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C. Wilke · SciRah

Researcher profile · Semantic Scholar

C. Wilke

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C. Wilke — researcher profile on SciRah

h-index: 54
Works: 237
Citations: 13K

Most-cited papers

Streamlined Plot Theme and Plot Annotations for 'ggplot2'
C. Wilke
20151,806 citations
Semantic Scholar
Create Elegant Data Visualisations Using the Grammar of Graphics [R package ggplot2 version 3.3.2]
H. Wickham, Winston Chang, Lionel Henry, Thomas Lin Pedersen +5 more
2020475 citations
Semantic Scholar
Systematic humanization of yeast genes reveals conserved functions and genetic modularity
Aashiq H. Kachroo, Jon M. Laurent, C. Yellman, A. Meyer +2 more
2015Science407 citations Open access
Semantic Scholar
Causes of evolutionary rate variation among protein sites
J. Echave, S. Spielman, C. Wilke
2016Nature reviews genetics308 citations Open access
Semantic Scholar
Dataset for: "BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains"
A. Hockenberry, C. Wilke
2020257 citations
Semantic Scholar
colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes
A. Zeileis, J. C. Fisher, K. Hornik, R. Ihaka +4 more
2019Journal of Statistical Software216 citations Open access
Semantic Scholar
The relationship between dN/dS and scaled selection coefficients.
S. Spielman, C. Wilke
2015Molecular biology and evolution130 citations Open access
Semantic Scholar
Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes
Benjamin R. Jack, A. Meyer, J. Echave, C. Wilke
2016PLoS Biology110 citations Open access
Semantic Scholar
Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence
J. Echave, C. Wilke
2016bioRxiv105 citations Open access
Semantic Scholar
Viral factors in influenza pandemic risk assessment
M. Lipsitch, W. Barclay, R. Raman, C. Russell +15 more
2016eLife100 citations Open access
Semantic Scholar
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
S. Spielman, C. Wilke
2015bioRxiv98 citations Open access
Semantic Scholar
Single-cell virology: on-chip investigation of viral infection dynamics
Feng Guo, Si-Xing Li, M. Caglar, Zhangming Mao +6 more
2017Cell Reports83 citations Open access
Semantic Scholar
Metagenomic discovery of CRISPR-associated transposons
James R. Rybarski, Kuang Hu, A. Hill, C. Wilke +1 more
2021Proceedings of the National Academy of Sciences of the United States of America80 citations Open access
Semantic Scholar
Limitations of alignment-free tools in total RNA-seq quantification
Douglas C. Wu, Jun Yao, Kevin S. Ho, A. Lambowitz +1 more
2018BMC Genomics66 citations Open access
Semantic Scholar
The E. coli molecular phenotype under different growth conditions
M. Caglar, John R. Houser, Craig Barnhart, D. Boutz +11 more
2016Scientific Reports64 citations Open access
Semantic Scholar
Using machine learning to predict the effects and consequences of mutations in proteins
D. Diaz, Anastasiya V. Kulikova, A. Ellington, C. Wilke
2023Current Opinion in Structural Biology54 citations Open access
Semantic Scholar
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs
Jon M. Laurent, Riddhiman K. Garge, Ashley I. Teufel, C. Wilke +2 more
2020PLoS Biology51 citations Open access
Semantic Scholar
Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin
A. Meyer, C. Wilke
2015bioRxiv46 citations Open access
Semantic Scholar
Predicting an epidemic trajectory is difficult
C. Wilke, Carl T. Bergstrom
2020Proceedings of the National Academy of Sciences of the United States of America44 citations Open access
Semantic Scholar
Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin
Claire D. McWhite, A. Meyer, C. Wilke
2016bioRxiv43 citations Open access
Semantic Scholar
Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions
Colin W. Brown, V. Sridhara, D. Boutz, M. Person +3 more
2016BMC Genomics42 citations Open access
Semantic Scholar
Time dependence of evolutionary metrics during the 2009 pandemic influenza virus outbreak
A. Meyer, S. Spielman, T. Bedford, C. Wilke
2015Virus Evolution37 citations Open access
Semantic Scholar
The many nuanced evolutionary consequences of duplicated genes
Ashley I. Teufel, Mackenzie M. Johnson, Jon M. Laurent, Aashiq H. Kachroo +2 more
2018bioRxiv34 citations Open access
Semantic Scholar
A systematic analysis of the beta hairpin motif in the Protein Data Bank
Cory D. DuPai, B. Davies, C. Wilke
2020bioRxiv32 citations Open access
Semantic Scholar
Avian Influenza Virus PB1 Gene in H3N2 Viruses Evolved in Humans To Reduce Interferon Inhibition by Skewing Codon Usage toward Interferon-Altered tRNA Pools
B. Smith, Guifang Chen, C. Wilke, R. M. Krug
2018mBio28 citations Open access
Semantic Scholar
Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization
Benjamin R. Jack, D. Boutz, Matthew L. Paff, B. Smith +2 more
2017G3: Genes, Genomes, Genetics25 citations Open access
Semantic Scholar
Measuring evolutionary rates of proteins in a structural context
Dariya K. Sydykova, Benjamin R. Jack, S. Spielman, C. Wilke
2017F1000Research23 citations Open access
Semantic Scholar
Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint.
S. Spielman, C. Wilke
2016Molecular biology and evolution23 citations Open access
Semantic Scholar
Learning the local landscape of protein structures with convolutional neural networks
Anastasiya V. Kulikova, D. Diaz, James M. Loy, A. Ellington +1 more
2021Journal of biological physics (Print)21 citations Open access
Semantic Scholar
More than efficacy revealed by single-cell analysis of antiviral therapeutics
Wu Liu, M. Caglar, Zhangming Mao, A. Woodman +3 more
2019Science Advances21 citations Open access
Semantic Scholar
Transcript degradation and codon usage regulate gene expression in a lytic phage
Benjamin R. Jack, D. Boutz, Matthew L. Paff, B. Smith +1 more
2019bioRxiv21 citations Open access
Semantic Scholar
Computational and Functional Analysis of the Virus-Receptor Interface Reveals Host Range Trade-Offs in New World Arenaviruses
Scott A. Kerr, Eleisha L. Jackson, Oana I. Lungu, A. Meyer +5 more
2015Journal of Virology21 citations Open access
Semantic Scholar
Evidence for Widespread Class II Microcins in Enterobacterales Genomes
T. Cole, Jennifer K. Parker, Aaron L. Feller, C. Wilke +1 more
2022Applied and Environmental Microbiology20 citations Open access
Semantic Scholar
Improved Text Rendering Support for 'ggplot2' [R package ggtext version 0.1.0]
C. Wilke
202020 citations
Semantic Scholar
Dissecting the roles of local packing density and longer-range effects in protein sequence evolution
A. Shahmoradi, C. Wilke
2015bioRxiv20 citations Open access
Semantic Scholar
Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors
S. Spielman, Keerthana Kumar, C. Wilke
2015PeerJ19 citations Open access
Semantic Scholar
Designing and identifying β-hairpin peptide macrocycles with antibiotic potential
Justin R Randall, Cory D. DuPai, T. Cole, G. Davidson +5 more
2023Science Advances18 citations Open access
Semantic Scholar
Within-Gene Shine–Dalgarno Sequences Are Not Selected for Function
A. Hockenberry, Michael C. Jewett, L. A. Nunes Amaral, C. Wilke
2018Molecular biology and evolution18 citations Open access
Semantic Scholar
Assessment of Raman Spectroscopy for Reducing Unnecessary Biopsies for Melanoma Screening
Yao Zhang, Austin J. Moy, Xu Feng, Hieu T. M. Nguyen +5 more
2020Molecules17 citations Open access
Semantic Scholar
Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses
A. Hockenberry, C. Wilke
2019bioRxiv17 citations Open access
Semantic Scholar
Accelerated simulation of evolutionary trajectories in origin–fixation models
Ashley I. Teufel, C. Wilke
2016bioRxiv17 citations Open access
Semantic Scholar
Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates
Dariya K. Sydykova, C. Wilke
2017PeerJ16 citations Open access
Semantic Scholar
Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein
Eleisha L. Jackson, S. Spielman, C. Wilke
2016bioRxiv16 citations Open access
Semantic Scholar
The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins
A. Meyer, C. Wilke
2015Journal of the Royal Society Interface16 citations Open access
Semantic Scholar
A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation
S. Spielman, S. Wan, C. Wilke
2015Genetics16 citations Open access
Semantic Scholar
Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences
Ashley I. Teufel, Andrew M. Ritchie, C. Wilke, D. Liberles
2018Genes15 citations Open access
Semantic Scholar
Evolutionary couplings detect side-chain interactions
A. Hockenberry, C. Wilke
2018bioRxiv13 citations Open access
Semantic Scholar
Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation
Qian Jiang, Ashley I. Teufel, Eleisha L. Jackson, C. Wilke
2018Genetics12 citations Open access
Semantic Scholar
Pinetree: a step-wise gene expression simulator with codon-specific translation rates
Benjamin R. Jack, C. Wilke
2018bioRxiv10 citations Open access
Semantic Scholar
At the mercy of viruses
C. Wilke, S. Sawyer
2016eLife10 citations Open access
Semantic Scholar

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