BioMet Toolbox: genome-wide analysis of metabolism. - Marija Cvijovic; Roberto Olivares-Hernández; Rasmus Agren; Niklas Dahr; Wanwipa Vongsangnak; Intawat Nookaew; Kiran Raosaheb Patil; Jens Nielsen (Nucleic Acids Res., 2010)

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes. - Sergio Bordel; Rasmus Agren; Jens Nielsen (PLoS Comput. Biol., 2010)

MEMOSys: Bioinformatics platform for genome-scale metabolic models. - Stephan Pabinger; Robert Rader; Rasmus Agren; Jens Nielsen; Zlatko Trajanoski (BMC Syst. Biol., 2011)

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. - Luis Caspeta; Saeed Shoaie; Rasmus Agren; Intawat Nookaew; Jens Nielsen (BMC Syst. Biol., 2012)

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT. - Rasmus Agren; Sergio Bordel; Adil Mardinoglu; Natapol Pornputtapong; Intawat Nookaew; Jens Nielsen (PLoS Comput. Biol., 2012)

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum. - Rasmus Agren; Liming Liu; Saeed Shoaie; Wanwipa Vongsangnak; Intawat Nookaew; Jens Nielsen (PLoS Comput. Biol., 2013)

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. - Stepan Tymoshenko; Rebecca D. Oppenheim; Rasmus Agren; Jens Nielsen; Dominique Soldati-Favre; Vassily Hatzimanikatis (PLoS Comput. Biol., 2015)

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. - Hao Wang 078; Simonas Marcisauskas; Benjamín J. Sánchez; Iván Domenzain; Daniel Hermansson; Rasmus Agren; Jens Nielsen; Eduard J. Kerkhoven (PLoS Comput. Biol., 2018)