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PlasmoDB: a functional genomic database for malaria parasites

C. Aurrecoechea, J. Brestelli, B. P. Brunk, J. Dommer, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O. S. Harb, M. Heiges, F. Innamorato (+13 others)
2009 Nucleic Acids Research  
PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale.  ...  PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http:// EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella.  ...  suggestions that have helped to improve the functionality of PlasmoDB.  ... 
doi:10.1093/nar/gkn814 pmid:18957442 pmcid:PMC2686598 fatcat:xeqgwoil5nebrcwyn4garimipe

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  
Acknowledgements The authors wish to acknowledge the many individuals who have contributed genomic-scale datasets to PlasmoDB, including the genome sequencing centers and the contributions of the dedicated  ...  database and website teams.  ...  PlasmoDB, a resource for malaria parasite genomic and functional genomics datasets, was released in August 2006. This new release includes additional Plasmodium genomes and a newly designed website.  ... 
doi:10.1016/j.pt.2006.09.005 pmid:17029963 fatcat:4o7fbvef5bhb3iyup2zo4adifq

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data

A. Bahl
2003 Nucleic Acids Research  
PlasmoDB currently houses information from five parasite species and provides tools for intra-and inter-species comparisons.  ...  PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium.  ...  PlasmoDB now provides direct links to external data sources and sites, including the Malaria Parasite Metabolic Pathways database (http://sites.huji.ac.il/malaria/) and the Malaria Research and Reference  ... 
doi:10.1093/nar/gkg081 pmid:12519984 pmcid:PMC165528 fatcat:dokyudxoxnbzzd4g5zu5uyacti

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data

2001 Nucleic Acids Research  
The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum.  ...  Tools have been designed to facilitate complex biological queries, including many that are specific to Plasmodium parasites and malaria as a disease.  ...  ACKNOWLEDGEMENTS The Plasmodium Genome Database, PlasmoDB, is supported by a grant from the Burroughs Wellcome Fund.  ... 
doi:10.1093/nar/29.1.66 fatcat:ivpq6uti3vbjfehehtgoqyuvpu

PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. The Plasmodium Genome Database Collaborative

2001 Nucleic Acids Research  
The GUS (Genomics Unified Schema) implementation of PlasmoDB provides a multi-species genomic relational database, incorporating data from human and mouse, as well as P.falciparum.  ...  Tools have been designed to facilitate complex biological queries, including many that are specific to PLASMODIUM: parasites and malaria as a disease.  ...  ACKNOWLEDGEMENTS The Plasmodium Genome Database, PlasmoDB, is supported by a grant from the Burroughs Wellcome Fund.  ... 
pmid:11125051 pmcid:PMC29846 fatcat:5z2zeeqlfnhzrfzcecoauaup5i

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)

A. Bahl
2002 Nucleic Acids Research  
PlasmoDB currently houses information from five parasite species and provides tools for cross-species comparisons.  ...  PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium.  ...  We wish to thank the scientists and funding agencies comprising the international Malaria Genome Project for making sequence data from the genome of P.falciparum (3D7) public prior to publication of the  ... 
doi:10.1093/nar/30.1.87 pmid:11752262 pmcid:PMC99106 fatcat:tjz2pqmornbi7o6nq74a2a77na

PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families

X. Xu, J. Wu, J. Xiao, Y. Tan, Q. Bao, F. Zhao, X. Li
2008 Bioinformatics  
Recently, with the arrival of several malaria parasite genomes, we established an integrated system named PlasmoGF for comparative genomics and phylogenetic analysis of Plasmodium gene families.  ...  The availability of such a highly integrated system would be of great interest for the community of researchers working on malaria parasite phylogenomics. Availability: PlasmoGF is freely available at  ...  ACKNOWLEDGEMENTS This work was supported by the National Natural Science Foundation of China (30600768), the Program of New Century Excellent Talents in University (Li XK) and Zhejiang Provincial Program for  ... 
doi:10.1093/bioinformatics/btn092 pmid:18337260 fatcat:4xmvra634nbsjlthpewraueqlq

DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites

Marcin Jąkalski, Hiroyuki Wakaguri, Tabea G. Kischka, Yoshifumi Nishikawa, Shin-ichiro Kawazu, Makoto Matsubayashi, Fumiya Kawahara, Naotoshi Tsuji, Shinuo Cao, Fujiko Sunaga, Xuenan Xuan, Kazuhiro Okubo (+8 others)
2014 Nucleic Acids Research  
The content of the database was substantially enriched with transcriptome information for new apicomplexan parasites.  ...  The previous release of our Full-parasites database (http://fullmal.hgc.jp/) brought enhanced functionality, an expanded full-length cDNA content, and new RNA-Seq datasets from several important apicomplexan  ...  Toya for their excellent programming work; to K. Abe for constructing the RNA-seq libraries; H. Suganuma for cultivation of the parasites and to K. Imamura, A. Kanai and M.  ... 
doi:10.1093/nar/gku1240 pmid:25414358 pmcid:PMC4383994 fatcat:ewd3dmrjzjbhdnc6ml3s27xcqu

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 currently houses information from five parasite species and provides tools for intra-and inter-species comparisons.  ...  PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium.  ...  PlasmoDB now provides direct links to external data sources and sites, including the Malaria Parasite Metabolic Pathways database (http://sites.huji.ac.il/malaria/) and the Malaria Research and Reference  ... 
doi:10.1128/9781555817558.ch2 fatcat:a37ookqqwbeujgpzqmc5vbhzpe

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.  ...  A genome and functional genomic database for Toxoplasma gondii, ToxoDB (http://ToxoDB.org), was first released in 2001.  ... 
doi:10.2174/138945009787581195 pmid:19275560 fatcat:7ayxjno4srecdlll4ptzhuwja4

MaGnET: Malaria Genome Exploration Tool

Joanna L. Sharman, Dietlind L. Gerloff
2013 Computer applications in the biosciences : CABIOS  
The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive 'exploration-style' visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum.  ...  MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein-protein interactions and more.  ...  The University of Edinburgh and UCSC were sites of development, and UCSC remains a data mirror for MaGnET.  ... 
doi:10.1093/bioinformatics/btt384 pmid:23894142 pmcid:PMC3753565 fatcat:ejadeptp7vafjmohf33xeeilia

Bioinformatic strategies to provide functional clues to the unknown genes inPlasmodium falciparumgenome

I. Florent, E. Maréchal, O. Gascuel, L. Bréhélin
2010 Parasite  
Summary: The fight against Plasmodium falciparum, the species responsible for 90 % of the lethal forms of human malaria, took a new direction with the publication of its genome in 2002.  ...  functionally annotated -less than 40 % upon the genome publication, just over 50 % eight years later.  ...  SGD stands for Saccharomyces Genomic Database (http://www.yeastgenome.org/) General repositories of genomic and post-genomic data for malaria eupathDB http://eupathdb.org/eupathdb/ PlasmoDB http://plasmodb.org  ... 
doi:10.1051/parasite/2010174273 pmid:21275233 fatcat:z3wnw4ozsjcene2nuajogc6hhi

Malaria.tools-comparative genomic and transcriptomic database for Plasmodium species

2019 Nucleic Acids Research  
Malaria is a tropical parasitic disease caused by the Plasmodium genus, which resulted in an estimated 219 million cases of malaria and 435 000 malaria-related deaths in 2017.  ...  Moreover, we exemplify how the tools can be used to easily identify genes relevant for pathogenicity and various life stages of the malaria parasite.  ...  We would like to thank Dr Daniela Mutwil-Anderwald for proofreading the manuscript. Furthermore, we would like to thank Dr Lei Zhu from Prof. Zbynek Bozdech lab, SBS, NTU for useful discussions.  ... 
doi:10.1093/nar/gkz662 pmid:31372645 pmcid:PMC6943069 fatcat:h4mfbkls5fek3fcw2gtnwqrvje

Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease

Christian Frech, Nansheng Chen, Christos A. Ouzounis
2011 PLoS Computational Biology  
With the availability of complete genome sequences of both human and non-human Plasmodium parasites, the causative agents of malaria, it is now possible to use comparative genomics as a tool to look for  ...  Confirmed subset-specific genes were then analyzed for their role in biological pathways and examined for molecular functions using publicly available databases.  ...  Fiona Brinkman for valuable advice and discussions. Special thanks go to Ismael A. Vergara for many fruitful discussions and for providing Perl scripts and OrthoCluster support.  ... 
doi:10.1371/journal.pcbi.1002320 pmid:22215999 pmcid:PMC3245289 fatcat:hhc55t646ngc3pwjjwhlbz34ru

Plasmodium post-genomics: an update

Daniel J. Carucci
2004 Trends in Parasitology  
Databases and comparative genomics PlasmoDB, the official database for malaria genome and functional genomics data, stores, organizes and displays a wide range of genomics data, and provides query tools  ...  an avian malaria parasite; and (iv) Plasmodium vivax, a human malaria parasite.  ... 
doi:10.1016/j.pt.2004.09.007 pmid:15522664 fatcat:wk4dv6qozfcllfmdr3zd3a74iu
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