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PlasmoDB v5: new looks, new genomes

Christian J. Stoeckert, Steve Fischer, Jessica C. Kissinger, Mark Heiges, Cristina Aurrecoechea, Bindu Gajria, David S. Roos
2006 Trends in Parasitology  
doi:10.1016/ pmid:17029963 fatcat:4o7fbvef5bhb3iyup2zo4adifq

EuPathDB: a portal to eukaryotic pathogen databases

Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice (+14 others)
2009 Nucleic Acids Research  
EuPathDB (; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB
more » ... ncludes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recentlyimplemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.
doi:10.1093/nar/gkp941 pmid:19914931 pmcid:PMC2808945 fatcat:wvtdhudoo5fgjiclufxahkzhuy

EuPathDB: the eukaryotic pathogen genomics database resource

Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb (+18 others)
2016 Nucleic Acids Research  
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are
more » ... with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polyso-mal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data.
doi:10.1093/nar/gkw1105 pmid:27903906 pmcid:PMC5210576 fatcat:gp4twmzt7rh2be7oga6xfszwpi

PlasmoDB: The Plasmodium Genome Resource [chapter]

Patricia L. Whetzel, Shailesh V. Date, Kobby Gajria, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, John Iodice, Philip T. Labo, Arthur J. Milgram, Christian J. Stoeckert, David S. Roos, Jessica C. Kissinger
Molecular Approaches to Malaria  
PlasmoDB ( is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra-and inter-species comparisons. Sequence information is integrated with other genomic-scale data
more » ... ng from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects.
doi:10.1128/9781555817558.ch2 fatcat:a37ookqqwbeujgpzqmc5vbhzpe

TriTrypDB: a functional genomic resource for the Trypanosomatidae

Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P. Brunk, Mark Carrington, Daniel P. Depledge, Steve Fischer, Bindu Gajria, Xin Gao, Malcolm J. Gardner, Alan Gingle (+32 others)
2009 Nucleic Acids Research  
TriTrypDB ( is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center ( to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional
more » ... datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
doi:10.1093/nar/gkp851 pmid:19843604 pmcid:PMC2808979 fatcat:qyypxtdzkrcelht7rbvhkok5tq

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites

L. Li
2004 Nucleic Acids Research  
ACKNOWLEDGEMENTS We thank members of the Roos and Stoeckert groups who provided useful advice on the development and utility of the ApiEST-DB resource, including Brian Brunk, Bindu Gajria and Jessica Kissinger  ... 
doi:10.1093/nar/gkh112 pmid:14681425 pmcid:PMC308846 fatcat:7ovk5palcnaxtemxntecadggqq

ApiDB: integrated resources for the apicomplexan bioinformatics resource center

Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John Miller, Eileen Kraemer, Christian J. Stoeckert, David S. Roos, Jessica C. Kissinger
2006 Nucleic Acids Research  
Mackey, Bindu Gajria, Thomas Gan, Jerric Gao, John Iodice and the entire development team for the component database sites.  ... 
doi:10.1093/nar/gkl880 pmid:17098930 pmcid:PMC1669770 fatcat:nqw2fblurvapzoxdsqdef3le2a

Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

A. Khan
2005 Nucleic Acids Research  
ACKNOWLEDGEMENTS We are grateful to Martin Franzholz and Bindu Gajria for assistance with ToxoDB, Sandra Clifton, Deana Pape and the EST Sequencing Team at The Washington University Genome Sequencing Center  ... 
doi:10.1093/nar/gki604 pmid:15911631 pmcid:PMC1137028 fatcat:hpbzised7vdrzghi3gply7ohyi

Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum

Kevin Brick, Junichi Watanabe, Elisabetta Pizzi
2008 Genome Biology  
Finally, we wish to thank Brian Brunk, Bindu Gajria, Omar Harb and David Roos for the incorporation of our data into PlasmoDB.  ... 
doi:10.1186/gb-2008-9-12-r178 pmid:19094208 pmcid:PMC2646282 fatcat:iu6mrcdawvh6xatsecuwqu7r6m