Functional genomics databases on the web
Functional genomics databases on the web Cell Microbiol. 2005 7(8), 1053-9 Stoeckert CJ Jr. Experiments involving high-throughput methods for measuring transcripts, proteins and metabolites constitute...
View ArticleThe transcriptome of Toxoplasma gondii
The transcriptome of Toxoplasma gondii BMC Bioinformatics 2005:3-26 Radke, J.R., M.S. Behnke, A.J. Mackey, J.B. Radke, D.S. Roos and M.W. White BACKGROUND: Toxoplasma gondii gives rise to...
View ArticleProtozoan genomics for drug discovery
Protozoan genomics for drug discovery Nature Biotechnol. 2005 23:1089-1091 Chaudhary, K., and D.S. Roos PMID: 16151400
View ArticleThemes and variations in apicomplexan parasite biology
Themes and variations in apicomplexan parasite biology Science. 2005 309:72-73 Roos, D.S. PMID: 15994520
View ArticleComposite genome map and recombination parameters derived from three...
Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii Nucl. Acids Res. 2005 33:2980-2992 Khan, A., S. Taylor, C. Su, A.J. Mackey, J. Boyle, R....
View ArticleGetting the most out of bioinformatics resources
Getting the most out of bioinformatics resourcesIn: Malaria Parasites, A.P. Waters & C.J. Janse, editors. Horizon, Norfolk UK. 2004 J.C. Kissinger and D.S. Roos ISBN: 0-9542464-6-2
View ArticlePlasmodium research in the postgenomic era
Plasmodium research in the postgenomic era Trends Parasitol. 2006 22(1):1-4 Duraisingh M, Ferdig MT, Stoeckert CJ, Volkman SK, McGovern VP The complete genomic sequence of Plasmodium falciparum strain...
View ArticleOrthoMCL-DB: querying a comprehensive multi-species collection of ortholog...
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups Nucleic Acids Res. 2006 Jan 1;34:D363-8 Feng Chen, Aaron J. Mackey, Christian J. Stoeckert Jr. and David S. Roos The...
View ArticleCryptoDB: a Cryptosporidium bioinformatics resource update
CryptoDB: a Cryptosporidium bioinformatics resource update Nucleic Acids Res. 2006 Jan 1;34:D419-22 Heiges M, Wang H, Robinson E, Aurrecoechea C, Gao X, Kaluskar N, Rhodes P, Wang S, He CZ, Su Y,...
View ArticleSynView: A GBrowse-compatible Approach to Visualizing Comparative Genome Data
SynView: A GBrowse-compatible Approach to Visualizing Comparative Genome Data Bioinformatics. 2006. 22(18):2308-2309 Haiming Wang, Yanqi Su, Aaron J. Mackey, Eileen T. Kraemer and Jessica C. Kissinger...
View ArticlePlasmoDB: The Plasmodium Genomics and Functional Genomics Resource
PlasmoDB: The Plasmodium Genomics and Functional Genomics Resource In silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Nicola Mulder and Rolf Apweiler (eds.). Nova Science...
View ArticlePlasmoDB v5: New Looks, New Genomes
PlasmoDB v5: New Looks, New Genomes Trends in Parasitology. 2006. 22(12): 543-546 Christian J. Stoeckert Jr., Steve Fisher, Jessica Kissinger, Mark Heiges, Cristina Aurrecoechea, Bindu Gajria, David S....
View ArticleApiDB: integrated resources for the apicomplexan bioinformatics resource center
ApiDB: integrated resources for the apicomplexan bioinformatics resource center Nucleic Acids Research. 2007. 35:D427-30 Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer,...
View ArticleToxoDB: an integrated Toxoplasma gondii database resource
ToxoDB: an integrated Toxoplasma gondii database resource Nucleic Acids Res. 2007. 36:D553-6 B. Gajria, A. Bahl, J. Brestelli, J. Dommer, S. Fischer, X. Gao, M. Heiges, J. Iodice, J. C. Kissinger, A....
View ArticleGiardiaDB and TrichDB: integrated genomic resources for the eukaryotic...
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis Nucleic Acids Res. 2009. 37:D526-D530 Aurrecoechea, C., J. Brestelli,...
View ArticlePlasmoDB: a functional genomic database for malaria parasites
PlasmoDB: a functional genomic database for malaria parasites Nucleic Acids Res. 2009. 37:D539-D543 Aurrecoechea, C., J. Brestelli, B. P. Brunk, J. Dommer, S. Fischer, B. Gajria, X. Gao, A. Gingle, G....
View ArticleTriTrypDB: a functional genomic resource for the Trypanosomatidae
TriTrypDB: a functional genomic resource for the Trypanosomatidae Nucleic Acids Research 2010 38(Database issue):D457-D462; doi:10.1093/nar/gkp851 Aslett M, Aurrecoechea C, Berriman M, Brestelli J,...
View ArticleEuPathDB: a portal to eukaryotic pathogen databases
EuPathDB: a portal to eukaryotic pathogen databases Nucleic Acids Research 2010 38(Database issue):D415-9 Aurrecoechea C. Brestelli J. Brunk BP. Fischer S. Gajria B. Gao X. Gingle A. Grant G. Harb OS....
View ArticleSynView - Synteny Browser with GBrowse Integration
SynView - Synteny Browser with GBrowse IntegrationA Practical Guide to Bioinformatics Analysis- 2010 iConcept Press Ltd. H. Wang, J. DeBarry, J. C. Kissinger Over the last decade, the field of...
View ArticleThe Strategies WDK: a graphical search interface and web development kit for...
The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. Database (Oxford). 2011 Jun 23;2011:bar027. Print 2011. PMID: 21705364 PMCID: PMC3122067...
View ArticleAmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and...
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Research. 39(Database issue):D612-9, 2011 Jan. Aurrecoechea C., Barreto A, Brestelli...
View ArticleUsing OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster...
Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr. Protoc. Bioinform. 35:6.12.1-6.12.19. © 2011 by John Wiley & Sons, Inc. PMID:...
View ArticleFungiDB: an integrated functional genomics database for fungi.
FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res. 2012 Jan;40(Database issue):D675-81. Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS, Kissinger JC, Li...
View ArticleSchistoDB: an updated genome resource for the three key schistosomes of humans.
SchistoDB: an updated genome resource for the three key schistosomes of humans. Nucleic Acids Res. 2013 Jan;41(Database issue):D728-31. Zerlotini A, Aguiar ER, Yu F, Xu H, Li Y, Young ND, Gasser RB,...
View ArticleEuPathDB: the eukaryotic pathogen database.
EuPathDB: the eukaryotic pathogen database. Nucleic Acids Res. 2013 Jan;41(Database issue):D684-91. Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X,...
View ArticleStandardized metadata for human pathogen/vector genomic sequences.
Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014 Jun 17;9(6):e99979. Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB,...
View ArticleThe Eukaryotic Pathogen Databases: a functional genomic resource integrating...
The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites. Methods Mol Biol. 2015;1201:1-18. Harb OS, Roos DS. Over the past 20 years,...
View ArticleEuPathDB: the eukaryotic pathogen genomics database resource.
EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res. 2016 Nov 29. pii: gkw1105. [Epub ahead of print] Aurrecoechea A, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S,...
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