Laia Carreté

Laia Carreté
Centre for Genomic Regulation | CRG · Bioinformatics and Genomics

PhD

About

30
Publications
2,595
Reads
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340
Citations
Citations since 2016
27 Research Items
339 Citations
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20162017201820192020202120220204060
20162017201820192020202120220204060
20162017201820192020202120220204060
Additional affiliations
January 2014 - December 2017
Centre for Genomic Regulation
Position
  • PhD Student

Publications

Publications (30)
Article
Full-text available
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish....
Article
Full-text available
The yeast Candida glabrata is an opportunistic human fungal pathogen whose incidence has increased in the last two decades. Despite its name, this yeast is only distantly related to the model fungal pathogen Candida albicans, and more closely related to Saccharomyces cerevisiae and other yeasts that underwent an ancient whole genome duplication. Un...
Article
Full-text available
The human pathogenic yeast Candida parapsilosis has gained significant importance over the past decades as one of the principal causes of fungal bloodstream infections. Isolates of C. parapsilosis are known to be able to switch between several different colony morphologies in vitro, which are correlated with different cell shapes, altered cell surf...
Article
Full-text available
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each het...
Article
Full-text available
Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting...
Article
Full-text available
Candida glabrata is an opportunistic fungal pathogen that currently ranks as the second most common cause of candidiasis. Although the mechanisms underlying virulence and drug resistance in C. glabrata are now starting to be elucidated, we still lack a good understanding of how this yeast adapts during the course of an infection. Outstanding questi...
Data
Detail of read mapping on the FKS1 gene region, visualized using IGV software (Thorvaldsdóttir et al., 2013) in the strains CMRL1, CMRL2, CMRL3, CMRL4, CMRL5, and CMRL6. Zoom-in square indicates private non-synonymous SNP S629P present only in CMRL1 (in blue).
Data
Correlation between genome-wide mutation density (SNPs/Kb) and days spanned between the first isolate and second isolate in serial isolates. As Figure 1B but strains are colored according to the presence of non-synonymous mutations in MSH2.
Data
Distribution of strains based on SNPs using a Multiple Correspondence Analysis (MCA). Each pair of strains used marked in different colors and names in plot. White circles in plot indicates strains used to provide a global comparison (Carreté et al., 2018).
Data
List of genes affected by private exonic INDELs. Columns indicates, in this order: pair of strains; INDEL position; systematic name; standard name; type of mutation; description of the gene affected.
Data
Single nucleotide polymorphisms (SNPs)/Kb value compared to reference genome CBS138. First column indicates list of C. glabrata isolates analyzed in this study. Second column indicates SNPs/Kb compared to reference genome (CBS138).
Data
List of genes affected by private non-synonymous mutations in clonal strains. Columns indicates: strain name; Systematic name of the gene affected by a private non-synonymous mutation; standard name of that gene; amino acid (AA) altered; description of the gene.
Data
List of genes deleted and duplicated in one of the two pair of isolates. First column indicates gene name; second column indicates description of the gene affected.
Data
Values from phenotypic analysis. Columns indicate: sample; condition used for the phenotypic analysis; carrying capacity (k), population size at time 0 (time 0); growth rate (r); time when the population density reaches ½ K (½ K time); fastest possible generation time; area under the logistic curve measured by taking the integral logistic equation...
Data
MIC value (μg/ml) for the different strains analyzed. Columns indicates: name of the strains analyzed, isolation site, drugs tested (fluconazole, Voriconazole, Amphotericin B, Anidulafungin, Micafungin, Caspofungin, 5-fluorocystosine, Posaconazole, Itraconazole, Isavuconazole); method used; and source data.
Data
Table S2. Synonymous versus Non-synonymous Variation per Gene, Related to Figure 5 The first column indicates the gene functional category (based on their function in S. cerevisiae). The following columns indicate gene ID, gene name (only for S. cerevisiae), and πN/πS for C. glabrata, C. albicans, and S. cerevisiae genes.
Data
Table S5. Levels of Nucleotide Variation per Strain and Mutations in MSH2, Related to Figure 6 Columns indicate, in this order: strain name; clade; non-synonymous variant; Saccharomycotina species presenting the same non-synonymous mutations (five-letter codes correspond to species mnemonic based on the UniProt taxonomy database [33]); reduced sen...
Data
Table S1. Information about the 32 Strains of C. albicans Re-analyzed in This Study, Related to Figure 5 Columns indicate, in this order: strain name or ID; host; isolation site; country of isolation; mating type (if any); experiment name in short read archive (SRA); number of SRA run.
Data
Columns indicate, in this order: condition used for the analysis; sample; clade; carrying capacity (K); population size at time 0 (n0); growth rate (r); time when the population density reaches ½K (t_mid); fastest possible generation time (t_gen); area under the logistic curve measured by taking the integral of the logistic equation (auc_l); empiri...
Data
Range of sensitivity levels (triplicate experiments) to amphotericin B (MIC90), 5-fluorocytosine, fluconazole, voriconazole, posaconazole, isavuconazole, micafungin, and caspofungin (all MIC50) and, where available (http://www.eucast.org/clinical_breakpoints), classification according to clinical breakpoints. S, sensitive; I, intermediate; R, resis...
Data
Columns indicate, in this order: duplication or deletion number in this study (corresponds to Figure 2); gene ID; gene name; name of S. cerevisiae one-to-one ortholog (if any); description.
Data
Data S2. Private Mutations per Strain, Non-synonymous SNPs and CNVs, Related to Figure 6 Columns of private non-synonymous SNPs indicate, in this order: strain ID; chromosome and position affected by the SNP; gene ID; amino acid substitution; gene name; description. The first column based on CNV indicates the strain analyzed. The following columns...
Article
Full-text available
Candida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae than to other Candida pathogens, and hence its ability to infect humans is thought to have emerged independently. Moreover, C....
Preprint
Full-text available
Candida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae than to other Candida pathogens, and hence its ability to infect humans is thought to have emerged independently. Morover, C....
Poster
Genome variation across global isolates in the emerging fungal pathogen Candida glabrata
Presentation
Genome variation across clinical and environmental isolates in the emerging fungal pathogen Candida glabrata.

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Projects

Project (1)
Project
Development of new bioinformatics tools to analyze NGS data.