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PHI-base update: additions to the pathogen host interaction database

R. Winnenburg, M. Urban, A. Beacham, T. K. Baldwin, S. Holland, M. Lindeberg, H. Hansen, C. Rawlings, K. E. Hammond-Kosack, J. Kohler
2007 Nucleic Acids Research  
The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens  ...  The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications.  ...  ACKNOWLEDGEMENTS The authors would like to thank the FRAC team for allowing inclusion of their data on fungicides and the PAMGO group for compiling a useful ontology on microbe-host interactions.  ... 
doi:10.1093/nar/gkm858 pmid:17942425 pmcid:PMC2238852 fatcat:3icb7nv7zrgvlpanwr3gy7ycee

PHI-base: the pathogen-host interactions database

2019 Nucleic Acids Research  
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org.  ...  PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles.  ...  ACKNOWLEDGEMENTS We thank all the species experts who contributed database annotations from their field of expertise into PHI-base.  ... 
doi:10.1093/nar/gkz904 pmid:31733065 pmcid:PMC7145647 fatcat:lytif2lhgbdahfxn2vhvcfi4ry

PHI-base: a new database for pathogen host interactions

R. Winnenburg
2006 Nucleic Acids Research  
PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions.  ...  To utilize effectively the growing number of verified genes that mediate an organism's ability to cause disease and/or to trigger host responses, we have developed PHI-base.  ...  All authors are grateful to Gavin Harrison and the Rothamsted Computing Services group for efficient provision and support with the computational infrastructure for PHI-base.  ... 
doi:10.1093/nar/gkj047 pmid:16381911 pmcid:PMC1347410 fatcat:ksqrzpewafhmfhxvmd56nyxwam

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

Martin Urban, Alayne Cuzick, Kim Rutherford, Alistair Irvine, Helder Pedro, Rashmi Pant, Vidyendra Sadanadan, Lokanath Khamari, Santoshkumar Billal, Sagar Mohanty, Kim E. Hammond-Kosack
2016 Nucleic Acids Research  
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org.  ...  PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles.  ...  ACKNOWLEDGEMENTS We thank all the species experts who contributed database annotations from their field of expertise into PHI-base.  ... 
doi:10.1093/nar/gkw1089 pmid:27915230 pmcid:PMC5210566 fatcat:wlgkt2ppprfexkharj4ej5axem

The Pathogen-Host Interactions Database (PHI-base) Provides Insights into Generic and Novel Themes of Pathogenicity

Thomas K. Baldwin, Rainer Winnenburg, Martin Urban, Chris Rawlings, Jacob Koehler, Kim E. Hammond-Kosack
2006 Molecular Plant-Microbe Interactions  
In this report, we describe the Pathogen-Host Interactions database (PHI-base), which systematically compiles such pathogenicity genes involved in pathogen-host interactions.  ...  Here, we focus on the biology that underlies this computational resource: the nature of pathogen-host interactions, the experimental methods that exist for the characterization of such pathogen-host interactions  ...  ACKNOWLEDGMENTS All authors are grateful to G. Harrison and the Rothamsted Computing Services group for efficient provision and support with the computational infrastructure for PHI-base.  ... 
doi:10.1094/mpmi-19-1451 pmid:17153929 fatcat:mnzj7yuz4vcqvojcm43r336s4q

Antimicrobial Peptides: An Update on Classifications and Databases

Ahmer Bin Hafeez, Xukai Jiang, Phillip J. Bergen, Yan Zhu
2021 International Journal of Molecular Sciences  
Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents.  ...  As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms222111691 pmid:34769122 pmcid:PMC8583803 fatcat:4ts7nuas7jdanhjgtpn3pntiqy

PHISTO: pathogen–host interaction search tool

Saliha Durmuş Tekir, Tunahan Çakır, Emre Ardıç, Ali Semih Sayılırbaş, Gökhan Konuk, Mithat Konuk, Hasret Sarıyer, Azat Uğurlu, İlknur Karadeniz, Arzucan Özgür, Fatih Erdoğan Sevilgen, Kutlu Ö. Ülgen
2013 Computer applications in the biosciences : CABIOS  
The pathogenhost interaction search tool (PHISTO) is a web-accessible platform that provides relevant information about pathogen-host interactions (PHIs).  ...  It enables access to the most up-to-date PHI data for all pathogen types for which experimentally verified protein interactions with human are available.  ...  Currently, there are a number of pathogen-host interaction (PHI) resources that are specific to some pathogens.  ... 
doi:10.1093/bioinformatics/btt137 pmid:23515528 fatcat:3rmxwibw7fdk5l6tlstnviwtve

Database resources of the National Center for Biotechnology Information: 2002 update

D. L. Wheeler
2002 Nucleic Acids Research  
Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets.  ...  the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases).  ...  HIV-1/Human Protein Interaction Database The HIV-1/Human Protein Interaction Database is an online presentation of documented interactions between HIV-1 proteins, host cell proteins, other HIV-1 proteins  ... 
doi:10.1093/nar/30.1.13 pmid:11752242 pmcid:PMC99094 fatcat:o3wyt5y72zhzrd7usrrsl57ake

PHIDIAS: a pathogen-host interaction data integration and analysis system

Zuoshuang Xiang, Yuying Tian, Yongqun He
2007 Genome Biology  
The Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based database system that serves as a centralized source to search, compare, and analyze integrated genome sequences  ...  , conserved domains, and gene expression data related to pathogen-host interactions (PHIs) for pathogen species designated as high priority agents for public health and biological security.  ...  We also acknowledge the public availability of many open-source programs (for example, GBrowse and NCBI BLAST) that have allowed the integration and extension into PHI-DIAS.  ... 
doi:10.1186/gb-2007-8-7-r150 pmid:17663773 pmcid:PMC2323235 fatcat:shajy4jgufclnlxgevalwfdu2y

Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement

Ahmad Ali, Mehran Khan, Rahat Sharif, Muhammad Mujtaba, San-Ji Gao
2019 Plants  
In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy.  ...  Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics.  ...  the plant-pathogen interaction [128] and the pathogen hijacked pathways in order to figure out the acquired resistance mechanisms [129] .  ... 
doi:10.3390/plants8090344 pmid:31547331 pmcid:PMC6784093 fatcat:26cir7eurngsjnkiymymagntli

PhytoPath: an integrative resource for plant pathogen genomics

Helder Pedro, Uma Maheswari, Martin Urban, Alistair George Irvine, Alayne Cuzick, Mark D. McDowall, Daniel M. Staines, Eugene Kulesha, Kim Elizabeth Hammond-Kosack, Paul Julian Kersey
2015 Nucleic Acids Research  
Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser.  ...  PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes  ...  ACKNOWLEDGEMENTS The authors would like to thank all the species experts who contributed additional database entries from their field of expertise into PHI-base; and the members of our Scientific Advisory  ... 
doi:10.1093/nar/gkv1052 pmid:26476449 pmcid:PMC4702788 fatcat:rr4yqb22afefzhena2rdm27mo4

Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference

Sylvain Brisse, Carina Brehony, Teresa Conceição, Meritxell Cubero, Corinna Glasner, Meriadeg Le Gouil, Aurélie Renvoisé, Sam Sheppard, Lucy A. Weinert
2014 Research in Microbiology  
Acknowledgments The authors would like to thank H. Fsihi for important editorial help and Richard Goering for providing material for Fig. 1 .  ...  , electronic tables to interact with the patient or nanotechnology-based in vivo and personalized diagnoses using nanocapsules.  ...  In addition, the need for genotyping standardization and for increasing the geographic representation and coverage of data was emphasized in order to improve the applicability of the database to support  ... 
doi:10.1016/j.resmic.2014.01.003 pmid:24486597 pmcid:PMC7126388 fatcat:zhq4q6scavd2pgxfqgvnwywynu

HPIDB 2.0: a curated database for host–pathogen interactions

Mais G. Ammari, Cathy R. Gresham, Fiona M. McCarthy, Bindu Nanduri
2016 Database: The Journal of Biological Databases and Curation  
Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70  ...  However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host-pathogen systems.  ...  Acknowledgements The authors thank the IntAct biocurators for training, support and access to the IntAct curation system.  ... 
doi:10.1093/database/baw103 pmid:27374121 pmcid:PMC4930832 fatcat:4jnd4gtbcnfwtn2e6eei2mlqse

PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets

Elzbieta I. Janowska-Sejda, Artem Lysenko, Martin Urban, Chris Rawlings, Sophia Tsoka, Kim E. Hammond-Kosack
2019 Frontiers in Microbiology  
To facilitate discovery and gain additional insights into globally important pathogenic fungi, we have reconstructed computationally inferred interactomes using an interolog and domain-based approach for  ...  In addition, for the best annotated organism, namely F. graminearum, the distribution of annotated genes with respect to network structure was profiled using a random walk with restart algorithm, which  ...  Interactions database (PHI-base 1 ) (Urban et al., 2017) .  ... 
doi:10.3389/fmicb.2019.02721 pmid:31866958 pmcid:PMC6908471 fatcat:ll5oi2ki6neq7btr3vmgdwlhr4

Limitations of a metabolic network-based reverse ecology method for inferring host–pathogen interactions

Kazuhiro Takemoto, Kazuki Aie
2017 BMC Bioinformatics  
Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions.  ...  host-pathogen interactions.  ...  Pathogen-Host Interactions database (PHI-base) [4] and Host Pathogen Interaction Database [5] .  ... 
doi:10.1186/s12859-017-1696-7 pmid:28545448 pmcid:PMC5445277 fatcat:bicmg6rs4zhbnoe4go56c2drbu
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