Claus O Wilke

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 55

Top Topics

Network Analysis

Gene Expression

Top Venues

bioRxiv : the preprint server for biology

Proceedings of the National Academy of Sciences of the United States of America

Science advances

Nature communications

This page only lists publications with an associated author ORCID identifier.

Publications

Claus O Wilke
The biophysical landscape of viral evolution. Proceedings of the National Academy of Sciences of the United States of America 121 (27) (2024)
Aaron L Feller, Claus O Wilke
Peptide-specific chemical language model successfully predicts membrane diffusion of cyclic peptides. bioRxiv : the preprint server for biology (2024)
Kuang Hu, Chia-Wei Chou, Claus O Wilke, Ilya J Finkelstein
Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons. Nature communications 15 (1) (2024)
Aaron L Feller, Claus O Wilke
Peptide-specific chemical language model successfully predicts membrane diffusion of cyclic peptides. bioRxiv : the preprint server for biology (2024)
Claus O Wilke
The biophysical landscape of viral evolution. Proceedings of the National Academy of Sciences of the United States of America 121 (27) (2024)
Kuang Hu, Chia-Wei Chou, Claus O Wilke, Ilya J Finkelstein
Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons. Nature communications 15 (1) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Aaron L Feller, Claus O Wilke
Peptide-specific chemical language model successfully predicts membrane diffusion of cyclic peptides. bioRxiv : the preprint server for biology (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Claus O Wilke
The biophysical landscape of viral evolution. Proceedings of the National Academy of Sciences of the United States of America 121 (27) (2024)
Kuang Hu, Chia-Wei Chou, Claus O Wilke, Ilya J Finkelstein
Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons. Nature communications 15 (1) (2024)
Anastasiya V Kulikova, Jennifer K Parker, Bryan W Davies, Claus O Wilke
Semantic search using protein large language models detects class II microcins in bacterial genomes. mSystems (2024)
Kuang Hu, Chia-Wei Chou, Claus O Wilke, Ilya J Finkelstein
Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons. Nature communications 15 (1) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Anastasiya V Kulikova, Daniel J Diaz, Tianlong Chen, T Jeffrey Cole, Andrew D Ellington, Claus O Wilke
Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry. Scientific reports 13 (1) (2023)
Justin R Randall, Cory D DuPai, T Jeffrey Cole, Gillian Davidson, Kyra E Groover, Sabrina L Slater, Despoina A I Mavridou, Claus O Wilke, Bryan W Davies
Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. Science advances 9 (2) (2023)
Justin R Randall, Luiz C Vieira, Claus O Wilke, Bryan W Davies
Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity. bioRxiv : the preprint server for biology (2023)
Justin R Randall, Cory D DuPai, T Jeffrey Cole, Gillian Davidson, Kyra E Groover, Sabrina L Slater, Despoina A I Mavridou, Claus O Wilke, Bryan W Davies
Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. Science advances 9 (2) (2023)
Anastasiya V Kulikova, Daniel J Diaz, Tianlong Chen, T Jeffrey Cole, Andrew D Ellington, Claus O Wilke
Sequence and structure based deep learning models represent different aspects of protein biochemistry. bioRxiv : the preprint server for biology (2023)
Mackenzie M Johnson, Adam J Hockenberry, Matthew J McGuffie, Luiz Carlos Vieira, Claus O Wilke
Growth-dependent gene expression variation influences the strength of codon usage biases. bioRxiv : the preprint server for biology (2023)
Mackenzie M Johnson, Adam J Hockenberry, Matthew J McGuffie, Luiz Carlos Vieira, Claus O Wilke
Growth-dependent gene expression variation influences the strength of codon usage biases. Molecular biology and evolution (2023)
Kuang Hu, Chia-Wei Chou, Claus O Wilke, Ilya J Finkelstein
Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons. bioRxiv : the preprint server for biology (2023)
Justin R Randall, Cory D DuPai, T Jeffrey Cole, Gillian Davidson, Kyra E Groover, Sabrina L Slater, Despoina A I Mavridou, Claus O Wilke, Bryan W Davies
Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. Science advances 9 (2) (2023)
Justin R Randall, Cory D DuPai, T Jeffrey Cole, Gillian Davidson, Kyra E Groover, Sabrina L Slater, Despoina A I Mavridou, Claus O Wilke, Bryan W Davies
Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. Science advances 9 (2) (2023)
Anastasiya V Kulikova, Jennifer K Parker, Bryan W Davies, Claus O Wilke
Semantic search using protein large language models detects class II microcins in bacterial genomes. bioRxiv : the preprint server for biology (2023)
James R Rybarski, Kuang Hu, Alexis M Hill, Claus O Wilke, Ilya J Finkelstein
Metagenomic discovery of CRISPR-associated transposons. Proceedings of the National Academy of Sciences of the United States of America 118 (49) (2022)
Sahil B Shah, Alexis M Hill, Claus O Wilke, Adam J Hockenberry
Generating dynamic gene expression patterns without the need for regulatory circuits. PloS one 17 (5) (2022)
T Jeffrey Cole, Jennifer K Parker, Aaron L Feller, Claus O Wilke, Bryan W Davies
Evidence for Widespread Class II Microcins in Enterobacterales Genomes. Applied and environmental microbiology (2022)
Anastasiya V Kulikova, Daniel J Diaz, James M Loy, Andrew D Ellington, Claus O Wilke
Learning the local landscape of protein structures with convolutional neural networks. Journal of biological physics 47 (4) (2021)
Cory D DuPai, Bryan W Davies, Claus O Wilke
A systematic analysis of the beta hairpin motif in the Protein Data Bank. Protein science : a publication of the Protein Society 30 (3) (2021)
Mackenzie M Johnson, Claus O Wilke
Site-Specific Amino Acid Distributions Follow a Universal Shape. Journal of molecular evolution 88 (10) (2020)
Jon M Laurent, Riddhiman K Garge, Ashley I Teufel, Claus O Wilke, Aashiq H Kachroo, Edward M Marcotte
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PLoS biology 18 (5) (2020)
Yao Zhang, Austin J Moy, Xu Feng, Hieu T M Nguyen, Katherine R Sebastian, Jason S Reichenberg, Claus O Wilke, Mia K Markey, James W Tunnell
Assessment of Raman Spectroscopy for Reducing Unnecessary Biopsies for Melanoma Screening. Molecules (Basel, Switzerland) 25 (12) (2020)
Cory D DuPai, Claus O Wilke, Bryan W Davies
A Comprehensive Coexpression Network Analysis in Vibrio cholerae. mSystems 5 (4) (2020)
Claus O Wilke, Carl T Bergstrom
Predicting an epidemic trajectory is difficult. Proceedings of the National Academy of Sciences of the United States of America 117 (46) (2020)
Cory D DuPai, Ashley L Cunningham, Aaron R Conrado, Claus O Wilke, Bryan W Davies
TsrA Regulates Virulence and Intestinal Colonization in Vibrio cholerae. mSphere 5 (6) (2020)
Adam J Hockenberry, Claus O Wilke
Evolutionary couplings detect side-chain interactions. PeerJ 7 (2019)
Wu Liu, Mehmet U Caglar, Zhangming Mao, Andrew Woodman, Jamie J Arnold, Claus O Wilke, Craig E Cameron
More than efficacy revealed by single-cell analysis of antiviral therapeutics. Science advances 5 (10) (2019)
Benjamin R Jack, Daniel R Boutz, Matthew L Paff, Bartram L Smith, Claus O Wilke
Transcript degradation and codon usage regulate gene expression in a lytic phage. Virus evolution 5 (2) (2019)
Adam J Hockenberry, Claus O Wilke
Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses. Entropy (Basel, Switzerland) 21 (10) (2019)
Cory D DuPai, Claire D McWhite, Catherine B Smith, Rebecca Garten, Sebastian Maurer-Stroh, Claus O Wilke
Influenza passaging annotations: what they tell us and why we should listen. Virus evolution 5 (1) (2019)
Ashley I Teufel, Andrew M Ritchie, Claus O Wilke, David A Liberles
Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences. Genes 9 (8) (2018)
Qian Jiang, Ashley I Teufel, Eleisha L Jackson, Claus O Wilke
Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation. Genetics 208 (4) (2018)
Mehmet U Caglar, Ashley I Teufel, Claus O Wilke
Sicegar: R package for sigmoidal and double-sigmoidal curve fitting. PeerJ 6 (2018)
Matthew L Paff, Benjamin R Jack, Bartram L Smith, James J Bull, Claus O Wilke
Combinatorial Approaches to Viral Attenuation. mSystems 3 (4) (2018)
Bartram L Smith, Guifang Chen, Claus O Wilke, Robert M Krug
Avian Influenza Virus PB1 Gene in H3N2 Viruses Evolved in Humans To Reduce Interferon Inhibition by Skewing Codon Usage toward Interferon-Altered tRNA Pools. mBio 9 (4) (2018)
Eleisha L Jackson, Stephanie J Spielman, Claus O Wilke
Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein. PloS one 12 (4) (2017)
Bartram L Smith, Claus O Wilke
A new twist in measuring mutation rates. eLife 6 (2017)
Dariya K Sydykova, Benjamin R Jack, Stephanie J Spielman, Claus O Wilke
Measuring evolutionary rates of proteins in a structural context. F1000Research 6 (2017)
Colin W Brown, Viswanadham Sridhara, Daniel R Boutz, Maria D Person, Edward M Marcotte, Jeffrey E Barrick, Claus O Wilke
Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. BMC genomics 18 (1) (2017)
Benjamin R Jack, Daniel R Boutz, Matthew L Paff, Bartram L Smith, James J Bull, Claus O Wilke
Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization. G3 (Bethesda, Md.) 7 (9) (2017)
Dariya K Sydykova, Benjamin R Jack, Stephanie J Spielman, Claus O Wilke
Measuring evolutionary rates of proteins in a structural context. F1000Research (2017)
Claus O Wilke, Sara L Sawyer
At the mercy of viruses. eLife 5 (2016)
Marc Lipsitch, Wendy Barclay, Rahul Raman, Charles J Russell, Jessica A Belser, Sarah Cobey, Peter M Kasson, James O Lloyd-Smith, Sebastian Maurer-Stroh, Steven Riley, Catherine A A Beauchemin, Trevor Bedford, Thomas C Friedrich, Andreas Handel, Sander Herfst, Pablo Ramiro Murcia, Benjamin Roche, Claus O Wilke, Colin A Russell
Viral factors in influenza pandemic risk assessment. eLife 5 (2016)