Mutual Information Analysis of Surrogate Gene Expression Data. - Dirk Holste; Dieter Beule; Wolfram Liebermeister; Johannes Schuchhardt; Hanspeter Herzel (German Conference on Bioinformatics, 1999)

Independent component analysis of gene expression data. - Wolfram Liebermeister (German Conference on Bioinformatics, 2001)

Linear modes of gene expression determined by independent component analysis. - Wolfram Liebermeister (Bioinform., 2002)

Predicting Physiological Concentrations of Metabolites from Their Molecular Structure. - Wolfram Liebermeister (J. Comput. Biol., 2005)

Integration of Enzyme Kinetic Data from Various Sources. - Simon Borger; Jannis Uhlendorf; Anselm Helbig; Wolfram Liebermeister (Silico Biol., 2007)

Systems Biology - a Textbook. - Edda Klipp; Wolfram Liebermeister; Christoph K. Wierling; Axel Kowald; Hans Lehrach (Wiley, 2009)

semanticsSBML 2.0 - A Collection of Online Services for SBML Models. - Falko Krause; Marvin Schulz; Timo Lubitz; Wolfram Liebermeister (SWAT4LS, 2010)

Annotation and merging of SBML models with semanticSBML. - Falko Krause; Jannis Uhlendorf; Timo Lubitz; Marvin Schulz; Edda Klipp; Wolfram Liebermeister (Bioinform., 2010)

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. - Wolfram Liebermeister; Jannis Uhlendorf; Edda Klipp (Bioinform., 2010)

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. - Keren Yizhak; Tomer Benyamini; Wolfram Liebermeister; Eytan Ruppin; Tomer Shlomi (Bioinform., 2010)

semanticSBML 2.0 - A Collection of Online Services for SBML Models - Falko Krause; Marvin Schulz; Timo Lubitz; Wolfram Liebermeister (CoRR, 2010)

Propagating semantic information in biochemical network models. - Marvin Schulz; Edda Klipp; Wolfram Liebermeister (BMC Bioinform., 2012)

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism. - Elad Noor; Arren Bar-Even; Avi I. Flamholz; Ed Reznik; Wolfram Liebermeister; Ron Milo (PLoS Comput. Biol., 2014)

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. - Lucian Paul Smith; Michael Hucka; Stefan Hoops; Andrew Finney; Martin Ginkel; Chris J. Myers; Ion I. Moraru; Wolfram Liebermeister (J. Integr. Bioinform., 2015)

SBtab: a flexible table format for data exchange in systems biology. - Timo Lubitz; Jens Hahn; Frank T. Bergmann; Elad Noor; Edda Klipp; Wolfram Liebermeister (Bioinform., 2016)

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization. - Elad Noor; Avi I. Flamholz; Arren Bar-Even; Dan Davidi; Ron Milo; Wolfram Liebermeister (PLoS Comput. Biol., 2016)

Toward Community Standards and Software for Whole-Cell Modeling. - Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes 001; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; et al. (IEEE Trans. Biomed. Eng., 2016)

Notions of similarity for systems biology models. - Ron Henkel; Robert Hoehndorf; Tim Kacprowski; Christian Knüpfer; Wolfram Liebermeister; Dagmar Waltemath (Briefings Bioinform., 2017)

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield. - Meike T. Wortel; Elad Noor; Michael Ferris 001; Frank J. Bruggeman; Wolfram Liebermeister (PLoS Comput. Biol., 2018)

Parameter balancing: consistent parameter sets for kinetic metabolic models. - Timo Lubitz; Wolfram Liebermeister (Bioinform., 2019)

Structured spreadsheets with ObjTables enable data reuse and integration. - Jonathan R. Karr; Wolfram Liebermeister; Arthur P. Goldberg; John A. P. Sekar; Bilal Shaikh (CoRR, 2020)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth. - Hugo Dourado; Wolfram Liebermeister; Oliver Ebenhöh; Martin J. Lercher (PLoS Comput. Biol., 2023)

Inferring Reaction Elasticities from Metabolic Correlations in Cells Through Multi-objective Evolutionary Optimization. - Arthur Lequertier; Wolfram Liebermeister; Alberto Tonda (EvoApplications (2), 2025)