The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. - Federico Baldini; Almut Heinken; Laurent Heirendt; Stefanía Magnúsdóttir; Ronan M. T. Fleming; Ines Thiele (Bioinform., 2019)

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. - Alberto Noronha; Jennifer Modamio; Yohan Jarosz; Elisabeth Guerard; Nicolas Sompairac; German A. Preciat Gonzalez; Anna Dröfn Daníelsdóttir; Max Krecke; Diane Merten; Hulda S. Haraldsdóttir; Almut Heinken; Laurent Heirendt; et al. (Nucleic Acids Res., 2019)

DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. - Almut Heinken; Stefanía Magnúsdóttir; Ronan M. T. Fleming; Ines Thiele (Bioinform., 2021)

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities. - Almut Heinken; Ines Thiele (Bioinform., 2022)

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. - William T. Scott Jr.; Sara Benito-Vaquerizo; Johannes Zimmermann; Djordje Bajic; Almut Heinken; María Suárez-Diez; Peter J. Schaap (PLoS Comput. Biol., 2023)