In cparsania/FungiExpresZ: FungiExpresZ: Fungal gene expression data analysis and visualizations

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

#library(FungiExpresZ)

Cite FungiExpresZ

• Chirag Parsania, Ruiwen Chen, Pooja Sethiya, Zhengqiang Miao, Liguo Dong, Koon Ho Wong, FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery, Briefings in Bioinformatics, 2023;bbad051, https://doi.org/10.1093/bib/bbad051

List of articles citing FungiExpresZ

2023

1. Maruti Nandan Rai, Rikky Rai, Pooja Sethiya, Chirag Parsania. Transcriptome analysis reveals a common adaptive transcriptional response of Candida glabrata to diverse environmental stresses. Research in Microbiology. 2023;104073. Article link

2. Siddharth Sinha, Jiaheng Li, Benjamin Tam, San Ming Wang. Classification of PTEN missense VUS through exascale simulations. Briefings in Bioinformatics,2023; bbad361. Article link

2022

1. Karahoda B, Pardeshi L, Ulas M et al. The KdmB-EcoA-RpdA-SntB chromatin complex binds regulatory genes and coordinates fungal development with mycotoxin synthesis. Nucleic Acids Research. 2022;17:9797-9813. Article link

2. Colabardini AC, Wang F, Miao Z, Pardeshi L, Valero C, de Castro PA, et al. Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. PLoS Genet. 2022;18(1): e1010001. Article link

2021

1. Assis LJ, Silva LP, Bayram O, Dowling P, et al. Carbon Catabolite Repression in Filamentous Fungi Is Regulated by Phosphorylation of the Transcription Factor CreA. mBio 2021;12:e03146-20. Article link{target="_blank"}

2. Wang, F., Sethiya, P., Hu, X. et al. Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments Nat Microbiol. 2021;6: 1066--1081. Article link

3. Maruti Nandan Rai, Chirag Parsania, Rikky Rai, et al. Temporal transcriptional response of Candida glabrata during macrophage infection reveals a multifaceted transcriptional regulator CgXbp1 important for macrophage response and drug resistance. BioRxiv 2021. Article link

4. Ana Cristina Colabardini, Fang Wang, Zhengqiang Miao et al. Chromatin profiling reveals genome stability heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. BioRxiv 2021. Article link

5. A bioinformatics-driven study of Candida glabrata response to infection-relevant conditions and antifungal drugs.Sethiya, & Wong, K. H. University of Macau 2021. Thesis (Ph.D).

6. Fungal spore transcription activity before dormancy drives phenotypic variation. Wang, & Wong, K. H. University of Macau 2021. Thesis (Ph.D.).

2020

1. Ries LNA, Pardeshi L, Dong Z, Tan K, Steenwyk JL, Colabardini AC, et al. The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence. PLoS Pathog 2020;16(7): e1008645. Article link{target="_blank"}

2. Systematic activation and characterization of the regulation of secondary metabolism gene clusters in Aspergillus nidulans. Guo, & Wong, K. H. University of Macau2020. Thesis (Ph.D.).

3. Genome-wide characterization of AreA function and regulation in Aspergillus nidulans. Li, A., & Wong, K. University of Macau 2020. Thesis (Ph.D.).

2019

1. P Sethiya, MN Rai, R Rai, C Parsania, K Tan, KH Wong. Transcriptomic analysis reveals global and temporal transcription changes during Candida glabrata adaptation to an oxidative environment. Fungal Biology, 2019;5:427-439. Article link{target="_blank"}

cparsania/FungiExpresZ documentation built on March 15, 2024, 5:48 p.m.