Fungal systems biology articles within Nature Communications

Featured

• Article
  20 July 2023 | Open Access

  Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome

  Here, the authors generate strain-specific genome-scale metabolic models of Aspergillus fumigatus and analyze fungal metabolism of infection of the lung of cystic fibrosis patients, finding that the fungus shapes the lung microbiome to promote its own growth.

  • Mohammad H. Mirhakkak
  • , Xiuqiang Chen
  •  & Gianni Panagiotou

• Article
  18 October 2022 | Open Access

  Proteome effects of genome-wide single gene perturbations

  Protein abundance is controlled at the transcriptional, translational and posttranslational levels. Here, Öztürk et al. determine proteome changes resulting from individual knockout of 3308 nonessential genes in the yeast S. pombe, infer gene functionality, and show that protein upregulation under stable transcript expression utilizes optimal codons.

  • Merve Öztürk
  • , Anja Freiwald
  •  & Falk Butter

• Article
  09 June 2022 | Open Access

  Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity

  Commensal bacteria such as Lactobacillus rhamnosus can inhibit the pathogenicity of the fungus Candida albicans. Here, Alonso-Roman et al. investigate the interplay between C. albicans, L. rhamnosus and intestinal epithelial cells, showing that changes in the metabolic environment, induced by the bacteria, trigger adaptations in C. albicans that reduce fungal pathogenicity.

  • Raquel Alonso-Roman
  • , Antonia Last
  •  & Mark S. Gresnigt

• Article
  11 November 2021 | Open Access

  Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets

  The analysis of essential genes in pathogens can be used to discover potential antimicrobial targets. Here, the authors use a machine learning model and chemogenomic analyses to generate genome-wide gene essentiality predictions for the fungal pathogen Candida albicans, define the function of three uncharacterized essential genes, and identify the target of a new antifungal compound.

  • Ci Fu
  • , Xiang Zhang
  •  & Leah E. Cowen

• Article
  23 March 2020 | Open Access

  Fungal kinases and transcription factors regulating brain infection in Cryptococcus neoformans

  Cryptococcus neoformans causes fatal fungal meningoencephalitis. Here, the authors identify fungal kinases and transcription factors involved in blood-brain barrier crossing and brain infection in mice.

  • Kyung-Tae Lee
  • , Joohyeon Hong
  •  & Yong-Sun Bahn

• Article
  21 March 2019 | Open Access

  A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae

  Whole-cell models hold great promise for fundamental and translational biology, but genome-scale modelling of signalling networks has been a challenge. Here, the authors present a genome-scale, mechanistic and executable model of the network controlling and executing the S. cerevisiae cell cycle.

  • Ulrike Münzner
  • , Edda Klipp
  •  & Marcus Krantz

• Article
  14 December 2017 | Open Access

  A general pharmacodynamic interaction model identifies perpetrators and victims in drug interactions

  Assessment of pharmacodynamic interactions is at the heart of combination therapy development. Here the authors introduce a general drug interaction scoring model that enables quantification of synergistic and antagonistic interactions and determination of the directionality of the interactions.

  • Sebastian G. Wicha
  • , Chunli Chen
  •  & Ulrika S. H. Simonsson