)
- TBrowse: an integrative genomics map of Mycobacterium tuberculosis.
PMID:19683474
[18]
(GBrowse-related)
- CMap 1.01: a comparative mapping application for the
Internet. PMID:19648141
[19]
- Apollo: a community resource for genome
annotation editing. PMID:19439563
[20]
- PopGenIE: The Populus Genome Integrative Explorer.
PMID:19383103
[21]
- Artemis and ACT: viewing, annotating and
comparing sequences stored in a relational database.
PMID:18845581
[22]
- GMODWeb: a web framework for the Generic Model
Organism Database. PMID:18570664
[23]
- FishMap: a community resource for zebrafish genomics.
PMID:18554176
[24]
(GBrowse-related)
- Using the Generic Genome Browser (GBrowse).
PMID:18428797
[25]
- MAKER: an easy-to-use annotation pipeline designed
for emerging model organism genomes. PMID:18025269
[26]
- SmedGD: the Schmidtea mediterranea genome database.
PMID:17881371
[27]
- The Princeton Protein Orthology Database (P-POD): a comparative
genomics analysis tool for biologists. PMID:17712414
[28]
- Analysis of expressed sequence tags of the cyclically parthenogenetic
rotifer Brachionus plicatilis. PMID:17668053
[29]
- A Chado case
study: an ontology-based modular schema for representing
genome-associated biological information. PMID:17646315
[30]
- Celsius: a community resource for Affymetrix
microarray data PMID:17570842
[31]
PDF
- Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used
Saccharomyces cerevisiae Strains. PMID:17389913
[32] (See YSB.)
- The development of BAC-end sequence-based microsatellite markers and
placement in the
physical and genetic maps of soybean.
PMID:17287974
[33]
- AphidBase: a database for aphid genomic resources.
PMID:17237053
[34]
- DroSpeGe: rapid access database for new Drosophila
species genomes. PMID:17202166
[35]
PDF
- T1DBase: integration and presentation of complex
data for type 1 diabetes research. PMID:17169983
[36]
- Gbrowse Moby: a Web-based browser for
BioMoby Services. PMID:17147784
[37]
- ParameciumDB: a community resource that
integrates the Paramecium tetraurelia genome sequence with genetic
data. PMID:17142227
[38]
PDF
- Expanded protein information at SGD: new pages and proteome browser.
PMID:17142221
[39]
- SwissRegulon: a database of genome-wide annotations
of regulatory sites. PMID:17130146
[40]
- KISS: the kinetoplastid RNA editing sequence search
tool. PMID:17123956
[41]
- BeetleBase: the model
organism database for Tribolium castaneum. PMID:17090595
[42]
PDF
- Xanthusbase: adapting wikipedia principles to a
model organism database. PMID:17090585
[43]
- SynView: a
GBrowse-compatible approach to visualizing
comparative genome data. PMID:16844709
[44]
- OryGenesDB: a database for rice reverse genetics.
PMID:16381969
[45]
- dictyBase, the model organism database for
Dictyostelium discoideum. PMID:16381903
[46]
- Galaxy: a platform for interactive large-scale
genome analysis. PMID:16169926
[47]
- SynBrowse: a
synteny
browser for comparative sequence analysis. PMID:15994196
[48]
PDF
- FPC Web tools for rice, maize, and distribution.
PMID:15888684
[49]
- 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. PMID:15805491
[50]
- wFleaBase: the Daphnia genome database.
PMID:15752432
[51]
PDF
- The Legume Information System (LIS): an integrated
information resource for comparative legume biology.
PMID:15608283
[52]
- Pseudomonas aeruginosa Genome Database and
PseudoCAP: facilitating community-based,
continually updated, genome annotation. PMID:15608211
[53]
- Development of an integrated genome informatics, data management and
workflow infrastructure: a toolbox for the study of complex disease
genetics. PMID:15601538
[54]
- Caryoscope: an Open Source Java application
for viewing microarray data in a genomic context. PMID:15488149
[55]
- ATIDB: Arabidopsis thaliana insertion database.
PMID:12582244
[56]
PDF
- Apollo: a sequence annotation editor.
PMID:12537571
[57]
PDF
- The generic genome browser (GBrowse): a
building block for a model organism system database.
PMID:12368253
[58]
PDF
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