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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, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and  ...  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  ...  from our scientific advisors and the scientific community at large, which have helped to improve the functionality of EuPathDB resources.  ... 
doi:10.1093/nar/gkw1105 pmid:27903906 pmcid:PMC5210576 fatcat:gp4twmzt7rh2be7oga6xfszwpi

EuPathDB: The Eukaryotic Pathogen Genomics Database Resource [chapter]

Susanne Warrenfeltz, Evelina Y. Basenko, Kathryn Crouch, Omar S. Harb, Jessica C. Kissinger, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco
2018 Msphere  
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and  ...  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  ...  from our scientific advisors and the scientific community at large, which have helped to improve the functionality of EuPathDB resources.  ... 
doi:10.1007/978-1-4939-7737-6_5 pmid:29761457 fatcat:c6zfevdra5c7xn7f3qozklsy6i

The Eukaryotic Pathogen Databases: A Functional Genomic Resource Integrating Data from Human and Veterinary Parasites [chapter]

Omar S. Harb, David S. Roos
2014 Msphere  
This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.  ...  Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale  ...  While EuPathDB includes a family of databases supporting various eukaryotic pathogens (Table 1) , the look and feel of these databases have been streamlined to facilitate mobility between databases without  ... 
doi:10.1007/978-1-4939-1438-8_1 pmid:25388105 pmcid:PMC6157018 fatcat:ntn2vegwp5hp3b7wbnygjowl4q

EuPathDB: The Eukaryotic Pathogen database

C. Aurrecoechea, A. Barreto, J. Brestelli, B. P. Brunk, S. Cade, R. Doherty, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O. S. Harb (+13 others)
2012 Nucleic Acids Research  
EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics.  ...  Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e.  ...  suggestions from our scientific advisors and the scientific community at large, which have helped to improve the functionality of EuPathDB resources.  ... 
doi:10.1093/nar/gks1113 pmid:23175615 pmcid:PMC3531183 fatcat:rvac774wtze43l4xqhes64gsge

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 (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas  ...  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  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge the contribution of numerous members of the eukaryotic pathogen research community, in the form of advice, suggestions and/or data-often made available  ... 
doi:10.1093/nar/gkp941 pmid:19914931 pmcid:PMC2808945 fatcat:wvtdhudoo5fgjiclufxahkzhuy

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

C. Aurrecoechea, J. Brestelli, B. P. Brunk, J. M. Carlton, J. Dommer, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O. S. Harb, M. Heiges (+16 others)
2009 Nucleic Acids Research  
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB  ...  GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases.  ...  We also thank past and present staff associated with the ApiDB-BRC project, and our research laboratory colleagues whose contributions have facilitated the creation and maintenance of this database resource  ... 
doi:10.1093/nar/gkn631 pmid:18824479 pmcid:PMC2686445 fatcat:6cdetdt2nvbbdipsjoja6pidkq

Removing contaminants from databases of draft genomes

Jennifer Lu, Steven L. Salzberg, Fengzhu Sun
2018 PLoS Computational Biology  
We demonstrate that when attempting to find eukaryotic pathogens in metagenomic samples, the new database provides better sensitivity than one using the original genomes while offering a dramatic reduction  ...  Using this pipeline, we have produced a database of "clean" eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools.  ...  This table lists all genomes included in the RefSeq Eukaryotic Pathogen database and the MicrobeDB database. (XLSX) S6 Table. Cornea sample reads.  ... 
doi:10.1371/journal.pcbi.1006277 pmid:29939994 pmcid:PMC6034898 fatcat:ylwjd4aqdjhgxkehzsf3wsgaey

Removing Contaminants from Metagenomic Databases [article]

Jennifer Lu, Steven Salzberg
2018 bioRxiv   pre-print
We demonstrate that when attempting to find eukaryotic pathogens in metagenomic samples, the new database provides better sensitivity than one using the original genomes while offering a dramatic reduction  ...  Using this pipeline, we have produced a database of "clean" eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools.  ...  All pseudo-reads from the eukaryotic pathogen genomes were then classified against both Kraken databases.  ... 
doi:10.1101/261859 fatcat:364k6kfj6fd2hjgcstx5kpcjse

Characterization of potential drug targeting folate transporter proteins from Eukaryotic Pathogens

Mofolusho O. Falade, Benson Otarigho
2017 F1000Research  
automated search strategies in the Eukaryotic Methods Pathogen Database Resources (EuPathDB) to construct a protein list and retrieve protein sequences of folate transporters encoded in the genomes of  ...  The availability of genome sequences of many eukaryotic microbes is providing critical biological information for understanding parasite biology and identifying new drug and vaccine targets. : We developed  ...  the Eukaryotic Pathogen Database (EuPathDB) resources.  ... 
doi:10.12688/f1000research.10561.2 fatcat:6qf5t7asyrbo7d6dbkxinlveiu

Genome-wide characterization of folate transporter proteins of eukaryotic pathogens

Mofolusho Falade, Benson Otarigho
2017 F1000Research  
We applied a combination of bioinformatics methods to examine the Methods: genomes of pathogens in the EupathDB for genes encoding homologues of proteins that mediate folate salvage in a bid to identify  ...  The availability of genome sequences of many eukaryotic protozoa is providing important data for understanding parasite biology and identifying new drug and vaccine targets.  ...  We also searched the 200 pathogen genome sequences archived at the Eukaryotic Pathogen Genome Database Resources (http://eupathdb.org/eupathdb/).  ... 
doi:10.12688/f1000research.10561.1 fatcat:q5orwv7ijrak5igayeduy7jnsy

Selecting Targets from Eukaryotic Parasites for Structural Genomics and Drug Discovery [chapter]

Isabelle Q. H. Phan, Robin Stacy, Peter J. Myler
2014 Msphere  
The selection of targets is the first step for any structural genomics project. The application of structural genomics approaches to drug discovery also starts with the selection of targets.  ...  Here, three protocols are described that were developed to select targets from eukaryotic pathogens. These protocols could also be applied to other drug discovery projects.  ...  Acknowledgments The SSGCID has been funded with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under  ... 
doi:10.1007/978-1-4939-0354-2_4 pmid:24590708 pmcid:PMC4601580 fatcat:rwqxyfsjind5ffheka5nfbbhwq

Genomic Databases and the Search of Protein Targets for Protozoan Parasites

Luis Fernando Timmers, Ivani Pauli, Guy Barcellos, Kelen Rocha, Rafael Caceres, Walter de Azevedo Jr., Milena Soares
2009 Current Drug Targets  
Here we review the current status of these research efforts to develop genomic databases for protozoan parasites, such as the apicomplexan parasites, Trypanosoma cruzi and Leishmania spp.  ...  The integration of genomic data, three-dimensional structures of proteins, biological activity, and drugs availability allows a system approach to the study of the biology.  ...  Eukaryotic Pathogens Database Resources (EuPathDB) The Eukatiotic Pathogens Database Resources (Eu-PathDB) is one of the eight databases available at Bioinformatics Resources Center (BRC) Central, a database  ... 
doi:10.2174/138945009787581195 pmid:19275560 fatcat:7ayxjno4srecdlll4ptzhuwja4

Systems analysis of host-parasite interactions

Justine Swann, Neema Jamshidi, Nathan E. Lewis, Elizabeth A. Winzeler
2015 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
to the Center for Biosustainability at the Technical University of Denmark.  ...  This work was completed with generous support from the National Institutes for Health, the Bill and Melinda Gates Foundation, The Medicines for Malaria Venture, and the Novo Nordisk Foundation provided  ...  Institute repository of mass spectrometry proteomics data http://www.ebi.ac.uk/pride/ archive/ EuPathDB (Eukaryotic Pathogen Database Resources) 57 Integrative database of eukaryotic pathogens  ... 
doi:10.1002/wsbm.1311 pmid:26306749 pmcid:PMC4679367 fatcat:krdi3s6pq5exhgeiprsfu34e7q

AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species

C. Aurrecoechea, A. Barreto, J. Brestelli, B. P. Brunk, E. V. Caler, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O. S. Harb, M. Heiges (+13 others)
2010 Nucleic Acids Research  
The databases belong to the National Institute of Allergy and Infectious Diseases (NIAID) funded EuPathDB (http:// EuPathDB.org) Bioinformatics Resource Center family of integrated databases and assume  ...  the same architectural and graphical design as other EuPathDB resources such as PlasmoDB and TriTrypDB.  ...  We also thank past and present staff associated with the EuPathDB BRC project, and our research laboratory colleagues whose contributions have facilitated the creation and maintenance of this database  ... 
doi:10.1093/nar/gkq1006 pmid:20974635 pmcid:PMC3013638 fatcat:dfxsbca33vg6rka3imf5pmrjni

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models [article]

Maureen A. Carey, Gregory L. Medlock, Michał Stolarczyk, William A. Petri, Jennifer L. Guler, Jason A. Papin
2019 bioRxiv   pre-print
This knowledgebase represents the largest collection of genome-scale metabolic models for both pathogens and eukaryotes; with this resource, we can predict species-specific functions, contextualize experimental  ...  Model in vitro or in vivo systems are frequently used to enhance experimental manipulability, but these systems generally use species related to, yet distinct from, the clinically relevant causal pathogen  ...  The authors  ... 
doi:10.1101/772467 fatcat:hjrasufn35bjlgjhqynkjehqte
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