title: EuPathDB: the eukaryotic pathogen genomics database resource.
abstract: 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 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 analyzed 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 polysomal 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. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host-pathogen interactions.
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Cristina
authors.initials: C
authors.lastname: Aurrecoechea
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Ana
authors.initials: A
authors.lastname: Barreto
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Evelina Y
authors.initials: EY
authors.lastname: Basenko
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: John
authors.initials: J
authors.lastname: Brestelli
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Brunk
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Shon
authors.initials: S
authors.lastname: Cade
authors.affiliation: Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow G12 8TA, UK.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Crouch
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Doherty
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Dave
authors.initials: D
authors.lastname: Falke
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Fischer
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Bindu
authors.initials: B
authors.lastname: Gajria
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA oharb@sas.upenn.edu.|Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Omar S
authors.initials: OS
authors.lastname: Harb
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Heiges
authors.affiliation: Centre for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Christiane
authors.initials: C
authors.lastname: Hertz-Fowler
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Sufen
authors.initials: S
authors.lastname: Hu
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: John
authors.initials: J
authors.lastname: Iodice
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.|Department of Genetics, University of Georgia, Athens, GA 30602, USA.|Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Kissinger
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Cris
authors.initials: C
authors.lastname: Lawrence
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Deborah F
authors.initials: DF
authors.lastname: Pinney
authors.affiliation: Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Jane A
authors.initials: JA
authors.lastname: Pulman
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Roos
authors.affiliation: Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Achchuthan
authors.initials: A
authors.lastname: Shanmugasundram
authors.affiliation: Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Fatima
authors.initials: F
authors.lastname: Silva-Franco
authors.affiliation: Wellcome Trust Sanger Institute, Parasite Genomics, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Sascha
authors.identifier: 0000-0002-2151-0574
authors.initials: S
authors.lastname: Steinbiss
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Stoeckert
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Drew
authors.initials: D
authors.lastname: Spruill
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Haiming
authors.initials: H
authors.lastname: Wang
authors.affiliation: Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
authors.forename: Susanne
authors.initials: S
authors.lastname: Warrenfeltz
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.|Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Zheng
mesh_terms: D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D056890:Eukaryota; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D054884:Host-Pathogen Interactions / Q000235:genetics*; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D040901:Proteomics; D012984:Software; D064878:Web Browser