FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery

ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data

(2022) Xian Liu et al.   NUCLEIC ACIDS RESEARCH

eVITTA: a web-based visualization and inference toolbox for transcriptome analysis

(2021) Xuanjin Cheng et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

(2020) Vahid Jalili et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

(2019) Brandon Monier et al.   PLoS Computational Biology

Digital expression explorer 2: a repository of uniformly processed RNA sequencing data

(2019) Mark Ziemann et al.   GigaScience

Transcriptomic analysis reveals global and temporal transcription changes during Candida glabrata adaptation to an oxidative environment

(2019) Pooja Sethiya et al.   Fungal Biology

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

(2018) Steven Xijin Ge et al.   BMC BIOINFORMATICS

Fungal secondary metabolism: regulation, function and drug discovery

(2018) Nancy P. Keller   NATURE REVIEWS MICROBIOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans

(2016) Michelle D. Leach et al.   Nature Communications

Function and Regulation of Cph2 in Candida albicans

(2015) Shelley Lane et al.   EUKARYOTIC CELL

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Text Mining Infrastructure inR

(2015) Ingo Feinerer et al.   Journal of Statistical Software

A Comprehensive Functional Portrait of Two Heat Shock Factor-Type Transcriptional Regulators Involved in Candida albicans Morphogenesis and Virulence

(2013) Sadri Znaidi et al.   PLoS Pathogens

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Cole Trapnell et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

FungiDB: an integrated functional genomics database for fungi

(2011) J. E. Stajich et al.   NUCLEIC ACIDS RESEARCH

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Role of the heat shock transcription factor, Hsf1, in a major fungal pathogen that is obligately associated with warm-blooded animals

(2009) Susan Nicholls et al.   MOLECULAR MICROBIOLOGY