Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks

P Schaepe, MJ Kwon, B Baumann… - Nucleic acids …, 2019 - academic.oup.com
A significant challenge in our understanding of biological systems is the high number of
genes with unknown function in many genomes. The fungal genus Aspergillus contains …

[HTML][HTML] Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

JC Wright, D Sugden, S Francis-McIntyre, I Riba-Garcia… - Bmc Genomics, 2009 - Springer
Background Proteomic data is a potentially rich, but arguably unexploited, data source for
genome annotation. Peptide identifications from tandem mass spectrometry provide prima …

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

GC Cerqueira, MB Arnaud, DO Inglis… - Nucleic acids …, 2014 - academic.oup.com
Abstract The Aspergillus Genome Database (AspGD; http://www. aspgd. org) is a freely
available web-based resource that was designed for Aspergillus researchers and is also a …

[HTML][HTML] Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans

H David, G Hofmann, AP Oliveira, H Jarmer, J Nielsen - Genome biology, 2006 - Springer
Background Aspergillus nidulans (the asexual form of Emericella nidulans) is a model
organism for aspergilli, which are an important group of filamentous fungi that encompasses …

[HTML][HTML] New resources for functional analysis of omics data for the genus Aspergillus

BM Nitsche, J Crabtree, GC Cerqueira, V Meyer… - BMC genomics, 2011 - Springer
Background Detailed and comprehensive genome annotation can be considered a
prerequisite for effective analysis and interpretation of omics data. As such, Gene Ontology …

Beyond the biosynthetic gene cluster paradigm: genome-wide coexpression networks connect clustered and unclustered transcription factors to secondary metabolic …

MJ Kwon, C Steiniger, TC Cairns… - Microbiology …, 2021 - Am Soc Microbiol
Fungal secondary metabolites are widely used as therapeutics and are vital components of
drug discovery programs. A major challenge hindering discovery of novel secondary …

[HTML][HTML] Analysis of Aspergillus nidulans metabolism at the genome-scale

H David, İŞ Özçelik, G Hofmann, J Nielsen - BMC genomics, 2008 - Springer
Background Aspergillus nidulans is a member of a diverse group of filamentous fungi,
sharing many of the properties of its close relatives with significance in the fields of …

[HTML][HTML] Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

W Vongsangnak, P Olsen, K Hansen, S Krogsgaard… - BMC genomics, 2008 - Springer
Background Since ancient times the filamentous fungus Aspergillus oryzae has been used
in the fermentation industry for the production of fermented sauces and the production of …

[HTML][HTML] A community-driven reconstruction of the Aspergillus niger metabolic network

J Brandl, MV Aguilar-Pontes, P Schäpe… - Fungal biology and …, 2018 - Springer
Background Aspergillus niger is an important fungus used in industrial applications for
enzyme and acid production. To enable rational metabolic engineering of the species …

[HTML][HTML] Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

TC Vesth, JL Nybo, S Theobald, JC Frisvad… - Nature Genetics, 2018 - nature.com
Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy,
health, and biotechnology. To learn more about what genetically sets these species apart …