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Bronze Contributor

Claus O Wilke

PeerJ Editor, Author & Reviewer

Summary

Professor and Department Chair, Department of Integrative Biology, The University of Texas at Austin. Received his PhD in Theoretical Physics from the University of Bochum, Germany, in 1999. Postdoc at Caltech, 2000-2005.

Biochemistry Bioinformatics Biophysics Computational Biology Evolutionary Studies Genetics Genomics Mathematical Biology Virology

Editorial Board Member

PeerJ - the Journal of Life & Environmental Sciences

Past or current institution affiliations

University of Texas at Austin

Work details

Professor

University of Texas at Austin

Department of Integrative Biology

Websites

PeerJ Contributions

May 6, 2021

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains

Adam J. Hockenberry, Claus O. Wilke

https://doi.org/10.7717/peerj.11396 PubMed 33996289

July 8, 2019

Evolutionary couplings detect side-chain interactions

Adam J. Hockenberry, Claus O. Wilke

https://doi.org/10.7717/peerj.7280 PubMed 31328041

January 16, 2018

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

M. Umut Caglar, Ashley I. Teufel, Claus O. Wilke

https://doi.org/10.7717/peerj.4251 PubMed 29362694

May 30, 2017

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates

Dariya K. Sydykova, Claus O. Wilke

https://doi.org/10.7717/peerj.3391 PubMed 28584717

April 18, 2017

The evolution of logic circuits for the purpose of protein contact map prediction

Samuel D. Chapman, Christoph Adami, Claus O. Wilke, Dukka B KC

https://doi.org/10.7717/peerj.3139 PubMed 28439455

January 4, 2016

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

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

https://doi.org/10.7717/peerj.1508 PubMed 26855855

February 17, 2015

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

Stephanie J. Spielman, Keerthana Kumar, Claus O. Wilke

https://doi.org/10.7717/peerj.773 PubMed 25737813

February 27, 2014

Analyzing machupo virus-receptor binding by molecular dynamics simulations

Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington, Claus O. Wilke

https://doi.org/10.7717/peerj.266 PubMed 24624315

November 12, 2013

Amino-acid site variability among natural and designed proteins

Eleisha L. Jackson, Noah Ollikainen, Arthur W. Covert, Tanja Kortemme, Claus O. Wilke

https://doi.org/10.7717/peerj.211 PubMed 24255821

May 21, 2013

PeptideBuilder: A simple Python library to generate model peptides

Matthew Z. Tien, Dariya K. Sydykova, Austin G. Meyer, Claus O. Wilke

https://doi.org/10.7717/peerj.80 PubMed 23717802

July 31, 2017 - Version: 1

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

M. Umut Caglar, Ashley I. Teufel, Claus O Wilke

https://doi.org/10.7287/peerj.preprints.3116v1

June 2, 2017 - Version: 1

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

Dariya K Sydykova, Claus O Wilke

https://doi.org/10.7287/peerj.preprints.3002v1

June 2, 2017 - Version: 1

Investigating viral attenuation by promoter knockout: a systems approach

Matthew L Paff, Benjamin R. Jack, Daniel R Boutz, Bartram L Smith, Claus O Wilke, James J Bull

https://doi.org/10.7287/peerj.preprints.3001v1

June 1, 2017 - Version: 1

Influenza A virus avian-derived PB1 gene has evolved to match its codon usage to interferon-altered human tRNA pools

Bartram L Smith, Guifang Chen, Claus O Wilke, Robert M Krug

https://doi.org/10.7287/peerj.preprints.3000v1

January 19, 2017 - Version: 1

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates

Dariya K. Sydykova, Claus O Wilke

https://doi.org/10.7287/peerj.preprints.2739v1

July 1, 2016 - Version: 1

The evolution of logic circuits for the purpose of protein contact map prediction

Samuel D Chapman, Christoph Adami, Claus O Wilke, Dukka B KC

https://doi.org/10.7287/peerj.preprints.2197v1

October 31, 2014 - Version: 1

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

Stephanie Spielman, Keerthana Kumar, Claus O. Wilke

https://doi.org/10.7287/peerj.preprints.571v1

January 27, 2014 - Version: 3

Analyzing Machupo virus-receptor binding by molecular dynamics simulations

Austin G Meyer, Sara L Sawyer, Andrew D Ellington, Claus O Wilke

https://doi.org/10.7287/peerj.preprints.138v3

October 3, 2013 - Version: 1

Amino-acid site variability among natural and designed proteins

Eleisha L. Jackson, Noah Ollikainen, Arthur W. Covert III, Tanja Kortemme, Claus O. Wilke

https://doi.org/10.7287/peerj.preprints.74v1

Academic Editor on

December 6, 2023

The development and application of pseudoviruses: assessment of SARS-CoV-2 pseudoviruses

Conglian Tan, Nian Wang, Shanshan Deng, Xiaoheng Wu, Changwu Yue, Xu Jia, Yuhong Lyu

https://doi.org/10.7717/peerj.16234 PubMed 38077431

September 25, 2023

Classification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis

Li-Yan Zhang, Benshun Tian, Yuan-Hong Huang, Bin Gu, Pei Ju, Yanfei Luo, Jiawei Tang, Liang Wang

https://doi.org/10.7717/peerj.16161 PubMed 37780376

August 4, 2022

In silico testing of flavonoids as potential inhibitors of protease and helicase domains of dengue and Zika viruses

Omar Cruz-Arreola, Abdu Orduña-Diaz, Fabiola Domínguez, Julio Reyes-Leyva, Verónica Vallejo-Ruiz, Lenin Domínguez-Ramírez, Gerardo Santos-López

https://doi.org/10.7717/peerj.13650 PubMed 35945938

February 17, 2022

PCAtest: testing the statistical significance of Principal Component Analysis in R

Arley Camargo

https://doi.org/10.7717/peerj.12967 PubMed 35194531

December 22, 2020

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis

Daniel Dimitrov, Quan Gu

https://doi.org/10.7717/peerj.10469 PubMed 33391870

February 3, 2020

ViSiElse: an innovative R-package to visualize raw behavioral data over time

Elodie M. Garnier, Nastasia Fouret, Médéric Descoins

https://doi.org/10.7717/peerj.8341 PubMed 32117603

September 12, 2019

Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses

Yanan Shi, Huanlong Liu, Yameng Gao, Yujiao Wang, Min Wu, Yan Xiang

https://doi.org/10.7717/peerj.7510 PubMed 31579567

March 18, 2019

Estimating probabilistic context-free grammars for proteins using contact map constraints

Witold Dyrka, Mateusz Pyzik, François Coste, Hugo Talibart

https://doi.org/10.7717/peerj.6559 PubMed 30918754

March 18, 2019

Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys

Xiao Wang, Boshi Wang, Zhijin Liu, Paul A. Garber, Huijuan Pan

https://doi.org/10.7717/peerj.6602 PubMed 30918756

October 5, 2018

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

María José Jiménez-Santos, Miguel Arenas, Ugo Bastolla

https://doi.org/10.7717/peerj.5549 PubMed 30310736

September 3, 2018

Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments

Jesse D. Bloom

https://doi.org/10.7717/peerj.5578 PubMed 30202659

April 27, 2018

FluxPyt: a Python-based free and open-source software for ¹³C-metabolic flux analyses

Trunil S. Desai, Shireesh Srivastava

https://doi.org/10.7717/peerj.4716 PubMed 29736347

April 25, 2018

phylopath: Easy phylogenetic path analysis in R

Wouter van der Bijl

https://doi.org/10.7717/peerj.4718 PubMed 29713568

April 13, 2018

Evolution of dopamine receptors: phylogenetic evidence suggests a later origin of the DRD_2l and DRD_4rs dopamine receptor gene lineages

Juan C. Opazo, Kattina Zavala, Soledad Miranda-Rottmann, Roberto Araya

https://doi.org/10.7717/peerj.4593 PubMed 29666757

January 12, 2018

RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration

Jing Zhang, Kenneth B. Storey

https://doi.org/10.7717/peerj.4262 PubMed 29340253

December 12, 2017

Substitutions into amino acids that are pathogenic in human mitochondrial proteins are more frequent in lineages closely related to human than in distant lineages

Galya V. Klink, Andrey V. Golovin, Georgii A. Bazykin

https://doi.org/10.7717/peerj.4143 PubMed 29250469

July 31, 2017

phydms: software for phylogenetic analyses informed by deep mutational scanning

Sarah K. Hilton, Michael B. Doud, Jesse D. Bloom

https://doi.org/10.7717/peerj.3657 PubMed 28785526

June 27, 2017

SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment

Scott Barlowe, Heather B. Coan, Robert T. Youker

https://doi.org/10.7717/peerj.3492 PubMed 28674656

June 20, 2017

Focus expansion and stability of the spread parameter estimate of the power law model for dispersal gradients

Peter S. Ojiambo, David H. Gent, Lucky K. Mehra, David Christie, Roger Magarey

https://doi.org/10.7717/peerj.3465 PubMed 28649473

May 16, 2017

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

Ranjan V. Mannige

https://doi.org/10.7717/peerj.3327 PubMed 28533975

March 9, 2017

Differential bicodon usage in lowly and highly abundant proteins

Luis A. Diambra

https://doi.org/10.7717/peerj.3081 PubMed 28289571

March 1, 2017

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species

Benjamin D. Redelings, Mark T. Holder

https://doi.org/10.7717/peerj.3058 PubMed 28265520

October 4, 2016

Did the 1918 influenza cause the twentieth century cardiovascular mortality epidemic in the United States?

Steven Tate, Jamie J. Namkung, Andrew Noymer

https://doi.org/10.7717/peerj.2531 PubMed 27761328

November 19, 2015

Rapid drop in the reproduction number during the Ebola outbreak in the Democratic Republic of Congo

Christian L. Althaus

https://doi.org/10.7717/peerj.1418 PubMed 26618087

October 22, 2015

Migration in the social stage of Dictyostelium discoideum amoebae impacts competition

Chandra N. Jack, Neil Buttery, Boahemaa Adu-Oppong, Michael Powers, Christopher R.L. Thompson, David C. Queller, Joan E. Strassmann

https://doi.org/10.7717/peerj.1352 PubMed 26528414

August 18, 2015

Coalescent: an open-science framework for importance sampling in coalescent theory

Susanta Tewari, John L. Spouge

https://doi.org/10.7717/peerj.1203 PubMed 26312189

August 4, 2015

Assessing the reproducibility of discriminant function analyses

Rose L. Andrew, Arianne Y.K. Albert, Sebastien Renaut, Diana J. Rennison, Dan G. Bock, Tim Vines

https://doi.org/10.7717/peerj.1137 PubMed 26290793

July 2, 2015

Multi-level machine learning prediction of protein–protein interactions in Saccharomyces cerevisiae

Julian Zubek, Marcin Tatjewski, Adam Boniecki, Maciej Mnich, Subhadip Basu, Dariusz Plewczynski

https://doi.org/10.7717/peerj.1041 PubMed 26157620

June 9, 2015

Research groups: How big should they be?

Isabelle Cook, Sam Grange, Adam Eyre-Walker

https://doi.org/10.7717/peerj.989 PubMed 26082872

May 27, 2015

Reconstructing the history of a WD40 beta-propeller tandem repeat using a phylogenetically informed algorithm

Philippe Lavoie-Mongrain, Mahdi Belcaid, Aïda Ouangraoua, Anne Bergeron, Guylaine Poisson

https://doi.org/10.7717/peerj-cs.6

April 30, 2015

The European and Japanese outbreaks of H5N8 derive from a single source population providing evidence for the dispersal along the long distance bird migratory flyways

Andrew R. Dalby, Munir Iqbal

https://doi.org/10.7717/peerj.934 PubMed 25945320

March 26, 2015

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

Peter A. Combs, Michael B. Eisen

https://doi.org/10.7717/peerj.869 PubMed 25834775

March 5, 2015

CauseMap: fast inference of causality from complex time series

M. Cyrus Maher, Ryan D. Hernandez

https://doi.org/10.7717/peerj.824 PubMed 25780776

February 17, 2015

X-to-autosome expression and msl-2 transcript abundance correlate among Drosophila melanogaster somatic tissues

Steven P. Vensko II, Eric A. Stone

https://doi.org/10.7717/peerj.771 PubMed 25737812

October 28, 2014

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

Matthew D. MacManes, Michael B. Eisen

https://doi.org/10.7717/peerj.642 PubMed 25374784

September 23, 2014

Removing batch effects for prediction problems with frozen surrogate variable analysis

Hilary S. Parker, Héctor Corrada Bravo, Jeffrey T. Leek

https://doi.org/10.7717/peerj.561 PubMed 25332844

September 2, 2014

Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene

Derek J. Taylor, Matthew J. Ballinger, Jack J. Zhan, Laura E. Hanzly, Jeremy A. Bruenn

https://doi.org/10.7717/peerj.556 PubMed 25237605

August 26, 2014

Rat sightings in New York City are associated with neighborhood sociodemographics, housing characteristics, and proximity to open public space

Michael G. Walsh

https://doi.org/10.7717/peerj.533 PubMed 25237595

June 17, 2014

Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters

Simon van Mourik, Cajo ter Braak, Hans Stigter, Jaap Molenaar

https://doi.org/10.7717/peerj.433 PubMed 25024907

May 29, 2014

Increasing the precision of orthology-based complex prediction through network alignment

Roland A. Pache, Patrick Aloy

https://doi.org/10.7717/peerj.413 PubMed 24918034

March 27, 2014

Severity of chronic Lyme disease compared to other chronic conditions: a quality of life survey

Lorraine Johnson, Spencer Wilcox, Jennifer Mankoff, Raphael B. Stricker

https://doi.org/10.7717/peerj.322 PubMed 24749006

Signed reviews submitted for articles published in PeerJ Note that some articles may not have the review itself made public unless authors have made them open as well.

August 28, 2018

A simple method for data partitioning based on relative evolutionary rates

Jadranka Rota, Tobias Malm, Nicolas Chazot, Carlos Peña, Niklas Wahlberg

https://doi.org/10.7717/peerj.5498 PubMed 30186687

March 4, 2014

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

Anders S. Christensen, Thomas Hamelryck, Jan H. Jensen

https://doi.org/10.7717/peerj.277 PubMed 24688855

1 Answer

Would a virtual machine be a useful link for this paper?