Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis (Q34109099)

31 July 2017

title

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis (English)

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31 July 2017

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Candida parapsilosis

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31 July 2017

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31 July 2017

Sarah L Maguire

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Matthew Berriman

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31 July 2017

Alessandro Guida

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31 July 2017

Claudia Lindstädt

series ordinal

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31 July 2017

Chen Ding

series ordinal

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31 July 2017

Nicola J Corton

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31 July 2017

language of work or name

English

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publication date

22 December 2011

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31 July 2017

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31 July 2017

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31 July 2017

page(s)

628

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describes a project that uses

31 July 2017

limma

object named as

Limma

2 references

22 June 2022

https://europepmc.org/article/PMC/3287387

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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Transcriptional profiling of azole-resistant Candida parapsilosis strains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Comparative functional genomics of the fission yeasts

5 July 2018

1 reference

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Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs

5 July 2018

1 reference

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Evolution of mating within the Candida parapsilosis species group

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Evolution of Yeast Noncoding RNAs Reveals an Alternative Mechanism for Widespread Intron Loss

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Regulation of the hypoxic response in Candida albicans

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Evaluation of models of the mechanisms underlying intron loss and gain in Aspergillus fungi.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

5 July 2018

1 reference

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The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays

5 July 2018

1 reference

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

5 July 2018

1 reference

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Gene duplication and the evolution of ribosomal protein gene regulation in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Tablet--next generation sequence assembly visualization

5 July 2018

1 reference

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Transcriptional regulation of carbohydrate metabolism in the human pathogen Candida albicans

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Transcriptome analysis by strand-specific sequencing of complementary DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

The Sequence Alignment/Map format and SAMtools

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Genome sequence of the recombinant protein production host Pichia pastoris

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

TopHat: discovering splice junctions with RNA-Seq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

A Candida albicans early stage biofilm detachment event in rich medium

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Mystery of intron gain: new data and new models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Candida parapsilosis, an emerging fungal pathogen

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Comparative genomic analysis of fungal genomes reveals intron-rich ancestors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Candida parapsilosis fungemia in neonates: genotyping results suggest healthcare workers hands as source, and review of published studies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Heme levels switch the function of Hap1 of Saccharomyces cerevisiae between transcriptional activator and transcriptional repressor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Transcriptional response of Candida parapsilosis following exposure to farnesol

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Epidemiology of invasive candidiasis: a persistent public health problem

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Candida albicans transcription factor Ace2 regulates metabolism and is required for filamentation in hypoxic conditions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Intron size, abundance, and distribution within untranslated regions of genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

A role for sterol levels in oxygen sensing in Saccharomyces cerevisiae.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Molecular genotyping of Candida parapsilosis group I clinical isolates by analysis of polymorphic microsatellite markers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

The evolution of spliceosomal introns: patterns, puzzles and progress

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Dual activators of the sterol biosynthetic pathway of Saccharomyces cerevisiae: similar activation/regulatory domains but different response mechanisms.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Candida albicans zinc cluster protein Upc2p confers resistance to antifungal drugs and is an activator of ergosterol biosynthetic genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Role of Candida albicans transcription factor Upc2p in drug resistance and sterol metabolism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Patterns of intron gain and loss in fungi

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Epidemiologic and molecular characterization of an outbreak of Candida parapsilosis bloodstream infections in a community hospital

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Genome evolution in yeasts

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

APSES proteins regulate morphogenesis and metabolism in Candida albicans

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Candida parapsilosis characterization in an outbreak setting

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Normalization of cDNA microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Horizontal transmission of Candida parapsilosis candidemia in a neonatal intensive care unit

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Invasive filamentous growth of Candida albicans is promoted by Czf1p-dependent relief of Efg1p-mediated repression.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Upc2p and Ecm22p, dual regulators of sterol biosynthesis in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Artemis: sequence visualization and annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

T-Coffee: A novel method for fast and accurate multiple sequence alignment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

5 July 2018

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Genomic heterogeneity in the yeast Candida parapsilosis

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Three distinct genotypes within Candida parapsilosis from clinical sources

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Regulation of gene expression by oxygen in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Variation in Candida spp. distribution and antifungal resistance rates among bloodstream infection isolates by patient age: report from the SENTRY Antimicrobial Surveillance Program (2008–2009)

5 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Correlation of restriction fragment length polymorphism genotyping with internal transcribed spacer sequence, randomly amplified polymorphic DNA and multilocus sequence groupings for Candida parapsilosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Correlation between biofilm formation and the hypoxic response in Candida parapsilosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

cis-Acting elements within the Candida albicans ERG11 promoter mediate the azole response through transcription factor Upc2p

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Evolutionary conservation of UTR intron boundaries in Cryptococcus

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Common introns within orthologous genes: software and application to plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Contribution of the glycolytic flux and hypoxia adaptation to efficient biofilm formation by Candida albicans

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Gene disruption in Candida albicans using a synthetic, codon-optimised Cre-loxP system

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

An outbreak of Candida parapsilosis prosthetic valve endocarditis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-12-628

Hypoxic adaptation by Efg1 regulates biofilm formation by Candida albicans

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

High-quality genome sequence of Pichia pastoris CBS7435

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3287387

Candida parapsilosis bloodstream infections in neonatal intensive care unit patients: epidemiologic and laboratory confirmation of a common source outbreak

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22192698

12 December 2020

inferred from PubMed ID database lookup

Transcriptional response of Candida albicans to hypoxia: linkage of oxygen sensing and Efg1p-regulatory networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22192698

12 December 2020

inferred from PubMed ID database lookup

Transcriptional Response of Candida parapsilosis following Exposure to Farnesol

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22192698

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1471-2164-12-628

1 reference

31 July 2017

1 reference

31 July 2017

1 reference