Beyond Digital Naturalism. - Walter Fontana; Günter P. Wagner; Leo W. Buss (Artif. Life, 1994)

Adaptation and the Modular Design of Organisms. - Günter P. Wagner (ECAL, 1995)

Recombination induced hypergraphs: A new approach to mutation-recombination isomorphism. - Paul Gitchoff; Günter P. Wagner (Complex., 1996)

Algebraic Theory of Recombination Spaces. - Peter F. Stadler; Günter P. Wagner (Evol. Comput., 1997)

Duplication of Modules Facilitates the Evolution of Functional Specialization. - Raffaele Calabretta; Stefano Nolfi; Domenico Parisi; Günter P. Wagner (Artif. Life, 2000)

The Right Stuff: Appropriate Mathematics for Evolutionary and Developmental Biology . - Chrystopher L. Nehaniv; Günter P. Wagner (Artif. Life, 2000)

Asymmetry of Configuration Space Induced by Unequal Crossover: Implications for Mathematical Theory of Evolutionary Innovation. - Max Shpak; Günter P. Wagner (Artif. Life, 2000)

Character identification in evolutionary biology: The role of the organism. - Günter P. Wagner; Manfred D. Laubichler (Theory Biosci., 2000)

Simon-Ando decomposability and fitness landscapes. - Max Shpak; Peter F. Stadler; Günter P. Wagner; Lee Altenberg (Theory Biosci., 2004)

Aggregation of variables and system decomposition: Applications to fitness landscape analysis. - Max Shpak; Peter F. Stadler; Günter P. Wagner; Joachim Hermisson (Theory Biosci., 2004)

Erratum to "Aggregation of variables and system decomposability: Applications to fitness landscape analysis. - Max Shpak; Peter F. Stadler; Günter P. Wagner; Joachim Hermisson (Theory Biosci., 2005)

The developmental evolution of avian digit homology: An update. - Günter P. Wagner (Theory Biosci., 2005)

Conceptual continuity as a mode of understanding complex systems: Applications to the dynamics sociopolitical systems. - Heinz Herrmann; Günter P. Wagner (Complex., 2006)

Emergence of Ultra-Conserved Protein Domains and Amino Acid Repeats: Adaptation, Competition and Thresholds. - Mary Rorick; Günter P. Wagner (AAAI Fall Symposium: Complex Adaptive Systems and the Threshold Effect, 2009)

Structural Robustness Confers Evolvability in Proteins. - Mary McLeod Rorick; Günter P. Wagner (AAAI Fall Symposium: Complex Adaptive Systems, 2010)

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. - Günter P. Wagner; Koryu Kin; Vincent J. Lynch (Theory Biosci., 2012)

A model based criterion for gene expression calls using RNA-seq data. - Günter P. Wagner; Koryu Kin; Vincent J. Lynch (Theory Biosci., 2013)

Normalizing need not be the norm: count-based math for analyzing single-cell data. - Samuel H. Church; Jasmine L. Mah; Günter P. Wagner; Casey W. Dunn (Theory Biosci., 2024)

In-Context Learning can distort the relationship between sequence likelihoods and biological fitness. - Pranav Kantroo; Günter P. Wagner; Benjamin B. Machta (CoRR, 2025)