Molecular Evolution in Time-Dependent Environments. - Claus O. Wilke; Christopher Ronnewinkel; Thomas Martinetz (ECAL, 1999)

Genetic Algorithms in Time-Dependent Environments - Christopher Ronnewinkel; Claus O. Wilke; Thomas Martinetz (CoRR, 1999)

Dynamische Fitnesslandschaften. - Claus O. Wilke (Künstliche Intell., 2000)

Adaptive evolution on neutral networks - Claus O. Wilke (CoRR, 2001)

Does the Red Queen Reign in the Kingdom of Digital Organisms? - Claus O. Wilke (ECAL, 2003)

Viral evolution under the pressure of an adaptive immune system: Optimal mutation rates for viral escape. - Christel Kamp; Claus O. Wilke; Christoph Adami; Stefan Bornholdt (Complex., 2003)

Experiments in Digital Evolution (Editors' Introduction to the Special Issue). - Christoph Adami; Claus O. Wilke (Artif. Life, 2004)

Evolution of Resource Competition between Mutually Dependent Digital Organisms. - Tyler J. Johnson; Claus O. Wilke (Artif. Life, 2004)

Digital Evolution in Time-Dependent Fitness Landscapes. - Ye Li; Claus O. Wilke (Artif. Life, 2004)

Avida: A Software Platform for Research in Computational Evolutionary Biology. - Charles Ofria; Claus O. Wilke (Artif. Life, 2004)

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes. - Wanjun Gu; Tong Zhou; Claus O. Wilke (PLoS Comput. Biol., 2010)

Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations? - Eamon B. O'Dea; Thomas E. Keller; Claus O. Wilke (PLoS Comput. Biol., 2010)

The role of deleterious mutations in the adaptation to a novel environment. - Arthur W. Covert III; Jared Carlson-Stevermer; Dakota Z. Derrberry; Claus O. Wilke (ALIFE, 2012)

What does sex have to do with it: tracking the fate of deleterious mutations in sexual populations. - Arthur W. Covert III; Jared Carlson-Stevermer; Dakota Z. Derrberry; Claus O. Wilke (ALIFE, 2012)

Bringing Molecules Back into Molecular Evolution. - Claus O. Wilke (PLoS Comput. Biol., 2012)

Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation and Self-Regulation. - Daifeng Wang; Mia K. Markey; Claus O. Wilke; Ari Arapostathis (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. - John R. Houser; Craig Barnhart; Daniel R. Boutz; Sean M. Carroll; Aurko Dasgupta; Joshua K. Michener; Brittany D. Needham; Ophelia Papoulas; Viswanadham Sridhara; Dariya K. Sydykova; Christopher J. Marx; M. Stephen Trent; et al. (PLoS Comput. Biol., 2015)

Pinetree: a step-wise gene expression simulator with codon-specific translation rates. - Benjamin R. Jack; Claus O. Wilke (Bioinform., 2019)

Phylogenetic Weighting Does Little to Improve the Accuracy of Evolutionary Coupling Analyses. - Adam J. Hockenberry; Claus O. Wilke (Entropy, 2019)

Welcome to the Tidyverse. - Hadley Wickham; Mara Averick; Jennifer Bryan; Winston Chang; Lucy D'Agostino McGowan; Romain François; Garrett Grolemund; Alex Hayes; Lionel Henry; Jim Hester; Max Kuhn; Thomas Lin Pedersen; et al. (J. Open Source Softw., 2019)

colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes. - Achim Zeileis; Jason C. Fisher; Kurt Hornik; Ross Ihaka; Claire D. McWhite; Paul Murrell; Reto Stauffer; Claus O. Wilke (J. Stat. Softw., 2020)

Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets. - Alexis Hill; James Rybarski; Kuang Hu; Ilya Finkelstein; Claus O. Wilke (J. Open Source Softw., 2021)

Prompt Engineering for Transformer-based Chemical Similarity Search Identifies Structurally Distinct Functional Analogues. - Clayton W. Kosonocky; Aaron L. Feller; Claus O. Wilke; Andrew D. Ellington (CoRR, 2023)

Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures. - Clayton W. Kosonocky; Claus O. Wilke; Edward M. Marcotte; Andrew D. Ellington (CoRR, 2023)

Using alternative SMILES representations to identify novel functional analogues in chemical similarity vector searches. - Clayton W. Kosonocky; Aaron L. Feller; Claus O. Wilke; Andrew D. Ellington (Patterns, 2023)

extendr: Frictionless bindings for R and Rust. - Mossa Merhi Reimert; Josiah D. Parry; Matt Denwood; Maya Katrin Gussmann; Claus O. Wilke; Ilia Kosenkov; Michael Milton; Amy Thomason (J. Open Source Softw., 2024)

Peptide-Aware Chemical Language Model Successfully Predicts Membrane Diffusion of Cyclic Peptides. - Aaron L. Feller; Claus O. Wilke (J. Chem. Inf. Model., 2025)

seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies. - Ira Zibbu; Claus O. Wilke; Jeffrey E. Barrick (J. Open Source Softw., 2025)