Designing optimal cell factories: integer programming couples elementary mode analysis with regulation. - Christian Jungreuthmayer; Jürgen Zanghellini (BMC Syst. Biol., 2012)

Designing an optimally ethanol producing E. coli strain using constrained minimal cut sets. - Christian Jungreuthmayer; Margot Sonnleitner; Gerald Striedner; Jürgen Mairhofer; Jürgen Zanghellini (EUSIPCO, 2013)

regEfmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic. - Christian Jungreuthmayer; David E. Ruckerbauer; Jürgen Zanghellini (Biosyst., 2013)

Comparison and improvement of algorithms for computing minimal cut sets. - Christian Jungreuthmayer; Govind Nair; Steffen Klamt; Jürgen Zanghellini (BMC Bioinform., 2013)

Designing minimal microbial strains of desired functionality using a genetic algorithm. - Govind Nair; Christian Jungreuthmayer; Michael Hanscho; Jürgen Zanghellini (Algorithms Mol. Biol., 2015)

tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks. - Matthias P. Gerstl; Christian Jungreuthmayer; Jürgen Zanghellini (Bioinform., 2015)

Exact quantification of cellular robustness in genome-scale metabolic networks. - Matthias P. Gerstl; Steffen Klamt; Christian Jungreuthmayer; Jürgen Zanghellini (Bioinform., 2016)

ICT: isotope correction toolbox. - Christian Jungreuthmayer; Stefan Neubauer; Teresa Mairinger; Jürgen Zanghellini; Stephan Hann (Bioinform., 2016)

CHOmine: an integrated data warehouse for CHO systems biology and modeling. - Matthias P. Gerstl; Michael Hanscho; David E. Ruckerbauer; Jürgen Zanghellini; Nicole Borth (Database J. Biol. Databases Curation, 2017)

Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization. - Govind Nair; Christian Jungreuthmayer; Jürgen Zanghellini (BMC Bioinform., 2017)

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. - Steffen Klamt; Georg Regensburger; Matthias P. Gerstl; Christian Jungreuthmayer; Stefan Schuster; Radhakrishnan Mahadevan; Jürgen Zanghellini; Stefan Müller 009 (PLoS Comput. Biol., 2017)

Flux tope analysis: studying the coordination of reaction directions in metabolic networks. - Matthias P. Gerstl; Stefan Müller 009; Georg Regensburger; Jürgen Zanghellini (Bioinform., 2019)

EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search. - Bianca A. Buchner; Jürgen Zanghellini (BMC Bioinform., 2021)

Inclusion of maintenance energy improves the intracellular flux predictions of CHO. - Diana Széliová; Jerneja Stor; Isabella Thiel; Marcus Weinguny; Michael Hanscho; Gabriele Lhota; Nicole Borth; Jürgen Zanghellini; David E. Ruckerbauer; Isabel Rocha (PLoS Comput. Biol., 2021)

PeakBot: machine-learning-based chromatographic peak picking. - Christoph Bueschl; Maria Doppler; Elisabeth Varga; Bernhard Seidl; Mira Flasch; Benedikt Warth; Jürgen Zanghellini (Bioinform., 2022)

Probabilistic quotient's work and pharmacokinetics' contribution: countering size effect in metabolic time series measurements. - Mathias Gotsmy; Julia Brunmair; Christoph Bueschl; Christopher Gerner; Jürgen Zanghellini (BMC Bioinform., 2022)

Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. - Stefan Müller 009; Diana Széliová; Jürgen Zanghellini (PLoS Comput. Biol., 2022)

Homologue series detection and management in LC-MS data with homologueDiscoverer. - Kevin Mildau; Justin J. J. van der Hooft; Mira Flasch; Benedikt Warth; Yasin El Abiead; Gunda Koellensperger; Jürgen Zanghellini; Christoph Bueschl (Bioinform., 2022)

ecmtool: fast and memory-efficient enumeration of elementary conversion modes. - Bianca A. Buchner; Tom J. Clement; Daan H. de Groot; Jürgen Zanghellini (Bioinform., 2023)

Flexible Nets to Improve GEM Cell Factories by Combining Kinetic and Proteomics Data. - Jorge Lázaro; Jorge Júlvez; Jürgen Zanghellini (CMSB, 2024)

Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine. - Steffen Klamt; Jürgen Zanghellini; Axel von Kamp (Briefings Bioinform., 2024)

Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways. - Leopold Zehetner; Diana Széliová; Barbara Kraus; Juan A. Hernandez Bort; Jürgen Zanghellini (PLoS Comput. Biol., 2024)