C. Wilke

C. Wilke, L. Kramer, A. Ciota, 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Evolutionary paths of least resistance

C. Wilke, 2015, Proceedings of the National Academy of Sciences.

The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution

Claus O Wilke, C. Wilke, T. Zhou, 2011, Genetics.

Genealogical process on a correlated fitness landscape.

C. Wilke, J. Fontanari, P. Campos, 2002, The Journal of experimental zoology.

Quasispecies theory in the context of population genetics

Claus O Wilke, C. Wilke, 2005, BMC Evolutionary Biology.

Analysis of Human Immunodeficiency Virus Type 1 Viremia and Provirus in Resting CD4+ T Cells Reveals a Novel Source of Residual Viremia in Patients on Antiretroviral Therapy

John O. Woods, R. Siliciano, C. Wilke, 2009, Journal of Virology.

Residual Human Immunodeficiency Virus Type 1 Viremia in Some Patients on Antiretroviral Therapy Is Dominated by a Small Number of Invariant Clones Rarely Found in Circulating CD4+ T Cells

Claus O. Wilke, Thomas C. Quinn, Tara L. Kieffer, 2006, Journal of Virology.

T cell dynamics and the response to HAART in a cohort of HIV-1-infected elite suppressors.

C. Wilke, J. Blankson, A. Sedaghat, 2009, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation

C. Wilke, A. Hockenberry, D. C. Weaver, 2021, bioRxiv.

Metagenomic discovery of CRISPR-associated transposons

James R. Rybarski, C. Wilke, I. Finkelstein, 2021, Proceedings of the National Academy of Sciences.

Slow fitness recovery in a codon-modified viral genome.

J. Bull, C. Wilke, I. Molineux, 2012, Molecular biology and evolution.

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

Claus O. Wilke, Edward M. Marcotte, Joshua K. Michener, 2015, PLoS Comput. Biol..

Phenotypic differences in viral immune escape explained by linking within-host dynamics to host-population immunity.

C. Wilke, J. Banavar, B. Grenfell, 2010, Journal of theoretical biology.

REPLICATION AT PERIODICALLY CHANGING MULTIPLICITY OF INFECTION PROMOTES STABLE COEXISTENCE OF COMPETING VIRAL POPULATIONS

C. Wilke, I. Novella, Daniel D. Reissig, 2004, Evolution; international journal of organic evolution.

The role of environmental factors on the evolution of phenotypic diversity in vesicular stomatitis virus populations.

C. Wilke, S. Khuder, I. Novella, 2013, The Journal of general virology.

Experiments in Digital Evolution (Editors' Introduction to the Special Issue)

Christoph Adami, Claus O. Wilke, C. Wilke, 2004, Artificial Life.

TsrA Regulates Virulence and Intestinal Colonization in Vibrio cholerae

C. Wilke, Ashley L. Cunningham, Cory D. DuPai, 2020, mSphere.

A Comprehensive Coexpression Network Analysis in Vibrio cholerae

C. Wilke, Cory D. DuPai, B. W. Davies, 2020, mSystems.

A comprehensive co-expression network analysis in Vibrio cholerae

C. Wilke, Cory D. DuPai, B. W. Davies, 2020, bioRxiv.

Avida: Evolution Experiments with Self-Replicating Computer Programs

Charles Ofria, Claus O. Wilke, C. Ofria, 2005, Artificial Life Models in Software.

Maternal effects in molecular evolution.

Claus O Wilke, C. Wilke, 2001, Physical review letters.

Generating complex patterns of gene expression without regulatory circuits

Claus O. Wilke, Adam J. Hockenberry, Sahil B. Shah, 2020, bioRxiv.

Evolution in time-dependent fitness landscapes

C. Wilke, 1998, physics/9811021.

Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART

Claus O Wilke, R. Siliciano, C. Wilke, 2008, BMC infectious diseases.

Avida

Charles Ofria, Claus O. Wilke, C. Ofria, 2004, Artificial Life.

Eigen-Genomic System Dynamic-Pattern Analysis (ESDA): Modeling mRNA Degradation and Self-Regulation

Ari Arapostathis, Mia K. Markey, Claus O. Wilke, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Modelling Stochastic Clonal Interference

C. Wilke, C. Adami, P. Campos, 2003, physics/0305001.

The Stochastic Edge in Adaptive Evolution

Claus O Wilke, Igor M Rouzine, Eric Brunet, 2007, Genetics.

Analyzing machupo virus-receptor binding by molecular dynamics simulations

Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington, 2013, PeerJ.

Predicting virus-receptor mutant binding by molecular dynamics simulation

C. Wilke, A. Ellington, S. Sawyer, 2013 .

Evolution of Resource Competition between Mutually Dependent Digital Organisms

Claus O. Wilke, Tyler J. Johnson, C. Wilke, 2004, Artificial Life.

A Linear Relationship between Fitness and the Logarithm of the Critical Bottleneck Size in Vesicular Stomatitis Virus Populations

Claus O. Wilke, C. Wilke, I. Novella, 2008, Journal of Virology.

Modeling poliovirus replication dynamics from live time-lapse single-cell imaging data

Ashley I. Teufel, C. Wilke, J. Draghi, 2021, Scientific Reports.

Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs

Ashley I. Teufel, C. Wilke, E. Marcotte, 2019, bioRxiv.

Optimal adaptive performance and delocalization in NK fitness landscapes

Christoph Adami, Claus O. Wilke, Paulo R. A. Campos, 2001, physics/0109020.

Risk factors for development of chronic rhinosinusitis in patients with allergic rhinitis

C. Wilke, A. Sedaghat, S. Gray, 2012, International forum of allergy & rhinology.

RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction

C. Wilke, R. A. Harris, R. Mayfield, 2013, Biology Direct.

PeptideBuilder: A simple Python library to generate model peptides

Austin G. Meyer, Claus O. Wilke, Dariya K. Sydykova, 2013, PeerJ.

Phylogenetic Weighting Does Little to Improve the Accuracy of Evolutionary Coupling Analyses

Claus O. Wilke, Adam J. Hockenberry, C. Wilke, 2019, bioRxiv.

Growth-dependent gene expression variation influences the strength of codon usage biases

Mackenzie M. Johnson, C. Wilke, A. Hockenberry, 2023, bioRxiv.

Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons

C. Wilke, Chia-Wei Chou, I. Finkelstein, 2023, bioRxiv.

Predicting an epidemic trajectory is difficult

Carl T. Bergstrom, Carl T Bergstrom, Claus O Wilke, 2020, Proceedings of the National Academy of Sciences.

Evaluation of Parvovirus B19 Infection in Children with Malignant or Hematological Disorders

C. Wilke, J. Blankson, A. Sedaghat, 2010 .

Does the Red Queen Reign in the Kingdom of Digital Organisms?

Claus O. Wilke, C. Wilke, 2003, ECAL.

Genetic Algorithms in Time-Dependent Environments

Thomas Martinetz, Claus O. Wilke, Christopher Ronnewinkel, 1999, ArXiv.

Molecular Evolution in Time-Dependent Environments

Thomas Martinetz, Claus O. Wilke, Christopher Ronnewinkel, 1999, ECAL.

Reproducibility of SNV-calling in multiple sequencing runs from single tumors

Matthew C. Cowperthwaite, Claus O. Wilke, Dakota Z. Derryberry, 2016, PeerJ.

Transcriptional Robustness Complements Nonsense-Mediated Decay in Humans

C. Wilke, 2011, PLoS genetics.

Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein

Stephanie J. Spielman, Claus O Wilke, Stephanie J Spielman, 2016, bioRxiv.

Lethal mutagenesis in a structured environment.

Claus O Wilke, C. Wilke, Shelby H Steinmeyer, 2009, Journal of theoretical biology.

Designing and identifying β-hairpin peptide macrocycles with antibiotic potential

C. Wilke, D. Mavridou, Cory D. DuPai, 2023, Science advances.

Limits on Replenishment of the Resting CD4+ T Cell Reservoir for HIV in Patients on HAART

Claus O Wilke, R. Siliciano, C. Wilke, 2007, PLoS pathogens.

Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza H3N2 hemagglutinin

Claire D. McWhite, C. Wilke, A. Meyer, 2016, bioRxiv.

Short communication: dynamic constraints on the second phase compartment of HIV-infected cells.

R. Siliciano, C. Wilke, A. Spivak, 2011, AIDS research and human retroviruses.

Evolutionary couplings detect side-chain interactions

Claus O. Wilke, Adam J. Hockenberry, C. Wilke, 2018, bioRxiv.

Geometric constraints dominate the antigenic evolution of 1 influenza H 3 N 2 hemagglutinin 2

C. Wilke, A. Meyer, 2015 .

Analysis of HIV-1 Viremia and Provirus in Resting CD4 + T Cells Reveals a Novel Source of Residual Viremia in Patients on Antiretroviral Therapy

John O. Woods, C. Wilke, J. Siliciano, 2009 .

Distributed under Creative Commons Cc-by 4.0 the Evolution of Logic Circuits for the Purpose of Protein Contact Map Prediction

Christoph Adami, Claus O. Wilke, Samuel D. Chapman, 2022 .

More than efficacy revealed by single-cell analysis of antiviral therapeutics

C. Wilke, J. Arnold, C. Cameron, 2019, Science Advances.

Limited utility of residue masking for positive-selection inference.

Eric T. Dawson, Stephanie J. Spielman, C. Wilke, 2014, Molecular biology and evolution.

Influenza passaging annotations: what they tell us and why we should listen

Sebastian Maurer-Stroh, Claus O Wilke, Cory D DuPai, 2019, Virus evolution.

Reply to Torre

C. Wilke, J. Blankson, A. Sedaghat, 2010 .

A new twist in measuring mutation rates

C. Wilke, B. Smith, 2017, eLife.

Supporting Text : Geometric constraints dominate the antigenic 1 evolution of influenza H 3 N 2 hemagglutinin 2

C. Wilke, A. Meyer, 2015 .

Increased evolutionary rate in the 2014 West African Ebola outbreak is due to transient polymorphism and not positive selection

Stephanie J. Spielman, C. Wilke, A. Meyer, 2014 .

Prompt Engineering for Transformer-based Chemical Similarity Search Identifies Structurally Distinct Functional Analogues

C. Wilke, A. Ellington, Clayton W Kosonocky, 2023, ArXiv.

Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry

C. Wilke, A. Ellington, Tianlong Chen, 2023, bioRxiv.

Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons

C. Wilke, Chia-Wei Chou, I. Finkelstein, 2023, bioRxiv.

Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets

James R. Rybarski, Ilya J. Finkelstein, C. Wilke, 2021, J. Open Source Softw..

The role of deleterious mutations in the adaptation to a novel environment

Arthur W. Covert, Claus O. Wilke, Jared Carlson-Stevermer, 2012, ALIFE.

Thermodynamic prediction of protein neutrality.

C. Wilke, C. Adami, F. Arnold, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Does Mutational Robustness Inhibit Extinction by Lethal Mutagenesis in Viral Populations?

Claus O. Wilke, Thomas E. Keller, Eamon B. O'Dea, 2010, PLoS Comput. Biol..

Improved Text Rendering Support for 'ggplot2' [R package ggtext version 0.1.0]

Claus O. Wilke, C. Wilke, 2020 .

Limitations of alignment-free tools in total RNA-seq quantification

Claus O. Wilke, Alan M. Lambowitz, C. Wilke, 2018, BMC Genomics.

Pinetree: a step-wise gene expression simulator with codon-specific translation rates

Claus O. Wilke, Benjamin R. Jack, C. Wilke, 2018, bioRxiv.

Kinetics of the viral cycle influence pharmacodynamics of antiretroviral therapy

C. Wilke, A. Sedaghat, 2011, Biology Direct.

Amino-acid site variability among natural and designed proteins

Arthur W. Covert, Tanja Kortemme, Claus O. Wilke, 2013, PeerJ.

Geometric Constraints Dominate the Antigenic Evolution of Influenza H3N2 Hemagglutinin

C. Wilke, A. Meyer, 2015, bioRxiv.

At the mercy of viruses

C. Wilke, S. Sawyer, 2016, eLife.

ADAPTIVE EVOLUTION At the mercy of viruses Viruses are responsible for many of the adaptive mutations in the human genome

C. Wilke, S. Sawyer, 2016 .

Reproductive pair correlations and the clustering of organisms

W. R. Young, A. J. Roberts, C. Ofria, 2001, Nature.

Sicegar: R package for sigmoidal and double-sigmoidal curve fitting

Ashley I. Teufel, C. Wilke, M. Caglar, 2018, PeerJ.

On the conservative nature of intragenic

C. Wilke, F. Arnold, J. Silberg, 2005 .

Large-scale evolution and extinction in a hierarchically structured environment

C. Wilke, T. Martinetz, S. Altmeyer, 1998, adap-org/9803001.

Simple model of evolution with variable system size

C. Wilke, T. Martinetz, C. Wilke, 1997, physics/9705008.

RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction

C. Wilke, R. Harris, R. Mayfield, 2013, Biology Direct.

Causes of evolutionary rate variation among protein sites

Stephanie J. Spielman, C. Wilke, J. Echave, 2016, Nature Reviews Genetics.

Beyond thermodynamic constraints: Evolutionary history shapes protein sequence variation

Ashley I. Teufel, Eleisha L. Jackson, C. Wilke, 2017, bioRxiv.

Predicting Evolutionary Site Variability from Structure in Viral Proteins: Buriedness, Packing, Flexibility, and Design

Eric T. Dawson, Stephanie J. Spielman, Dariya K. Sydykova, 2014, Journal of Molecular Evolution.

Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors

Stephanie J. Spielman, C. Wilke, Keerthana Kumar, 2015, PeerJ.

T cell dynamics and the response to HAART in a cohort of HIV-1-infected elite suppressors.

C. Wilke, J. Blankson, A. Sedaghat, 2009, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases

Mackenzie M. Johnson, C. Wilke, A. Hockenberry, 2023, bioRxiv.

The Stochastic Edge in Adaptive Evolution

C. Wilke, I. M. Rouzine, E. Brunet, 2007, Genetics.

Theory of measurement for site-specific evolutionary rates in amino-acid sequences

Dariya K. Sydykova, C. Wilke, 2017, bioRxiv.

Analysis of Human Immunodeficiency Virus Type 1 Viremia and Provirus in Resting CD4+ T Cells Reveals a Novel Source of Residual Viremia in Patients on Antiretroviral Therapy

John O. Woods, R. Siliciano, C. Wilke, 2009, Journal of Virology.

Detecting positive and purifying selection at synonymous sites in yeast and worm.

C. Wilke, W. Gu, Tong Zhou, 2010, Molecular biology and evolution.

New Hampshire Scholars

M. Eisen, C. Wilke, M. MacManes, 2022 .

Dataset for: "BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains"

C. Wilke, A. Hockenberry, 2020 .

Long-term control of viral replication in a Group O, human immunodeficiency virus type 1-infected individual.

C. Wilke, O. Laeyendecker, J. Blankson, 2014, AIDS research and human retroviruses.

Comprehensive , structurally-curated alignment and phylogeny of vertebrate biogenic amine receptors

Stephanie J. Spielman, C. Wilke, Keerthana Kumar, 2017 .