4.7 Article

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

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

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

Xian Liu et al.

Summary: In the era of life-omics, biologists face challenges in extracting biological insights from the vast amount of multi-omics data. To address this, the biologist-oriented platform, ExpressVis, provides visualization functions and allows users to perform various analyses and integrate expression data with interaction networks and pathway maps. ExpressVis displays results in interactive figures and tables and offers comprehensive interactive operations. It is freely accessible and can be used for multi-omics studies in clinical cohorts.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

The Gene Ontology resource: enriching a GOld mine

Seth Carbon et al.

Summary: The Gene Ontology Consortium has made advancements in the last two years, such as improving the GO-CAM annotation framework, increasing the number of annotations and annotated gene products, and reviewing older annotations for consistency.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

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

Xuanjin Cheng et al.

Summary: Transcriptome profiling is crucial for gene regulation studies, but current tools have limitations. eVITTA addresses these limitations by providing modular analysis and visualization options, allowing customized comparisons across multiple datasets and exploration of data stored in NCBI GEO.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

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

Vahid Jalili et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemical Research Methods

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

Brandon Monier et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Review Microbiology

Fungal secondary metabolism: regulation, function and drug discovery

Nancy P. Keller

NATURE REVIEWS MICROBIOLOGY (2019)

Article Biochemical Research Methods

'Multi-omic' data analysis using O-miner

Ajanthah Sangaralingam et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Biochemical Research Methods

A global perspective on evolving bioinformatics and data science training needs

Teresa K. Attwood et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Biochemical Research Methods

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

Steven Xijin Ge et al.

BMC BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Near-optimal probabilistic RNA-seq quantification

Nicolas L. Bray et al.

NATURE BIOTECHNOLOGY (2016)

Article Microbiology

Function and Regulation of Cph2 in Candida albicans

Shelley Lane et al.

EUKARYOTIC CELL (2015)

Article Biotechnology & Applied Microbiology

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

Mihaela Pertea et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

Big Data: Astronomical or Genomical?

Zachary D. Stephens et al.

PLOS BIOLOGY (2015)

Article Statistics & Probability

Text Mining Infrastructure inR

Ingo Feinerer et al.

Journal of Statistical Software (2015)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

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

Daehwan Kim et al.

GENOME BIOLOGY (2013)

Article Biochemical Research Methods

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

Cole Trapnell et al.

NATURE PROTOCOLS (2012)

Article Biochemistry & Molecular Biology

FungiDB: an integrated functional genomics database for fungi

Jason E. Stajich et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

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

Guangchuang Yu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

The real cost of sequencing: higher than you think!

Andrea Sboner et al.

GENOME BIOLOGY (2011)

Article Genetics & Heredity

SMURF: Genomic mapping of fungal secondary metabolite clusters

Nora Khaldi et al.

FUNGAL GENETICS AND BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Opaque cells signal white cells to form biofilms in Candida albicans

Karla J. Daniels et al.

EMBO JOURNAL (2006)

Article Cell Biology

Transcription profiling of Candida albicans cells undergoing the yeast-to-hyphal transition

A Nantel et al.

MOLECULAR BIOLOGY OF THE CELL (2002)