Claus O. Wilke

30 papers C 2Journal 26Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Peptide-Aware Chemical Language Model Successfully Predicts Membrane Diffusion of Cyclic Peptides. J. Chem. Inf. Model. Aaron L. Feller, Claus O. Wilke
2025	J	`jnl`	p2smi: A toolkit enabling SMILES generation and property analysis for noncanonical and cyclized peptides. J. Open Source Softw. Aaron L. Feller, Claus O. Wilke
2025	J	`jnl`	seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies. J. Open Source Softw. Ira Zibbu, Claus O. Wilke, Jeffrey E. Barrick
2024	J	`jnl`	extendr: Frictionless bindings for R and Rust. J. Open Source Softw. Mossa Merhi Reimert, Josiah D. Parry, Matt Denwood, Maya Katrin Gussmann, Claus O. Wilke, Ilia Kosenkov, Michael Milton, Amy Thomason
2023	J	`jnl`	Mining Patents with Large Language Models Demonstrates Congruence of Functional Labels and Chemical Structures. CoRR Clayton W. Kosonocky, Claus O. Wilke, Edward M. Marcotte, Andrew D. Ellington
2023	J	`jnl`	Prompt Engineering for Transformer-based Chemical Similarity Search Identifies Structurally Distinct Functional Analogues. CoRR Clayton W. Kosonocky, Aaron L. Feller, Claus O. Wilke, Andrew D. Ellington
2023	J	`jnl`	Using alternative SMILES representations to identify novel functional analogues in chemical similarity vector searches. Patterns Clayton W. Kosonocky, Aaron L. Feller, Claus O. Wilke, Andrew D. Ellington
2021	J	`jnl`	Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets. J. Open Source Softw. Alexis Hill, James Rybarski, Kuang Hu, Ilya Finkelstein, Claus O. Wilke
2020	J	`jnl`	colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes. J. Stat. Softw. Achim Zeileis, Jason C. Fisher, Kurt Hornik, Ross Ihaka, Claire D. McWhite, Paul Murrell, Reto Stauffer, Claus O. Wilke
2019	J	`jnl`	Phylogenetic Weighting Does Little to Improve the Accuracy of Evolutionary Coupling Analyses. Entropy Adam J. Hockenberry, Claus O. Wilke
2019	J	`jnl`	Pinetree: a step-wise gene expression simulator with codon-specific translation rates. Bioinform. Benjamin R. Jack, Claus O. Wilke
2019	J	`jnl`	Welcome to the Tidyverse. J. Open Source Softw. 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, Evan Miller, Stephan Bache, Kirill Müller, Jeroen Ooms, David Robinson, Dana Paige Seidel, Vitalie Spinu, Kohske Takahashi, Davis Vaughan, Claus O. Wilke, Kara H. Woo, Hiroaki Yutani
2019	J	`jnl`	colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes. CoRR Achim Zeileis, Jason C. Fisher, Kurt Hornik, Ross Ihaka, Claire D. McWhite, Paul Murrell, Reto Stauffer, Claus O. Wilke
2015	J	`jnl`	Controlled Measurement and Comparative Analysis of Cellular Components in PLoS Comput. Biol. 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, Jeffrey E. Barrick, Edward M. Marcotte, Claus O. Wilke
2012	J	`jnl`	Bringing Molecules Back into Molecular Evolution. PLoS Comput. Biol. Claus O. Wilke
2012	J	`jnl`	Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation and Self-Regulation. IEEE ACM Trans. Comput. Biol. Bioinform. Daifeng Wang, Mia K. Markey, Claus O. Wilke, Ari Arapostathis
2012	C	`conf`	The role of deleterious mutations in the adaptation to a novel environment. ALIFE Arthur W. Covert III, Jared Carlson-Stevermer, Dakota Z. Derrberry, Claus O. Wilke
2012	C	`conf`	What does sex have to do with it: tracking the fate of deleterious mutations in sexual populations. ALIFE Arthur W. Covert III, Jared Carlson-Stevermer, Dakota Z. Derrberry, Claus O. Wilke
2010	J	`jnl`	A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes. PLoS Comput. Biol. Wanjun Gu, Tong Zhou, Claus O. Wilke
2010	J	`jnl`	Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations? PLoS Comput. Biol. Eamon B. O'Dea, Thomas E. Keller, Claus O. Wilke
2004	J	`jnl`	Avida: A Software Platform for Research in Computational Evolutionary Biology. Artif. Life Charles Ofria, Claus O. Wilke
2004	J	`jnl`	Digital Evolution in Time-Dependent Fitness Landscapes. Artif. Life Ye Li, Claus O. Wilke
2004	J	`jnl`	Evolution of Resource Competition between Mutually Dependent Digital Organisms. Artif. Life Tyler J. Johnson, Claus O. Wilke
2004	J	`jnl`	Experiments in Digital Evolution (Editors' Introduction to the Special Issue). Artif. Life Christoph Adami, Claus O. Wilke
2003	—	`conf`	Does the Red Queen Reign in the Kingdom of Digital Organisms? ECAL Claus O. Wilke
2003	J	`jnl`	Viral evolution under the pressure of an adaptive immune system: Optimal mutation rates for viral escape. Complex. Christel Kamp, Claus O. Wilke, Christoph Adami, Stefan Bornholdt
2001	J	`jnl`	Adaptive evolution on neutral networks CoRR Claus O. Wilke
2000	J	`jnl`	Dynamische Fitnesslandschaften. Künstliche Intell. Claus O. Wilke
1999	J	`jnl`	Genetic Algorithms in Time-Dependent Environments CoRR Christopher Ronnewinkel, Claus O. Wilke, Thomas Martinetz
1999	—	`conf`	Molecular Evolution in Time-Dependent Environments. ECAL Claus O. Wilke, Christopher Ronnewinkel, Thomas Martinetz