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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...

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The 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...

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Protozoan genomics for drug discovery

Protozoan genomics for drug discovery Nature Biotechnol. 2005 23:1089-1091 Chaudhary, K., and D.S. Roos PMID: 16151400

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Themes and variations in apicomplexan parasite biology

Themes and variations in apicomplexan parasite biology Science. 2005 309:72-73 Roos, D.S. PMID: 15994520

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Composite 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....

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Getting 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

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Plasmodium 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...

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OrthoMCL-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...

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CryptoDB: 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,...

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SynView: 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...

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PlasmoDB: 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...

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PlasmoDB 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....

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ApiDB: 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,...

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ToxoDB: 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....

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GiardiaDB 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,...

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PlasmoDB: 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....

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TriTrypDB: 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,...

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EuPathDB: 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....

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SynView - 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...

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The 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...

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AmoebaDB 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...

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Using 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:...

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FungiDB: 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...

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SchistoDB: 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,...

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EuPathDB: 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,...

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Standardized 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,...

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The 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,...

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EuPathDB: 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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