Cited by 458Fungal and yeast genetics researchGenomics and Phylogenetic StudiesYeasts and Rust Fungi Studies

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 access

Skrzypek, Marek S., Binkley, Jonathan, Binkley, Gail, Miyasato, Stuart R., Simison, Matt, Sherlock, Gavin·2017·Nucleic Acids Research

DOI 10.1093/nar/gkw924PMC PMC5210628

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1093/nar/gkw924

Cites

45 of 45 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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).”
Background
Candida 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-citation
Antifungal 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
Candida bloodstream infections in intensive care units: Analysis of the extended prevalence of infection in intensive care unit study*
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

Flagged first, then by citations

Show all 45 references

Sorted by citations

Items 301–400 of 458

The zinc cluster transcription factor Znc1 regulates Rta3-dependent miltefosine resistance in Candida albicans
Ramı́rez-Zavala, B., Krüger, I., Schwanfelder, S., Barker, K. S., Rogers, P. D., & Morschhäuser, J. (2024) · mSphere · doi:10.1128/msphere.00270-24 · Cited by 5
A NovelcisElement Achieves the Same Solution as an AncestralcisElement During Thiamine Starvation inCandida glabrata
Iosue, C. L., Gulotta, A. P., Selhorst, K. B., Mody, A. C., Barbour, K. M., Marcotte, M. J., Bui, L. N., Leone, S. G., Lang, E. C., Hughes, G. H., et al. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400897 · Cited by 4
CaMad2 Promotes Multiple Aspects of Genome Stability Beyond Its Direct Function in Chromosome Segregation
Vossen, M. L., Alhosawi, H. M., Aney, K. J., & Burrack, L. S. (2019) · Genes · doi:10.3390/genes10121013 · Cited by 4
Photochromic Fluorophores Enable Imaging of Lowly Expressed Proteins in the Autofluorescent Fungus Candida albicans
Genechten, W. V., Demuyser, L., Duwé, S., Vandenberg, W., Dijck, P. V., & Dedecker, P. (2021) · mSphere · doi:10.1128/msphere.00146-21 · Cited by 4
Plasmid-Based CRISPR–Cas9 Editing in Multiple Candida Species
Lombardi, L., & Butler, G. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2549-1_2 · Cited by 4
The Ypk1 protein kinase signaling pathway is rewired and not essential for viability in Candida albicans
Ramı́rez-Zavala, B., Krüger, I., Wollner, A., Schwanfelder, S., & Morschhäuser, J. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010890 · Cited by 4
In silico genome wide identification of long non-coding RNAs differentially expressed during Candida auris host pathogenesis
Mathur, K., Singh, B., Puria, R., & Nain, V. (2024) · Archives of Microbiology · doi:10.1007/s00203-024-03969-7 · Cited by 4
Carbon Dioxide Controls Fungal Fitness and Skin Tropism of Candida aurisPreprint
Phan-Canh, T., Penninger, P., Seiser, S., Khunweeraphong, N., Moser, D., Bitencourt, T. A., Arzani, H., Chen, W., Zenz, L.-M., Knarr, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.12.589292 · Cited by 4
Expression of 1,3-β-glucan synthase subunits in Candida glabrata is regulated by the cell cycle and growth conditions and at both transcriptional and post-transcriptional levels
Gonzalez-Jimenez, I., Keniya, M. V., Aptekmann, A. A., Quinteros, C., Wilkerson, A., Arastehfar, A., Daneshnia, F., Perlin, D. S., & Shor, E. (2025) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00500-25 · Cited by 4
Host–Candida auris interactions in the skin
Thangamani, S., Balakumar, A., Datta, A., Bryak, G., & Lionakis, M. S. (2026) · PLOS Pathogens · doi:10.1371/journal.ppat.1014075 · Cited by 3
Pathogenic Features, Experimental Models, and Molecular Tools of Human Fungal Pathogens: Who’s on WHO’s Radar?
Narayanan, A., Shaji, A. A., Pullepu, D., Bhattacharya, J., & Sanyal, K. (2025) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5c00081 · Cited by 3
An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in Candida albicans during host infection
Chakraborty, S., Palanikumar, I., Gune, Y., Venkatesh, K. V., Raman, K., & Idicula‐Thomas, S. (2025) · Cell Communication and Signaling · doi:10.1186/s12964-025-02306-9 · Cited by 3
Small pangenome of Candida parapsilosis reflects overall low intraspecific diversity
Ryan, A. P., Bergin, S. A., Scully, J., Zuniga‐Soto, E., Hession, C., Barber, A. E., Gómez-Molero, E., Bader, O., Morio, F., Zhai, B., et al. (2025) · mBio · doi:10.1128/mbio.01320-25 · Cited by 4
Phylogenomic analysis and genetic mechanisms of antifungal resistance in clinical isolates of Candida glabrata ( Nakaseomyces glabratus ) from across Canada, 2013–2020
Luca, D. G. D., Alexander, D. C., Dingle, T. C., Dufresne, P. J., Fuller, J., German, G. J., Haldane, D. J. M., Hoang, L., Jiao, L., Kus, J. V., et al. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.01803-25 · Cited by 3
Structural insights into mechanisms of zinc scavenging by the Candida albicans zincophore Pra1
Nore, A., Roselletti, E., Chakraborty, T., Särkkä, N., Perera, R. L., Wilson, D., & Syrjänen, J. L. (2025) · Nature Communications · doi:10.1038/s41467-025-65782-0 · Cited by 3
A fungal pathobiont promotes Streptococcus vaginal persistence and pathogenesis through physical and metabolic interactions
Cohen, S., Crossen, A. J., Jensen, O., Neely, M. N., Doaré, K. L., Nobbs, A. H., Ost, K. S., & Doran, K. S. (2026) · Cell Host & Microbe · doi:10.1016/j.chom.2026.04.013 · Cited by 4
A targeted drug-repurposing strategy identifies Tavaborole (Kerydin) as a potent fungistatic agent against Candida auris
Mazumdar, R., & Bjelanović, A. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1830629 · Cited by 2
Mitochondrial targeting of Candida albicans SPFH proteins and requirement of stomatins for SDS-induced stress tolerance
Kim, H.-J., Heredia, M. Y., Chen, X., Ahmed, M., Qasim, M. N., Callender, T. L., Hernday, A. D., & Rauceo, J. M. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.01733-24 · Cited by 4
Expansion of the functional genomics GRACE library reveals genes relevant for temperature-dependent fitness in Candida albicans
Fu, C., Xiong, E. H., Kupczok, L., Archambault, L. S., Wang, T. R. W., Holleran, C., Carruthers-Lay, D., Zhuang, T. X., Marcoccia, S., Zhang, H., et al. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003409 · Cited by 2
Evaluation of novel L-histidine-based Schiff base derivatives as microbial-HO inhibitors and their antimicrobial and molecular docking studies
Vidhya, K., Kumar, K. P., Piramanayagam, S., Arulkumar, M., Balraj, J., Jairaman, K., Subashini, G., & Angayarkanni, J. (2022) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2022.133890 · Cited by 3
Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples
Hovhannisyan, H., Rodríguez, A., Saus, E., Vaneechoutte, M., & Gabaldón, T. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1093178 · Cited by 3
A cell wall-targeting urease-derived peptide as a potential antifungal agent against Candida species
Perin, A. P. A., Reuwsaat, J. C. V., Motta, H., Lopes, F. C., Grahl, M. V. C., Tavanti, A. G., Vainstein, M. H., Staats, C. C., Carlini, C. R., Ligabue‐Braun, R., et al. (2025) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2025.100399 · Cited by 3
‘The awesome power of yeast’
Macreadie, I. G., & Dhakal, S. (2022) · Microbiology Australia · doi:10.1071/ma22007 · Cited by 3
Pixel: a content management platform for quantitative omics data
Denecker, T., Durand, W., Maupetit, J., Hébert, C., Camadro, J., Poulain, P., & Lelandais, G. (2019) · PeerJ · doi:10.7717/peerj.6623 · Cited by 3
Functional genetic characterization of stress tolerance and biofilm formation in Nakaseomyces glabrata via a novel CRISPR activation systemPreprint
Maroc, L., Shaker, H., & Shapiro, R. S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.07.569977 · Cited by 3
Structural and Biophysical Dynamics of Fungal Plasma Membrane Proteins and Implications for Echinocandin Action in Candida glabrataPreprint
Jiang, J. B., Keniya, M. V., Puri, A., Zhan, X., Cheng, J., Wang, H., Lin, G., Lee, Y.-K., Jaber, N., Hassoun, Y., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.29.596243 · Cited by 3
A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans
Correia, I., Oliveira, C., Reis, A., Guimarães, A. R., Aveiro, S. S., Domingues, P. M., Bezerra, A. R., Vitorino, R. M. P., Moura, G. R., & Santos, M. A. S. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100818 · Cited by 2
EpiCandIn: An open online resource for epidemiology of Candida infections in India
Rahate, K., Arshi, A., Barai, R. S., Chakraborty, S., & Idicula‐Thomas, S. (2024) · The Indian Journal of Medical Research · doi:10.25259/ijmr_886_23 · Cited by 2
DNA Sequence Perplexity Reveals Evolutionarily Conserved Patterns in cis-Regulatory Regions Across Diverse Species
Gummadi, A. S. C., & Yella, V. R. (2025) · Biochemical Genetics · doi:10.1007/s10528-025-11231-y · Cited by 3
In Vitro Exposure to Vaped Tetrahydrocannabinol Increases Candida albicans (SC5314) Growth, Metabolic Activity, Biofilm Formation, and the Expression of Virulence Genes
Laaboudi, F.-Z., Amri, O., & Rouabhia, M. (2025) · Microorganisms · doi:10.3390/microorganisms13102278 · Cited by 2
Molecular Mechanism of Action of HOCl from Neutral-pH Electrolysed Oxidising Water Against Candida albicans
Krishnan, C. S., Milne, T. J., Tompkins, G. R., Cannon, R. D., & Lamping, E. (2025) · Journal of Fungi · doi:10.3390/jof11110761 · Cited by 2
Immunogold labeling of extracellular vesicles from the fungal pathogen Fusarium graminearum reveals the presence of the protein marker Sur7
Garcia‐Ceron, D., Wilson, S. M., Bleackley, M. R., & Anderson, M. A. (2025) · Fungal Biology and Biotechnology · doi:10.1186/s40694-025-00206-8 · Cited by 2
Recurrent mutations in the stress regulator Cap1 reveal a trade-off between azole resistance and oxidative stress response in Candida albicans
Zhou, X., Hilk, A. L., Solis, N. V., Scott, N. E., Zajac, C., Filler, S. G., & Selmecki, A. M. (2026) · PLoS Biology · doi:10.1371/journal.pbio.3003631 · Cited by 2
Profound cell wall remodeling in Candida parapsilosis during systemic infection confers simultaneous tolerance to echinocandins and host immunity
Daneshnia, F., Cai, L., Gunasekaran, D., Gautam, I., Perry, A. M., Ghahfarokhy, P. M., Ebadati, A., Munoz, J., Padilla, D., Hilmioglu-Polat, S., et al. (2026) · Microbiology Spectrum · doi:10.1128/spectrum.03043-25 · Cited by 3
“Should I stay or should I go”—a kinase delays escape of Candida glabrata from macrophages
Lange, T., Clairet, C., Fischer, L., Vij, R., Sonnberger, J., Mantke, J., Jablonowski, N., Seemann, E. A., Qualmann, B., d’Enfert, C., et al. (2026) · mBio · doi:10.1128/mbio.03885-25 · Cited by 3
Persistence and spread of fluconazole-resistant Candida parapsilosis clinical isolates associated with increased ERG11 copies in Qatar
Zhang, Z., Wang, Y., Abid, F. B., Salah, H., Ismail, K. A., Eldos, H. I., Samuel, B. G., Zhou, R., Sundararaju, S., Suleimen, M., et al. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001653 · Cited by 2
mGem: Fungal adhesins in Candidozyma auris confer unique fitness for skin colonization
Balakumar, A., & Thangamani, S. (2026) · mBio · doi:10.1128/mbio.03805-25 · Cited by 2
Pneumo Wiki: a pan-genome-based database for the pathogen Streptococcus pneumoniae
Mehlan, H., Hirschmann, S., Busch, L. M., Hennig, A., Nieselt, K., Völker, U., Hammerschmidt, S., & Mäder, U. (2026) · Microbiology Spectrum · doi:10.1128/spectrum.02957-25 · Cited by 2
ORF19.2286 Gene: Isolation and Purification of Deoxyhypusine Hydroxylase from the Human Pathogenic Yeast Candida albicans
Agboigba, E., Kuchaev, E., Гараева, Н. С., Андреевна, К. Э., Varfolomeev, A., Сергеевич, У. К., Yusupov, M., & Validov, S. Z. (2022) · Molecular Biology · doi:10.1134/s0026893322020029 · Cited by 2
Transcriptional noise adjusted for expression levels reveals genes with high transcriptional noise that are highly expressed, functionally related, and co-regulated in yeast
Palenchar, P. M., & DeStefanis, T. (2022) · Current Genetics · doi:10.1007/s00294-022-01255-x · Cited by 2
A Computational Workflow for Analysis of 3′ Tag‐Seq Data
Paropkari, A. D., Bapat, P. S., Sindi, S., & Nobile, C. J. (2023) · Current Protocols · doi:10.1002/cpz1.664 · Cited by 2
Protocol to identify genes important for Candida albicans fitness in diverse environmental conditions using pooled bar-seq screening approach
Xiong, E. H., Zhang, X., Robbins, N., Myers, C. L., & Cowen, L. E. (2025) · STAR Protocols · doi:10.1016/j.xpro.2025.103645 · Cited by 2
Nakaseomyces glabratus (Candida glabrata) MLST Genotypes in Central Poland
Kuthan, R. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26094407 · Cited by 2
Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9 reveals the functional impact of allelic variation
Després, P. C., Gervais, N. C., Fogal, M., Rogers, R. K. J., Cuomo, C. A., & Shapiro, R. S. (2025) · Genetics · doi:10.1093/genetics/iyaf154 · Cited by 2
Genoma de Candida albicans y resistencia a las drogas
Quintana, S. M. C., Sjostrom, P. D., Baldeón, G. M. M., Socarrás, D. A., Paz, M. M. C., & Molina, A. H. (2017) · DOAJ (DOAJ: Directory of Open Access Journals) · Cited by 2
Candida glabrata Hst1-Rfm1-Sum1 complex evolved to control virulence-related genes
Vázquez-Franco, N., Gutiérrez‐Escobedo, G., Juárez‐Reyes, A., Orta‐Zavalza, E., Castaño, I., & Peñas, A. D. L. (2021) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2021.103656 · Cited by 2
PerSVade: Personalized Structural Variation detection in your species of interestPreprint
Schikora-Tamarit, M. À., & Gabaldón, T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.23.469703 · Cited by 2
A modular cloning toolbox including CRISPRi for the engineering of the human fungal pathogen and biotechnology host Candida glabrataPreprint
Billerbeck, S., Prins, R. C., & Marquardt, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.17.512482 · Cited by 2
Xenosiderophore transporter gene expression and clade-specific filamentation in Candida auris killifish infectionPreprint
Gifford, H., Bedekovic, T., Helmstetter, N., Gregory, J., Ma, Q., Brand, A., Wilson, D., Rhodes, J. L., Ramsdale, M., Kudoh, T., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.22.619744 · Cited by 2
Cotranslational assembly confers specificity for in vivo target heterodimerization of paralogous H2B-like TAF12 proteins in the human fungal pathogen Candida albicansPreprint
Bhardwaj, V., Swanson, S. K., Florens, L. A., Washburn, M. P., Workman, J. L., & Natarajan, K. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.23.660276 · Cited by 2
Cytochrome bc1 Catalytic Subunit Rip1 Modulates Antifungal Tolerance in Candida auris
Phan-Canh, T., Lackner, M., Chauhan, M., Zenz, L.-M., Chauhan, N., & Kuchler, K. (2026) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.5c01058 · Cited by 1
Calcineurin‐Dependent Stress Adaptation Enables Caspofungin Heteroresistance Leading to Stable Resistance in Candida Glabrata
Su, Y., Li, Y., Xiao, M., Guo, D., Perlin, D. S., Shor, E., Xu, Y., & Li, Y. (2026) · Advanced Science · doi:10.1002/advs.76369 · Cited by 2
Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts
Łabędzka-Dmoch, K., Bui, T. H. D., Piątkowski, J., Dilling, M., Jagiełło, P., Kabza, W., & Golik, P. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag005 · Cited by 1
Development of a Shuttle Vector That Transforms at High Frequency for the Emerging Human Fungal Pathogen: Candida auris
Determann, B. F., Fu, J., & Wickes, B. L. (2024) · Journal of Fungi · doi:10.3390/jof10070477 · Cited by 1
Identification of Homeobox Transcription Factors in a Dimorphic Fungus Talaromyces marneffei and Protein-Protein Interaction Prediction of RfeB
Pongpom, M., Khamto, N., Sukantamala, P., Kalawil, T., & Wangsanut, T. (2024) · Journal of Fungi · doi:10.3390/jof10100687 · Cited by 1
PPI network identifies interacting pathogenic signaling pathways in Candida albicans
Chattopadhyay, D., Das, S., Mondal, P. S., Mondal, T., Samanta, S., Mondal, A., Goswami, A. M., & Saha, T. (2025) · Molecular Omics · doi:10.1039/d5mo00042d · Cited by 1
Histone acetylation by SAGA complex but not by NuA4 complex is required for filamentation program in Candida albicans
Nagar, P., Teli, B. B., Dinesh, D., & Natarajan, K. (2025) · Genetics · doi:10.1093/genetics/iyaf159 · Cited by 1
Migration and standing variation in vaginal and rectal yeast populations in recurrent vulvovaginal candidiasis
Bukari, A.-R. A., Kukurudz-Gorowski, R., de Graaf, A., Habon, D. A., Manyaz, B., Syvolos, Y., Sumanarathne, A., Poliquin, V., & Gerstein, A. C. (2025) · mSystems · doi:10.1128/msystems.00157-25 · Cited by 2
The antifungal mechanism of EntV-derived peptides is associated with a reduction in extracellular vesicle release
Cesare, G. B. D., Cruz, M. R., Cristy, S. A., Vega, L. A., Żarnowski, R., Zito, A., Guha, S., Andes, D. R., Garsin, D. A., & Lorenz, M. C. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013519 · Cited by 1
Genome Sequences and Antifungal Susceptibility of Candida auris from a Patient with Atopic Dermatitis
Kim, T., Bae, M., Bang, J., Jeon, J., Cho, Y., Park, J. M., & Jung, W. H. (2025) · Mycopathologia · doi:10.1007/s11046-025-01000-1 · Cited by 1
Frog-killing chytrid fungus deploys different strategies to regulate intracellular pressure in developmental states that have or lack a cell wall
Prostak, S. M., Velle, K., & Fritz‐Laylin, L. K. (2025) · Current Biology · doi:10.1016/j.cub.2025.10.013 · Cited by 1
Uncovering actionable trade-offs of antifungal resistance in a yeast pathogen
Nunez‐Rodriguez, J. C., Schikora-Tamarit, M. À., & Gabaldón, T. (2026) · Molecular Systems Biology · doi:10.1038/s44320-025-00185-3 · Cited by 1
The oleaginous yeast Cutaneotrichosporon oleaginosum modifies corn stover alkali lignin
Gluth, A., Pu, Y., Hu, D., Chen, X., Johnson, Z., Li, X., Ragauskas, A. J., Qian, W., Zhang, T., & Yang, B. (2026) · Scientific Reports · doi:10.1038/s41598-026-36483-5 · Cited by 1
Wastewater intelligence predicts the emergence of clinically-relevant and drug-resistant Candidozyma auris at healthcare facilities
Chang, C.-L., Moshi, M., Nguyen, Q., Oh, J., Nguyen, H., Paranjape, P., Abushanab, M., Tang, A. J., Itorralba, J. Y., Massic, L., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-71960-5 · Cited by 2
Towards accurate genomic detection of fungal antimicrobial resistance: progress in fungal resistance databases and bioinformatic tools
Gador‐Whyte, A., Rhodes, J., Farrer, R. A., Bakker, S., Wirth, W., Coldbeck-Shackley, R. C., Howden, B. P., Kwong, J. C., Sherry, N. L., & Seemann, T. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001710 · Cited by 2
Metabolic Network Modeling for Rational Drug Design against Candida albicans
Verma, R., Pradhan, D., Singh, H., Jain, A. K., & Khan, L. A. (2021) · Infectious diseases · doi:10.5772/intechopen.96749 · Cited by 1
Betulinic acid and Drummondin E: Potential inhibitors of Unfolded Protein Response Pathway of Candida auris
Akhtar, N., Joshi, A., Kaushik, V., Mohan, S., & Mannan, M. A.-U. (2023) · Research Journal of Pharmacy and Technology · doi:10.52711/0974-360x.2023.00472 · Cited by 1
The putative prenyltransferase Nus1 is required for filamentation in the human fungal pathogen Candida albicans
Farheen, A., Case, N. T., MacAlpine, J., Fu, C., Robbins, N., & Cowen, L. E. (2024) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkae124 · Cited by 1
SUMO-targeted Ubiquitin Ligases as crucial mediators of protein homeostasis in Candida glabrata
Gupta, D., Shukla, R., & Mishra, K. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012742 · Cited by 1
Transcriptional control of C. albicans white-opaque switching and modulation by environmental cues and strain background
Sharma, A., Homayoon, A., Weyler, M., Frazer, C., Ramírez-Zavala, B., Morschhäuser, J., & Bennett, R. J. (2025) · mBio · doi:10.1128/mbio.00581-25 · Cited by 1
Transcriptional Approach in the Identification of Drug Targets in Candida spp.
Patel, M., Mannan, M. A.-U., & Datta, B. (2021) · Springer eBooks · doi:10.1007/978-981-16-0691-5_9 · Cited by 1
m6Acancer-Net: Identification of m6A-mediated cancer driver genes from gene-site heterogeneous network
Ma, Q., Zhang, S., & Zhang, S.-Y. (2022) · Methods · doi:10.1016/j.ymeth.2022.04.002 · Cited by 1
Prediction of Gene and Genomic Regulation in Candida Species, Using the PathoYeastract Database: A Comparative Genomics Approach
Pais, P., Oliveira, J. S., Viana, R., Costa, I. V., Sá‐Correia, I., Monteiro, P. T., & Teixeira, M. C. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2257-5_23 · Cited by 1
Sequencing and de novo assembly reveals genomic variations associated with differential responses of Candida albicans ATCC 10231 towards fluconazole, pH and non-invasive growthPreprint
Zore, G. B., Thakre, A. D., Patil, R., Pradeep, C., & Balan, B. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/302943 · Cited by 1
Bioinformatics Approaches for Fungal Biotechnology
Li, J., de Vries, R. P., & Peng, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819990-9.00012-3 · Cited by 2
Filamentation in Candida albicans is modulated by adaptive translation of farnesol signalling genesPreprint
Oliveíra, C., Guimarães, A. R., Correia, I., Sousa, I., Poim, A., Rocha, S. M., Moura, G. R., Santos, M. A. S., & Bezerra, A. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.20.427544 · Cited by 1
Validation and Application of a Novel Target-Based Whole-Cell Screen to Identify Antifungal Compounds
DeJarnette, C. A. (2020) · doi:10.21007/etd.cghs.2020.0518 · Cited by 1
Functional genomics in Schizophyllum commune
Vonk, P. J. (2022) · Utrecht University Repository (Utrecht University) · doi:10.33540/1035 · Cited by 1
Structural insights into mechanisms of zinc scavenging by the Candida albicans zincophore Pra1Preprint
Syrjänen, J. L., Nore, A., Roselletti, E., Chakraborty, T., Perera, R. L., & Wilson, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.09.632233 · Cited by 1
Targeted loss of heterozygosity in Candida albicans using CRISPR-Cas9Preprint
Després, P. C., Gervais, N. C., Fogal, M., Rogers, R. K. J., Cuomo, C. A., & Shapiro, R. S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.13.653461 · Cited by 1
Manganese-modulated proteome and phosphoproteome dataset in the opportunistic yeast Candida albicans
Henry, M., Woods, M., Gutierrez‐Gongora, D., Geddes‐McAlister, J., & Sellam, A. (2025) · Data in Brief · doi:10.1016/j.dib.2025.111862 · Cited by 1
Wastewater intelligence predicts the emergence of clinically-relevant and drug-resistant Candida auris at healthcare facilitiesPreprint
Chang, C.-L., Moshi, M. A., Nguyen, Q., Oh, J., Nguyen, H., Paranjape, P. S., Abushanab, M., Tang, A. J., Itorralba, J. Y., Massic, L., et al. (2025) · medRxiv · doi:10.1101/2025.07.29.25332388 · Cited by 1
Pooled CRISPRi screening reveals fungal-specific vulnerabilities across environments and genetic backgroundsPreprint
Wensing, L. F., Després, P. C., Francis, D., Fogal, M., Hendriks, A., Gervais, N. C., Fikry, C., Bukari, A.-R. A., Gerstein, A. C., Cuomo, C. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.19.695556 · Cited by 1
Candida auris can acquire antifungal resistance without selection pressurePreprint
Phan-Canh, T., Nguyen-Le, D.-M., Chauhan, M., Luu, P., Chowdhary, A., Chauhan, N., & Kuchler, K. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.07.695227 · Cited by 1
Peer Review #2 of "Pixel: a content management platform for quantitative omics data (v0.1)"
(2019) · PeerJ · doi:10.7287/peerj.6623v0.1/reviews/2
Peer Review #1 of "Pixel: a content management platform for quantitative omics data (v0.1)"
(2019) · PeerJ · doi:10.7287/peerj.6623v0.1/reviews/1
Phagocytic predation by the fungivorous amoeba Protostelium aurantium targets metal ion and redox homeostasisPreprint
Radosa, S., Sprague, J. L., Tóth, R., Wolf, T., Sprenger, M., Brunke, S., Panagiotou, G., Linde, J., Gácser, A., & Hillmann, F. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/690503
DeORFanizing Candida albicans Genes using Co-ExpressionPreprint
O’Meara, T. R., & O’Meara, M. J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.04.412718
Photochromic fluorophores enable imaging of lowly-expressed proteins in the autofluorescent fungus Candida albicansPreprint
Genechten, W. V., Demuyser, L., Duwé, S., Vandenberg, W., Dijck, P. V., & Dedecker, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.26.433138
Application of Systems Biology Approaches for Host-Fungal Interaction in Animals
Kumar, R., & Ruhel, R. (2021) · Fungal biology · doi:10.1007/978-3-030-69507-1_4
Using Open Resources to Teach Mycology
Norflus, F. (2021) · The American Biology Teacher · doi:10.1525/abt.2021.83.8.504
Virtual screening of new targets and inhibitors for Candida albicans infection control
Torres-Osorio, L., Múnera, M., Fennix-Agudelo, M., & Chavarro‐Mesa, E. (2021) · IEEE International Congress of Biomedical Engineering and Bioengineering (CI-IB&BI) · doi:10.1109/ci-ibbi54220.2021.9626093
Faculty Opinions recommendation of Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans.
Bassilana, M. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734324385.793559869
Faculty Opinions recommendation of Titrating Gene Function in the Human Fungal Pathogen Candida albicans through Poly-Adenosine Tract Insertion.
Hynes, M. J. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736546914.793564791
Faculty Opinions recommendation of Candida albicans-Induced Epithelial Damage Mediates Translocation through Intestinal Barriers.
Bassilana, M. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733394828.793559882
Fungal eicosanoid biosynthesis Influences the virulence of Candida Parapsilosis
Chakraborty, T. (2019) · SZTE Repository of Dissertations (University of Szeged) · doi:10.14232/phd.9952
Faculty Opinions recommendation of New CRISPR Mutagenesis Strategies Reveal Variation in Repair Mechanisms among Fungi.
Mitchell, A. P. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733115592.793545570
Faculty Opinions recommendation of Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans.
Idnurm, A. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734324385.793552543
Volume 43 Number 1
(2022) · Microbiology Australia · doi:10.1071/mav43n1
A Cloning-Free Recyclable System for CRISPR-Cas9 Mediated Mutant and Reversion Construction in Candida albicans Clinical Isolates
Vogel, A. K. (2022) · doi:10.21007/etd.cghs.2022.0612

Authors: Skrzypek, M. S., Binkley, J., Binkley, G., Miyasato, S. R., Simison, M., & Sherlock, G.
Affiliations: Stanford Medicine (US)
Corresponding author: Sherlock, Gavin
ORCID: Skrzypek, Marek S.
Miyasato, Stuart R.
Simison, Matt
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
DOI: 10.1093/nar/gkw924
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: cc-by-nc
creativecommons.org/licenses/by-nc/4.0/ (vor, 83 d)
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

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks