Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells. - Liam G. Fearnley; Mark A. Ragan; Lars Keld Nielsen (BIOINFORMATICS, 2014)

Extracting reaction networks from databases-opening Pandora's box. - Liam G. Fearnley; Melissa J. Davis; Mark A. Ragan; Lars Keld Nielsen (Briefings Bioinform., 2014)

A depth-first search algorithm to compute elementary flux modes by linear programming. - Lake-Ee Quek; Lars Keld Nielsen (BMC Syst. Biol., 2014)

A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions. - Pedro A. Saa; Lars Keld Nielsen (PLoS Comput. Biol., 2015)

ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks. - Pedro A. Saa; Lars Keld Nielsen (Bioinform., 2016)

Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models. - Pedro A. Saa; Lars Keld Nielsen (Bioinform., 2016)

multiTFA: a Python package for multi-variate thermodynamics-based flux analysis. - Vishnuvardhan Mahamkali; Tim McCubbin; Moritz Emanuel Beber; Elad Noor; Esteban Marcellin; Lars Keld Nielsen (Bioinform., 2021)

The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility. - Verónica S. Martínez; Pedro A. Saa; Jason Jooste; Kanupriya Tiwari; Lake-Ee Quek; Lars Keld Nielsen (PLoS Comput. Biol., 2022)

LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models. - Pedro A. Saa; Sebastian Zapararte; Christopher C. Drovandi; Lars Keld Nielsen (BMC Bioinform., 2024)

Unsupervised learning bioreactor regimes. - Víctor Puig I Laborda; Lars Puiman; Teddy Groves; Cees Haringa; Lars Keld Nielsen (Comput. Chem. Eng., 2025)