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

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

(2012) David A Fitzpatrick et al.   BMC GENOMICS

Evolution of Mating within the Candida parapsilosis Species Group

(2011) Sixiang Sai et al.   EUKARYOTIC CELL

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

(2011) Julie Bonhomme et al.   MOLECULAR MICROBIOLOGY

Sequencing Illustrates the Transcriptional Response of Legionella pneumophila during Infection and Identifies Seventy Novel Small Non-Coding RNAs

(2011) Barbara A. Weissenmayer et al.   PLoS One

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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)

(2010) Michael A. Pfaller et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Regulation of the Hypoxic Response in Candida albicans

(2010) John M. Synnott et al.   EUKARYOTIC CELL

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

(2010) V. M. Bruno et al.   GENOME RESEARCH

Evaluation of Models of the Mechanisms Underlying Intron Loss and Gain in Aspergillus Fungi

(2010) Lei-Ying Zhang et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2010) I. Wapinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Q. M. Mitrovich et al.   SCIENCE

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

(2010) Brian B. Tuch et al.   PLoS Genetics

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

(2010) Adnane Sellam et al.   GENOME BIOLOGY

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Candida albicans early stage biofilm detachment event in rich medium

(2009) Adnane Sellam et al.   BMC MICROBIOLOGY

Common introns within orthologous genes: software and application to plants

(2009) M. D. Wilkerson et al.   BRIEFINGS IN BIOINFORMATICS

Correlation between Biofilm Formation and the Hypoxic Response inCandida parapsilosis

(2009) Tristan Rossignol et al.   EUKARYOTIC CELL

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

(2009) A. P. Jackson et al.   GENOME RESEARCH

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

(2009) Diethard Mattanovich et al.   Microbial Cell Factories

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

(2009) Eveline C. van Asbeck et al.   MYCOSES

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Genome sequence of the recombinant protein production host Pichia pastoris

(2009) Kristof De Schutter et al.   NATURE BIOTECHNOLOGY

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Regulation of Carbohydrate Metabolism in the Human Pathogen Candida albicans

(2009) Christopher Askew et al.   PLoS Pathogens

Candida parapsilosis, an Emerging Fungal Pathogen

(2008) D. Trofa et al.   CLINICAL MICROBIOLOGY REVIEWS

Mystery of intron gain: new data and new models

(2008) Scott William Roy et al.   TRENDS IN GENETICS