The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data
Open accessAbstract
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 tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations. Here, we report the incorporation into CGD of Assembly 22, the first chromosome-level, phased diploid assembly of the C. albicans genome, coupled with improvements that we have made to the assembly using additional available sequence data. 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. Finally, we describe the incorporation of JBrowse into CGD, which allows online browsing of mapped high throughput sequencing data, and its implementation for several RNA-Seq data sets, as well as the whole genome sequencing data that was used in the construction of Assembly 22.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“C. glabrata harbors five PIR paralogs (PIR1–PIR5) [47], all annotated as orthologs of Neurospora crassa NCU04033—a protein shown to function as a cell wall stabilizer with significant functional redundancy among family members [48].”
From Calcineurin‐Dependent Stress Adaptation Enables Caspofungin Heteroresistance Leading to Stable Resistance in Candida Glabrata (2026) · cites this paper as [47]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Since skin microbial communities can restrict bacterial pathogens through metabolic competition and immune modulation [69–72]”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [71]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Although fewer than 1% of C. auris open reading frames have been functionally characterized [71]”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [71]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Epidemiology of Invasive Candidiasis: a Persistent Public Health Problem
Pfaller, M. A., & Diekema, D. J. (2007) · Clinical Microbiology Reviews · doi:10.1128/cmr.00029-06 · Cited by 4,174 · cited 2×
“The frequency of fungal infections has risen dramatically over the past few decades, with the current annual incidence of invasive Candida infections recently estimated to range between 72 and 228 infections per million (3,4).”
BackgroundCandida albicans pathogenicity mechanisms
Mayer, F. L., Wilson, D., & Hube, B. (2013) · Virulence · doi:10.4161/viru.22913 · Cited by 1,848
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
Butler, G., Rasmussen, M. D., Lin, M. F., Santos, M. A. S., Sakthikumar, S., Munro, C. A., Rheinbay, E., Grabherr, M., Forche, A., Reedy, J. L., et al. (2009) · Nature · doi:10.1038/nature08064 · Cited by 1,065
Self-citationAntifungal drug resistance: mechanisms, epidemiology, and consequences for treatment
Pfaller, M. A. (2012) · The American Journal of Medicine · doi:10.1016/j.amjmed.2011.11.001 · Cited by 903
The diploid genome sequence of Candida albicans
Jones, T., Federspiel, N. A., Chibana, H., Dungan, J. M., Kalman, S., Magee, B. B., Newport, G., Thorstenson, Y. R., Agabian, N. M., Magee, P. T., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401648101 · Cited by 784
JBrowse: a dynamic web platform for genome visualization and analysis
Buels, R., Yao, E., Diesh, C. M., Hayes, R. D., Muñoz-Torres, M. C., Helt, G. A., Goodstein, D. M., Elsik, C. G., Lewis, S., Stein, L. D., et al. (2016) · Genome biology · doi:10.1186/s13059-016-0924-1 · Cited by 742
JBrowse: A next-generation genome browserPreprint
Skinner, M. E., Uzilov, A. V., Stein, L. D., Mungall, C., & Holmes, I. H. (2009) · Genome Research · doi:10.1101/gr.094607.109 · Cited by 718
Candida albicans: A molecular revolution built on lessons from budding yeast
Berman, J., & Sudbery, P. E. (2002) · Nature Reviews Genetics · doi:10.1038/nrg948 · Cited by 578
Kett, D. H., Azoulay, E., Echeverria, P. M., & Vincent, J.-L. (2011) · Critical Care Medicine · doi:10.1097/ccm.0b013e318206c1ca · Cited by 389
The direct cost and incidence of systemic fungal infections
Wilson, L. S., Reyes, C. M., Stolpman, M., Speckman, J., Allen, K., & Beney, J. (2002) · Value in Health · doi:10.1046/j.1524-4733.2002.51108.x · Cited by 374
Bennett, R. J., & Johnson, A. D. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg235 · Cited by 343
A Human-Curated Annotation of the Candida albicans Genome
Braun, B. R., van het Hoog, M., d'Enfert, C., Martchenko, M., Dungan, J., Kuo, A., Inglis, D. O., Uhl, M. A., Hogues, H., Berriman, M., et al. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010001 · Cited by 342
Self-citationYeast Model Uncovers Dual Roles of Mitochondria in the Action of Artemisinin
Li, W., Mo, W., Shen, D., Sun, L., Wang, J., Lu, S., Gitschier, J. M., & Zhou, B. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010036 · Cited by 304
Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage
Ihmels, J., Bergmann, S., Gerami‐Nejad, M., Yanai, I., McClellan, M., Berman, J. G., & Barkai, N. (2005) · Science · doi:10.1126/science.1113833 · Cited by 295
The ‘obligate diploid’ Candida albicans forms mating-competent haploids
Hickman, M. A., Zeng, G., Forche, A., Hirakawa, M. P., Abbey, D., Harrison, B. D., Wang, Y.-M., Su, C.-H., Bennett, R. J., Wang, Y., et al. (2013) · Nature · doi:10.1038/nature11865 · Cited by 284
Evolution of alternative transcriptional circuits with identical logic
Tsong, A. E., Tuch, B. B., Li, H., & Johnson, A. D. (2006) · Nature · doi:10.1038/nature05099 · Cited by 262
Two unlike cousins: Candida albicans and C . glabrata infection strategies
Brunke, S., & Hube, B. (2013) · Cellular Microbiology · doi:10.1111/cmi.12091 · Cited by 239
Bruno, V. M., Wang, Z., Marjani, S. L., Euskirchen, G. M., Martin, J. V., Sherlock, G., & Snyder, M. P. (2010) · Genome Research · doi:10.1101/gr.109553.110 · Cited by 212
Self-citationAssembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes
Hoog, M. V. H., Rast, T. J., Martchenko, M., Grindle, S. M., Dignard, D., Hogues, H., Cuomo, C. A., Berriman, M., Scherer, S., Magee, B. B., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-4-r52 · Cited by 173
Candida albicans: A Model Organism for Studying Fungal Pathogens
Kabir, M. A., Hussain, M. A., & Ahmad, Z. (2012) · ISRN Microbiology · doi:10.5402/2012/538694 · Cited by 170
Transcriptional Rewiring of Fungal Galactose-Metabolism Circuitry
Martchenko, M., Levitin, A., Hogues, H., Nantel, A., & Whiteway, M. S. (2007) · Current Biology · doi:10.1016/j.cub.2007.05.017 · Cited by 170
Opportunistic Candidiasis: An Epidemic of the 1980s
Fisher‐Hoch, S. P., & Hutwagner, L. (1995) · Clinical Infectious Diseases · doi:10.1093/clinids/21.4.897 · Cited by 164
Xie, J., Li, T., Nobile, C. J., Tong, Y., Guan, G., Sun, Y., Cao, C., Hernday, A. D., Johnson, A. D., Zhang, L., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001525 · Cited by 135
Holland, L., Schröder, M., Turner, S. A., Taff, H. T., Andes, D. R., Grózer, Z., Gácser, A., Ames, L., Haynes, K., Higgins, D. G., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004365 · Cited by 134
Insights into Candida tropicalis nosocomial infections and virulence factors
Negri, M., Silva, S., Henriques, M., & Oliveira, R. (2012) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-011-1455-z · Cited by 132
A review of Candida species causing blood stream infection
Giri, S., & Kindo, A. J. (2012) · Indian Journal of Medical Microbiology · doi:10.4103/0255-0857.99484 · Cited by 132
Arnaud, M. B. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki003 · Cited by 124
Muzzey, D., Schwartz, K., Weissman, J. S., & Sherlock, G. (2013) · Genome biology · doi:10.1186/gb-2013-14-9-r97 · Cited by 123
Self-citationEmerging targets for the development of novel antifungal therapeutics
Groll, A. H., Lucca, A. J. D., & Walsh, T. J. (1998) · Trends in Microbiology · doi:10.1016/s0966-842x(97)01206-7 · Cited by 90
Regulatory Role of Glycerol in Candida albicans Biofilm Formation
Desai, J. V., Bruno, V. M., Ganguly, S., Stamper, R. J., Mitchell, K. F., Solis, N. V., Hill, E. M., Xu, W., Filler, S. G., Andes, D. R., et al. (2013) · mBio · doi:10.1128/mbio.00637-12 · Cited by 86
Invasive fungal infections in patients with cancer in the Intensive Care Unit
Sipsas, N. V., & Kontoyiannis, D. P. (2012) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2011.11.017 · Cited by 82
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq
Linde, J., Duggan, S., Weber, M., Horn, F., Sieber, P. A., Hellwig, D., Riege, K., Marz, M., Martin, R., Guthke, R., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1357 · Cited by 77
Extensive DNA-binding specificity divergence of a conserved transcription regulator
Baker, C. R., Tuch, B. B., & Johnson, A. D. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019177108 · Cited by 75
Sequence resources at the Candida Genome Database
Arnaud, M. B., Costanzo, M. C., Skrzypek, M. S., Shah, P., Binkley, G., Lane, C. D., Miyasato, S. R., & Sherlock, G. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl899 · Cited by 72
Self-citationOccurrence, presentation and treatment of candidemia
Mikulska, M., Del Bono, V., Ratto, S., & Viscoli, C. (2012) · Expert Review of Clinical Immunology · doi:10.1586/eci.12.52 · Cited by 71
Management of candidiasis in the intensive care unit
Schelenz, S. (2007) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkm430 · Cited by 68
Chen, M.-W., Anné, J., Volckaert, G., Huysmans, E., Vandenberghe, A., & Wächter, R. D. (1984) · Nucleic Acids Research · doi:10.1093/nar/12.12.4881 · Cited by 64
MovieMaker: a web server for rapid rendering of protein motions and interactions
Maiti, R., Domselaar, G. H. V., & Wishart, D. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki485 · Cited by 62
Muzzey, D., Sherlock, G., & Weissman, J. S. (2014) · Genome Research · doi:10.1101/gr.166322.113 · Cited by 59
Self-citationHendriks, L., Goris, A., de Peer, Y. V., Neefs, J., Vancanneyt, M., Kersters, K., Hennebert, G. L., & Wächter, R. D. (1991) · Journal of General Microbiology · doi:10.1099/00221287-137-5-1223 · Cited by 53
The potential impact of antifungal drug resistance mechanisms on the host immune response to Candida
Lewis, R. E., Viale, P., & Kontoyiannis, D. P. (2012) · Virulence · doi:10.4161/viru.20746 · Cited by 51
Chow, B. D. W., Linden, J. R., & Bliss, J. M. (2012) · Expert Review of Anti-infective Therapy · doi:10.1586/eri.12.74 · Cited by 51
Lohse, M. B., & Johnson, A. D. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.024885 · Cited by 49
TheSaccharomycesGenome Database Variant Viewer
Sheppard, T. K., Hitz, B. C., Engel, S. R., Song, G., Balakrishnan, R., Binkley, G., Costanzo, M. C., Dalusag, K. S., Demeter, J., Hellerstedt, S. T., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1250 · Cited by 22
Self-citationGeneXplorer: an interactive web application for microarray data visualization and analysis
Rees, C. A., Demeter, J., Matese, J. C., Botstein, D., & Sherlock, G. J. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-141 · Cited by 19
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
The Gene Ontology knowledgebase in 2023
Aleksander, S., Balhoff, J. P., Carbon, S., Cherry, J. M., Drabkin, H., Ebert, D., Feuermann, M., Gaudet, P., Harris, N. L., Hill, D. P., et al. (2023) · Genetics · doi:10.1093/genetics/iyad031 · Cited by 2,873
Self-citationThe BioGRID interaction database: 2019 update
Oughtred, R., Stark, C., Breitkreutz, B., Rust, J., Boucher, L., Chang, C., Kolas, N. K., O’Donnell, L., Leung, G. C., McAdam, R. F., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1079 · Cited by 1,474
The BioGRID interaction database: 2017 update
Chatr‐aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N. K., O’Donnell, L., Oster, S. K., Theesfeld, C. L., Sellam, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1102 · Cited by 985
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center
Amos, B., Aurrecoechea, C., Barba, M., Barreto, A., Basenko, E. Y., Bażant, W., Belnap, R., Blevins, A. S., Böhme, U., Brestelli, J. E., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab929 · Cited by 460
Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1835-8 · Cited by 452
Metadata
- Authors
- Skrzypek, M. S., Binkley, J., Binkley, G., Miyasato, S. R., Simison, M., & Sherlock, G.
- Affiliations
- Stanford Medicine (US)
- Corresponding author
- Sherlock, Gavin
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-10-13
- Volume
- 45
- Issue
- D1
- Pages
- D592-D596
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5210628
- OpenAlex
- W2530772399
- Cited by
- 455
- References
- 45
- Citations by year
- 2026: 35 · 2025: 61 · 2024: 68 · 2023: 44 · 2022: 45 · 2021: 69 · 2020: 38 · 2019: 45 · 2018: 39 · 2017: 10 · 2016: 1
- FWCI
- 16.64
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institute of Dental and Craniofacial Research (R01DE015873)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Immunology and Microbiology › Microbiology › Yeasts and Rust Fungi Studies
- Keywords
- Candida albicans, genome assembly, JBrowse, RNA-seq, genome annotation, fungal genomics
- MeSH terms
- Candida, Fungal Proteins, Software, Open Reading Frames, Genome, Fungal, Computational Biology, Genomics, Databases, Nucleic Acid, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing, Web Browser
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
