Defining the transcriptomic landscape of Candida glabrata by RNA-Seq

Candida albicans promotes invasion and colonisation of Candida glabrata in a reconstituted human vaginal epithelium

(2014) Carlos Tiago Alves et al.   JOURNAL OF INFECTION

Neutrophil Responses to Aspergillosis: New Roles for Old Players

(2014) Cristina Cunha et al.   MYCOPATHOLOGIA

Regulatory Networks Controlling Nitrogen Sensing and Uptake in Candida albicans

(2014) Shruthi Ramachandra et al.   PLoS One

A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood

(2014) Kerstin Hünniger et al.   PLoS Computational Biology

Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)

(2014) Volker U. Schwartze et al.   PLoS Genetics

SplicingCompass: differential splicing detection using RNA-Seq data

(2013) Moritz Aschoff et al.   BIOINFORMATICS

snoStrip: a snoRNA annotation pipeline

(2013) S. Bartschat et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Species and condition specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis

(2013) Christian Grumaz et al.   BMC GENOMICS

Trancriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing

(2013) Michaela Novodvorska et al.   BMC GENOMICS

Fungal Alternative Splicing is Associated with Multicellular Complexity and Virulence: A Genome-Wide Multi-Species Study

(2013) K. Grutzmann et al.   DNA RESEARCH

Immune Evasion, Stress Resistance, and Efficient Nutrient Acquisition Are Crucial for Intracellular Survival of Candida glabrata within Macrophages

(2013) Katja Seider et al.   EUKARYOTIC CELL

Transcriptomic profiling of Aspergillus flavus in response to 5-azacytidine

(2013) Jian-Qing Lin et al.   FUNGAL GENETICS AND BIOLOGY

Transcriptional Profiling of Candida glabrata during Phagocytosis by Neutrophils and in the Infected Mouse Spleen

(2013) Yuichi Fukuda et al.   INFECTION AND IMMUNITY

Intracellular pH homeostasis in Candida glabrata in infection-associated conditions

(2013) A. Ullah et al.   MICROBIOLOGY-SGM

TheAspergillusGenome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

(2013) Gustavo C. Cerqueira et al.   NUCLEIC ACIDS RESEARCH

A Core Filamentation Response Network in Candida albicans Is Restricted to Eight Genes

(2013) Ronny Martin et al.   PLoS One

Family matters: structural and functional conservation of centromere-associated proteins from yeast to humans

(2013) Stefan Westermann et al.   TRENDS IN CELL BIOLOGY

Expression Plasmids for Use in Candida glabrata

(2013) Rebecca E. Zordan et al.   G3-Genes Genomes Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression

(2012) Sebastian Müller et al.   BMC GENOMICS

Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach

(2012) Jörg Linde et al.   BMC Systems Biology

Two unlike cousins:Candida albicansandC. glabratainfection strategies

(2012) Sascha Brunke et al.   CELLULAR MICROBIOLOGY

The process of kinetochore assembly in yeasts

(2012) Babhrubahan Roy et al.   FEMS MICROBIOLOGY LETTERS

CENP-T proteins are conserved centromere receptors of the Ndc80 complex

(2012) Alexander Schleiffer et al.   NATURE CELL BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Cellular Responses of Candida albicans to Phagocytosis and the Extracellular Activities of Neutrophils Are Critical to Counteract Carbohydrate Starvation, Oxidative and Nitrosative Stress

(2012) Pedro Miramón et al.   PLoS One

Tackling Human Fungal Infections

(2012) G. D. Brown et al.   SCIENCE

Systems Biology of Fungal Infection

(2012) Fabian Horn et al.   Frontiers in Microbiology

The role of the protein kinase A pathway in the response to alkaline pH stress in yeast

(2011) Carlos Casado et al.   BIOCHEMICAL JOURNAL

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

(2011) Alessandro Guida et al.   BMC GENOMICS

The Facultative Intracellular Pathogen Candida glabrata Subverts Macrophage Cytokine Production and Phagolysosome Maturation

(2011) K. Seider et al.   JOURNAL OF IMMUNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Expanding fungal pathogenesis: Cryptococcus breaks out of the opportunistic box

(2011) James W. Kronstad et al.   NATURE REVIEWS MICROBIOLOGY

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

(2011) D. O. Inglis et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Pathogenesis of Candida albicans Infections in the Alternative Chorio-Allantoic Membrane Chicken Embryo Model Resembles Systemic Murine Infections

(2011) Ilse D. Jacobsen et al.   PLoS One

Premitotic Assembly of Human CENPs -T and -W Switches Centromeric Chromatin to a Mitotic State

(2011) Lisa Prendergast et al.   PLOS BIOLOGY

Microarray and Molecular Analyses of the Azole Resistance Mechanism in Candida glabrata Oropharyngeal Isolates

(2010) H.-F. Tsai et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bcheck: a wrapper tool for detecting RNase P RNA genes

(2010) Dilmurat Yusuf et al.   BMC GENOMICS

Genomewide Expression Profile Analysis of the Candida glabrata Pdr1 Regulon

(2010) Kelly E. Caudle 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

Candida glabratatryptophan-based pigment production via the Ehrlich pathway

(2010) Sascha Brunke et al.   MOLECULAR MICROBIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

(2010) Bin Wang et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Comparison of costs, length of stay, and mortality associated with Candida glabrata and Candida albicans bloodstream infections

(2009) Cassandra Moran et al.   AMERICAN JOURNAL OF INFECTION CONTROL

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Autophagy supportsCandida glabratasurvival during phagocytosis

(2009) Andreas Roetzer et al.   CELLULAR MICROBIOLOGY

The Glycosylphosphatidylinositol-Anchored Protease Sap9 Modulates the Interaction of Candida albicans with Human Neutrophils

(2009) A. Hornbach et al.   INFECTION AND IMMUNITY

Candida glabrata Persistence in Mice Does Not Depend on Host Immunosuppression and Is Unaffected by Fungal Amino Acid Auxotrophy

(2009) I. D. Jacobsen et al.   INFECTION AND IMMUNITY

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

The Cell Wall of the Human PathogenCandida glabrata: Differential Incorporation of Novel Adhesin-Like Wall Proteins

(2008) Piet W. J. de Groot et al.   EUKARYOTIC CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Proteomic analysis of the pH response in the fungal pathogenCandida glabrata

(2008) Pia Schmidt et al.   PROTEOMICS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY

Induction of ERK-kinase signalling triggers morphotype-specific killing of Candida albicans filaments by human neutrophils

(2007) Iwona Wozniok et al.   CELLULAR MICROBIOLOGY