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The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information

M. B. Arnaud
2004 Nucleic Acids Research  
The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans.  ...  CGD also provides community resources, including a reservation system for gene names and a colleague registry through which Candida researchers can share contact information and research interests.  ...  ACKNOWLEDGEMENTS CGD thanks the Candida Annotation Working Group, especially Andre Nantel, for their generosity in sharing their entire data set and their enthusiasm for letting CGD house this resource  ... 
doi:10.1093/nar/gki003 pmid:15608216 pmcid:PMC539957 fatcat:uyutdlkpene2tjbz53prj5qcwe

Using the Candida Genome Database [chapter]

Marek S. Skrzypek, Jonathan Binkley, Gavin Sherlock
2018 Msphere  
The Candida Genome Database (CGD) curates the Candida literature, and integrates functional information about Candida genes and their products with a set of analysis tools that facilitate searching for  ...  Studying Candida biology requires access to genomic sequence data in conjunction with experimental information that together provide functional context to genes and proteins, and aid in interpreting newly  ...  Acknowledgements This work was supported by National Institute of Dental and Craniofacial Research at the US National Institutes of Health (grant no. R01 DE015873). References  ... 
doi:10.1007/978-1-4939-7737-6_3 pmid:29761455 pmcid:PMC6005354 fatcat:xhlbkdoipra6jjs4vn6yxok6gu

Sequence resources at the Candida Genome Database

M. B. Arnaud, M. C. Costanzo, M. S. Skrzypek, P. Shah, G. Binkley, C. Lane, S. R. Miyasato, G. Sherlock
2007 Nucleic Acids Research  
The Candida Genome Database (CGD, http://www. candidagenome.org/) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology  ...  In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD  ...  ACKNOWLEDGEMENTS We would like to thank the Candida Annotation Working Group, in particular Andre Nantel and Marco van het Hoog, for providing sequence and annotation files to CGD and helping to check  ... 
doi:10.1093/nar/gkl899 pmid:17090582 pmcid:PMC1669745 fatcat:wr5gl2rnvbfqta6duvzamgh7ou

How to Use the Candida Genome Database [chapter]

Marek S. Skrzypek, Jonathan Binkley, Gavin Sherlock
2016 Msphere  
The Candida Genome Database (CGD) integrates functional information about Candida genes and their products with a set of analysis tools that facilitate searching for sets of genes and exploring their biological  ...  Studying Candida biology requires access to genomic sequence data in conjunction with experimental information that provides functional context to genes and proteins.  ...  Acknowledgments This work was supported by National Institute of Dental and Craniofacial Research at the US National Institutes of Health (grant no. R01 DE015873).  ... 
doi:10.1007/978-1-4939-3052-4_1 pmid:26519061 pmcid:PMC4896156 fatcat:762r63gssbfvncdjjgab4uvi3q

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

D. O. Inglis, M. B. Arnaud, J. Binkley, P. Shah, M. S. Skrzypek, F. Wymore, G. Binkley, S. R. Miyasato, M. Simison, G. Sherlock
2011 Nucleic Acids Research  
genes and proteins of the fungal pathogen Candida albicans and other Candida species.  ...  The Candida Genome Database (CGD, http://www .candidagenome.org/) is an internet-based resource that provides centralized access to genomic sequence data and manually curated functional information about  ...  CGD is grateful to the many members of the Candida research community who have generously provided their feedback and support for the project.  ... 
doi:10.1093/nar/gkr945 pmid:22064862 pmcid:PMC3245171 fatcat:qfogwktijnbufkeevqgqiey5ka

New tools at the Candida Genome Database: biochemical pathways and full-text literature search

Marek S. Skrzypek, Martha B. Arnaud, Maria C. Costanzo, Diane O. Inglis, Prachi Shah, Gail Binkley, Stuart R. Miyasato, Gavin Sherlock
2009 Nucleic Acids Research  
The Candida Genome Database (CGD, http://www .candidagenome.org/) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen  ...  Candida albicans.  ...  other members of the SGD group for their help and support.  ... 
doi:10.1093/nar/gkp836 pmid:19808938 pmcid:PMC2808937 fatcat:2b4oftzhwjfo5b4pswxcx5rdby

TheCandidaGenome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data

Marek S. Skrzypek, Jonathan Binkley, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock
2016 Nucleic Acids Research  
The Candida Genome Database (CGD, http://www. candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based  ...  We also report the creation of systematic identifiers for C. albicans genes and sequence features using a system similar to that adopted by the yeast community over two decades ago.  ...  ACKNOWLEDGEMENTS CGD thanks the Candida research community for their advice, support and enthusiasm.  ... 
doi:10.1093/nar/gkw924 pmid:27738138 pmcid:PMC5210628 fatcat:wjlitcamdzgr3lks2omz35n64y

TheCandidaGenome Database: The new homology information page highlights protein similarity and phylogeny

Jonathan Binkley, Martha B. Arnaud, Diane O. Inglis, Marek S. Skrzypek, Prachi Shah, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock
2013 Nucleic Acids Research  
The Candida Genome Database (CGD, http://www. candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based  ...  tabs display more in-depth information, including protein product details for coding genes, notes on changes to the sequence or structure of the gene and a comprehensive reference list.  ...  The authors also thank the Candida research community for their advice, support and enthusiasm.  ... 
doi:10.1093/nar/gkt1046 pmid:24185697 pmcid:PMC3965001 fatcat:vf7ybvr3vnasxpa4wr7telpqxm

CandidaDB: a multi-genome database for Candida species and related Saccharomycotina

T. Rossignol, P. Lechat, C. Cuomo, Q. Zeng, I. Moszer, C. d'Enfert
2007 Nucleic Acids Research  
ACKNOWLEDGEMENTS We are grateful to Louis Jones for help in making the database publicly available.  ...  Funding to pay the Open Access publication charges for this article was provided by Institut Pasteur. Conflict of interest statement. None declared.  ...  CandidaDB is a convenient entry point for the community working on other Candida species than C. albicans since any Candida genome can be used as the favourite genome.  ... 
doi:10.1093/nar/gkm1010 pmid:18039716 pmcid:PMC2238939 fatcat:byq7ixgkvvbifjyn5a6v5aho7e

Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans

Martha B. Arnaud, Maria C. Costanzo, Prachi Shah, Marek S. Skrzypek, Gavin Sherlock
2009 Trends in Microbiology  
The unicellular fungus Candida albicans is similar in many ways to the model organism Saccharomyces cerevisiae, but as both a commensal and a pathogen of humans, differs greatly in its lifestyle.  ...  The Gene Ontology (GO) is a structured controlled vocabulary developed to describe the roles and locations of gene products in a consistent fashion, in a way that can be shared across organisms.  ...  Acknowledgments The Candida Genome Database staff thanks our close collaborators, Mike Cherry and the other members of the Saccharomyces Genome Database Group.  ... 
doi:10.1016/j.tim.2009.04.007 pmid:19577928 pmcid:PMC3907193 fatcat:zszwegcy35b5rhfdqykt6qkmyu

Improved Gene Ontology Annotation for Biofilm Formation, Filamentous Growth, and Phenotypic Switching in Candida albicans

Diane O. Inglis, Marek S. Skrzypek, Martha B. Arnaud, Jonathan Binkley, Prachi Shah, Farrell Wymore, Gavin Sherlock
2012 Eukaryotic Cell  
The Gene Ontology (GO) ( www.geneontology.org ) is a standardized vocabulary that the Candida Genome Database (CGD) ( www.candidagenome.org ) and other groups use to describe the functions of gene products  ...  The opportunistic fungal pathogen Candida albicans is a significant medical threat, especially for immunocompromised patients.  ...  ACKNOWLEDGMENTS We thank Gail Binkley for CGD Oracle database administration, Stuart Miyasoto and Matt Simison for CGD database software and hardware maintenance, and Jane Lomax, Rebecca Foulger, and Paola  ... 
doi:10.1128/ec.00238-12 pmid:23143685 pmcid:PMC3535841 fatcat:xtrjcvufhjfzjgfl4m3iyttjpa

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

David A Fitzpatrick, Peadar O'Gaora, Kevin P Byrne, Geraldine Butler
2010 BMC Genomics  
We also identified one example of intron gain in C. albicans. Conclusions: Our analysis provides an important resource that is now available for the Candida community. CGOB is available at  ...  CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida  ...  YGOB and for reading the manuscript.  ... 
doi:10.1186/1471-2164-11-290 pmid:20459735 pmcid:PMC2880306 fatcat:apdsaxmedzbvpa66dp6fxstg7i

Budding off: bringing functional genomics toCandida albicans

Matthew Z. Anderson, Richard J. Bennett
2015 Briefings in Functional Genomics  
Candida albicans resides as a commensal of the human gastrointestinal tract but is a frequent cause of opportunistic mucosal and systemic infections.  ...  Such studies include comparative genomics (both between and within Candida species), analysis of total RNA expression, and regulation and delineation of protein-DNA interactions.  ...  and addressing genomic diversity within C. albicans and the Candida Genome Database (CGD) for the construction and maintenance of an invaluable resource to the Candida community for investigation and  ... 
doi:10.1093/bfgp/elv035 pmid:26424829 pmcid:PMC5065355 fatcat:kwz7sknn3zfdzcelytu6u7c44m

A Candida albicans PeptideAtlas

Vital Vialas, Zhi Sun, Carla Verónica Loureiro y Penha, Montserrat Carrascal, Joaquín Abián, Lucía Monteoliva, Eric W. Deutsch, Ruedi Aebersold, Robert L. Moritz, Concha Gil
2014 Journal of Proteomics  
Based on data from 16 experiments, we attained coverage of 41% of the C. albicans open reading frame sequences (ORFs) in the database used for the searches.  ...  We report here the creation of a C. albicans PeptideAtlas comprising near 22,000 distinct peptides at a 0.24% False Discovery Rate (FDR) that account for over 2500 canonical proteins at a 1.2% FDR.  ...  We are thankful to María Luisa Hernáez and Jose Antonio Reales for helping in sample obtention from the hyphal and yeast form protein extracts and to Antonio Serna for providing the tandem mass spectra  ... 
doi:10.1016/j.jprot.2013.06.020 pmid:23811049 pmcid:PMC3951211 fatcat:a4ghewbbjjcg7ixtdfdshpd4im

YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts

2019 Nucleic Acids Research  
The YEASTRACT+ information system (http://YEASTRACT-PLUS.org/) is a wide-scope tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in yeasts of  ...  YEASTRACT+ continues to make available tools for the prediction of the TFs involved in the regulation of gene/genomic expression.  ...  Genome Database (CGD), Candida Gene Order Browser (CGOB) and GO Consortium.  ... 
doi:10.1093/nar/gkz859 pmid:31586406 pmcid:PMC6943032 fatcat:mhtwusu475cq5o55jl4lfkghma
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