The diploid genome sequence of Candida albicans.

By Ted Jones, N. Federspiel, H. Chibana, J. Dungan, S. Kalman, B. Magee, G. Newport, Y. Thorstenson, N. Agabian, P. T. Magee and 2 more. Proceedings of the National Academy of Sciences of the United States of America, 2004

818 citations recorded by the source corpus.

Subfields: Cell Biology, Epidemiology, Infectious Diseases

View Paper: https://www.semanticscholar.org/paper/36718af5d807c35a939de9c89b9fbeeb033c8d54

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In Cell Biology

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Citations in the corpus

• Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement (2014, neutral): “somes display loss of heterozygosity [21,22].”
• Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing (2016, background): “While the problem of assembling diploid and polymorphic genomes is not new 14-16 , it has not been adequately solved with a generic and scalable solution.”
• FungiDB: an integrated functional genomics database for fungi (2011, neutral): “32 6444 (19) Saccharomyces cerevisiae S288c 12.”
• The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. (2005, background): “Near-complete genome sequences are currently available for 14 species (Goffeau et al. 1996; Cliften et al. 2003; Kellis et al. 2003, 2004; Dietrich et al. 2004; Dujon et al. 2004; Jones et al. 2004).”
• Evolution of pathogenicity and sexual reproduction in eight Candida genomes (2009, background): “%) of the WO-1 assembly is homozygous for SNPs, approximately twice that found in SC5314 (Supplementary Information, section 7, and refs 7, 13, 14).”
• De novo assembly and genotyping of variants using colored de Bruijn graphs (2012, background): “Some variation-aware de novo assembly algorithms have been developed 31,33–36 , but these do not represent a general solution to sequencing experiments in which genetic variation is either the primary concern or unavoidable (for example, in outbred diploid samples, pooled data or ecological…”
• Genomics of the fungal kingdom: Insights into eukaryotic biology (2005, neutral): “albicans (Jones et al. 2004).”
• Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity (2010, methodology): “When this work was begun, the genome of clinical strain SC5314 had been sequenced and partially assembled by the Stanford Genome Technology Cente”
• Direct determination of diploid genome sequences (2016, neutral): “In a few cases, these diploid de novo assemblies have been demonstrated for small and midsized genomes (Jones et al. 2004; Chin et al. 2016).”
• The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data (2016, methodology): “CGD was originally based upon Assembly 19, a diploid, contiglevel assembly built from the genomic sequence that had just been completed (27), and which included gene models, sequence corrections, and functional annotations provided by a group of volunteer researchers known as the Annotation Working ”
• Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities (2005, background): “The assembly of communities has strong similarities to the assembly of highly polymorphic diploid eukaryotes, such as Ciona savigny [26] and Candida albicans [31], if we view prokaryotic strains as analogous to eukaryotic haplotypes.”