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CryptoDB: a Cryptosporidium bioinformatics resource update

M. Heiges
2006 Nucleic Acids Research  
AFFILIATIONS CryptoDB is a member of, an NIH/NIAID funded Bioinformatics Resource Center (BRC) for Biodefense and 35 Emerging or Re-Emerging Infectious Diseases (www.niaid.  ...  Data exchange and interoperability with other NIAID Bioinformatics Resource Centers will be a continued effort. 85 Figure 1 . 1 Database functionality.  ... 
doi:10.1093/nar/gkj078 pmid:16381902 pmcid:PMC1347441 fatcat:nab2wuwlfzhxvkgl4tah737jse

Accessing Cryptosporidium Omic and Isolate Data via [chapter]

Susanne Warrenfeltz, On Behalf of the EuPathDB Team, Jessica C. Kissinger
2019 Msphere  
CryptoDB merged with the EuPathDB Bioinformatics Resource Center family of databases ( ) and has been maintained and updated regularly since its establishment.  ...  Cryptosporidium has historically been a difficult organism to work with, and molecular genomic data for this important pathogen have typically lagged behind other prominent protist pathogens.  ...  CryptoDB is updated roughly every 2 months with new data and new features.  ... 
doi:10.1007/978-1-4939-9748-0_10 pmid:31452162 fatcat:p7auusbbsnfedfcuf3udpp4iwq

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  
CryptoDB [13] (Box 1h) houses genome resources for Cryptosporidium parvum Iowa II [19] and Cryptosporidium hominis TU502 [20] .  ...  CryptoDB cross-references with CryptoCyc (Box 1i), a companion database of Cryptosporidium metabolic pathways.  ... 
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  
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  ...  The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience.  ...  INTRODUCTION The Eukaryotic Pathogen Database (EuPathDB) has been developed as a Bioinformatics Resource Center (BRC), with support from the US National Institutes of Health (NIH).  ... 
doi:10.1093/nar/gkp941 pmid:19914931 pmcid:PMC2808945 fatcat:wvtdhudoo5fgjiclufxahkzhuy

Cryptosporidium hominisgene catalog: a resource for the selection of novelCryptosporidiumvaccine candidates

Olukemi O. Ifeonu, Raphael Simon, Sharon M. Tennant, Abhineet S. Sheoran, Maria C. Daly, Victor Felix, Jessica C. Kissinger, Giovanni Widmer, Myron M. Levine, Saul Tzipori, Joana C. Silva
2016 Database: The Journal of Biological Databases and Curation  
Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates.  ...  Abstract Human cryptosporidiosis, caused primarily by Cryptosporidium hominis and a subset of Cryptosporidium parvum, is a major cause of moderate-to-severe diarrhea in children under 5 years of age in  ...  Acknowledgement The authors thank the signatories of the 2011 community white paper on the comparative genomics of Cryptosporidium.  ... 
doi:10.1093/database/baw137 pmid:28095366 pmcid:PMC5070614 fatcat:seuqadmvirdvrpbnmlzdmwvsw4

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs

J. Watanabe, H. Wakaguri, M. Sasaki, Y. Suzuki, S. Sugano
2007 Nucleic Acids Research  
By specifying keywords and other search conditions, Comparasite retrieves putative counterpart gene groups containing a given feature in common or in a species-specific manner.  ...  produced and sequenced: 12 484 cDNA sequences from Plasmodium falciparum, 11 262 from Plasmodium yoelii, 9633 from Plasmodium vivax, 1518 from Plasmodium berghei, 7400 from Toxoplasma gondii, 5921 from Cryptosporidium  ..., CryptoDB (http://cryptodb. org/cryptodb/) and ToxoDB ( release4-0/home.jsp)].  ... 
doi:10.1093/nar/gkl1039 pmid:17151081 pmcid:PMC1781114 fatcat:muoaulc4svg7tkzaz453fvzfpq

ApicoTFdb: The comprehensive web repository of apicomplexan transcription factors and regulators [article]

Rahila Sardar, Abhinav Kaushik, Rajan Pandey, Asif Mohmmed, Shakir Ali, Dinesh Gupta
2019 bioRxiv   pre-print
significant progress in apicomplexans genome sequencing and genomics, the current list of experimentally validated TFs in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a  ...  We have performed systematic bioinformatics aided prediction of TFs and TAFs in apicomplexan genomes, and developed ApicoTFdb database which consists of experimentally validated as well as computationally  ...  Heiges M, Wang H, Robinson E, Aurrecoechea C, Gao X, Kaluskar N, Rhodes P, Wang S, He C-Z, 354 Su Y et al: CryptoDB: a Cryptosporidium bioinformatics resource update.  ... 
doi:10.1101/530006 fatcat:fkxae7lwirdedbyxktgfyrexti

An Evaluation of Multiple Approaches for Federating Biological Data

Zhiming Wang, Xin Gao, Congzhou He, John A. Miller, Jessica C. Kissinger, Mark Heiges, Cristina Aurrecoechea, Eileen T. Kraemer, C. Pennington
2009 Journal of Information Technology Research  
A significant result of our study is that the most flexible approach, Web Services, performs very competitively.  ...  research areas (Stevens currently are provided by three distinct databases, CryptoDB, PlasmoDB and ToxoDB 1 , which represent the Apicomplexan parasites Cryptosporidium, Plasmodium and Toxoplasma, respectively  ...  We have implemented and evaluated four approaches for the ApiDB project (a member of the National Institute of Allergy and Infectious Disease's (NIAID) Bioinformatics Resource Centers (BRC) http: //  ... 
doi:10.4018/jitr.2009040104 fatcat:v5eu6yiixfek7lnijk6vtid7jq

The State of Research for AIDS-Associated Opportunistic Infections and the Importance of Sustaining Smaller Research Communities

Anthony P. Sinai, Edna S. Kaneshiro, Honorine Ward, Louis M. Weiss, Melanie T. Cushion
2011 Eukaryotic Cell  
The community as a whole participates in the building of this resource, which is constantly updated based on its feedback.  ...  resource (29) , have greatly expedited a number of avenues of Cryptosporidium research.  ... 
doi:10.1128/ec.05143-11 pmid:22158712 pmcid:PMC3272903 fatcat:6hduzmeje5ahlljswmunuhwpsi

Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009

H. Wakaguri, Y. Suzuki, T. Katayama, S. Kawashima, E. Kibukawa, K. Hiranuka, M. Sasaki, S. Sugano, J. Watanabe
2009 Nucleic Acids Research  
Full-Malaria/Parasites is a database for transcriptome studies of apicomplexa and other parasites, which is based on our original full-length cDNA sequences and physical cDNA clone resources.  ...  Furthermore, we have launched Full-Arthropods, a full-length cDNA database for arthropods of medical importance.  ...  Comparasite, which is a database for the comparative studies of the parasites, was updated accordingly.  ... 
doi:10.1093/nar/gkn856 pmid:18987005 pmcid:PMC2686583 fatcat:vibtihhbhbfwlo3x3wxvgm3hbe

Comparative analyses of parasites with a comprehensive database of geno-scale metabolic models

Maureen A. Carey, Gregory L. Medlock, Michał Stolarczyk, William A. Petri, Jennifer L. Guler, Jason A. Papin, Pedro Mendes
2022 PLoS Computational Biology  
genome including Plasmodium, Toxoplasma, Cryptosporidium, Entamoeba, Trypanosoma, Leishmania, Giardia, and other species.  ...  To address this challenge and to accelerate parasitology research broadly, we present a functional comparative analysis of 192 genomes, representing every high-quality, publicly-available protozoan parasite  ...  The large genome of Chromera velia CCMP2878 (a non-parasitic organism on CryptoDB with 31,799 ORFs and 3,064 reactions) corresponds to a reconstruction with the second most unique reactions with 58.  ... 
doi:10.1371/journal.pcbi.1009870 pmid:35196325 pmcid:PMC8901074 fatcat:vsvudzipevaedit423yaw2u7ny

National Institute of Allergy and Infectious Diseases Bioinformatics Resource Centers: New Assets for Pathogen Informatics

J. M. Greene, F. Collins, E. J. Lefkowitz, D. Roos, R. H. Scheuermann, B. Sobral, R. Stevens, O. White, V. Di Francesco
2007 Infection and Immunity  
A federation of three databases (PlasmoDB, CryptoDB, and ToxoDB) in ApiDB permits users to simultaneously query across all three.  ...  Eight Bioinformatics Resource Centers for Biodefense and Emerging/Re-Emerging Infectious Disease (BRCs) were funded to provide the research community working on a variety of pathogens access to integrated  ... 
doi:10.1128/iai.00105-07 pmid:17420237 pmcid:PMC1932942 fatcat:ywmscqywenflnlxo7frpehvnii

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: Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.  ...  As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge  ...  Fig. 12 . 12 Screenshots of an isolate query in CryptoDB.  ... 
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  
Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e.  ...  EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data.  ...  sets, often prior to publication and for numerous comments and 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

Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites

Achchuthan Shanmugasundram, Faviel F. Gonzalez-Galarza, Jonathan M. Wastling, Olga Vasieva, Andrew R. Jones
2012 Nucleic Acids Research  
We expect this new database will become a valuable resource for fundamental and applied research on the Apicomplexa.  ...  We have adopted an approach called metabolic reconstruction, in which genes are systematically assigned to functions within pathways/networks for Toxoplasma gondii, Neospora caninum, Cryptosporidium and  ...  LAMP provides a balance between a highly curated organismspecific resource and general automatic reconstruction resource such as KEGG.  ... 
doi:10.1093/nar/gks1139 pmid:23193253 pmcid:PMC3531055 fatcat:z4nfyocjdjchtdvwdhr4kofn6q
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