2 citations · 2 across the 4 of their papers we have counts for
6 papers
DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming +1
Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manuall…
ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software
Laurent Heirendt, Sylvain Arreckx, Christophe Trefois +6
Motivation: Automatically testing changes to code is an essential feature of continuous integration. For open-source code, without licensed dependencies, a variety of continuous in…
From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohn's disease
Eugen Bauer, Ines Thiele
Crohn's disease (CD) is associated with an ecological imbalance of the intestinal microbiota, consisting of hundreds of species. The underlying complexity as well as individual dif…
Comparative genomic analysis of the human gut microbiome reveals a broad distribution of metabolic pathways for the degradation of host-synthetized mucin glycans
Dmitry A. Ravcheev, Ines Thiele
The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic m…
MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models
Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of ana…
ReconMap: An interactive visualisation of human metabolism
Alberto Noronha, Anna Dröfn Danielsdóttir, Freyr Jóhannsson +8
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation re…