Site-Specific Amino Acid Distributions Follow a Universal Shape

[1]  Vadim Puller,et al.  Efficient inference, potential, and limitations of site-specific substitution models , 2020, bioRxiv.

[2]  Kohske Takahashi,et al.  Welcome to the Tidyverse , 2019, J. Open Source Softw..

[3]  Ugo Bastolla,et al.  The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. , 2018, Methods in molecular biology.

[4]  Lorenz Wernisch,et al.  GPseudoRank: a permutation sampler for single cell orderings , 2018, Bioinform..

[5]  M. Jiménez,et al.  Substitution Rates Predicted by Stability‐Constrained Models of Protein Evolution Are Not Consistent with Empirical Data , 2018, Molecular biology and evolution.

[6]  Claus O Wilke,et al.  Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation , 2018, Genetics.

[7]  Stephanie J. Spielman,et al.  Relative evolutionary rate inference in HyPhy with LEISR , 2017, bioRxiv.

[8]  C. Wilke,et al.  Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence , 2016, bioRxiv.

[9]  Claus O. Wilke,et al.  Accelerated simulation of evolutionary trajectories in origin–fixation models , 2016, bioRxiv.

[10]  Stephanie J. Spielman,et al.  Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint. , 2016, Molecular biology and evolution.

[11]  R. Goldstein,et al.  The tangled bank of amino acids , 2016, Protein science : a publication of the Protein Society.

[12]  Itay Mayrose,et al.  ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..

[13]  M. Arenas.  Trends in substitution models of molecular evolution , 2015, Front. Genet..

[14]  U. Bastolla,et al.  Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. , 2015, Molecular biology and evolution.

[15]  Stephanie J. Spielman,et al.  The relationship between dN/dS and scaled selection coefficients. , 2015, Molecular biology and evolution.

[16]  Eleisha L. Jackson,et al.  Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites , 2014, bioRxiv.

[17]  D. Posada,et al.  Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories , 2014, Molecular biology and evolution.

[18]  Asif U. Tamuri,et al.  A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data , 2014, Genetics.

[19]  Nicolas Lartillot,et al.  Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package , 2013, Bioinform..

[20]  Arthur W. Covert,et al.  Amino-acid site variability among natural and designed proteins , 2013, PeerJ.

[21]  N. Rodrigue.  On the Statistical Interpretation of Site-Specific Variables in Phylogeny-Based Substitution Models , 2013, Genetics.

[22]  Richard A. Goldstein,et al.  Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models , 2012, Genetics.

[23]  Claus O Wilke,et al.  The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution , 2011, Genetics.

[24]  Hervé Philippe,et al.  Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles , 2010, Proceedings of the National Academy of Sciences.

[25]  Trevor Hastie,et al.  Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.

[26]  Peter F Stadler,et al.  Solvent exposure imparts similar selective pressures across a range of yeast proteins. , 2009, Molecular biology and evolution.

[27]  J. Plotkin,et al.  The Population Genetics of dN/dS , 2008, PLoS genetics.

[28]  Ziheng Yang,et al.  Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. , 2008, Molecular biology and evolution.

[29]  Daniel J. Wilson,et al.  Estimating Diversifying Selection and Functional Constraint in the Presence of Recombination , 2006, Genetics.

[30]  Sergei L. Kosakovsky Pond,et al.  Not so different after all: a comparison of methods for detecting amino acid sites under selection. , 2005, Molecular biology and evolution.

[31]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[32]  Michele Vendruscolo,et al.  Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences. , 2004, Molecular biology and evolution.

[33]  Itay Mayrose,et al.  Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues , 2002, ISMB.

[34]  E. Shakhnovich,et al.  Understanding hierarchical protein evolution from first principles. , 2001, Journal of molecular biology.

[35]  Ziheng Yang,et al.  Statistical methods for detecting molecular adaptation , 2000, Trends in Ecology & Evolution.

[36]  L. Mirny,et al.  Understanding conserved amino acids in proteins , 2000, cond-mat/0007084.

[37]  R A Goldstein,et al.  Models of natural mutations including site heterogeneity , 1998, Proteins.

[38]  A. Halpern,et al.  Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. , 1998, Molecular biology and evolution.

[39]  W. Bruno.  Modeling residue usage in aligned protein sequences via maximum likelihood. , 1996, Molecular biology and evolution.

[40]  T G Dewey,et al.  The Shannon information entropy of protein sequences. , 1996, Biophysical journal.

[41]  N. Goldman,et al.  A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.

[42]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[43]  S. Jeffery.  Evolution of Protein Molecules , 1979 .

[44]  M. Kimura.  Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution , 1977, Nature.

[45]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[46]  Claus O Wilke,et al.  Integrating sequence variation and protein structure to identify sites under selection. , 2013, Molecular biology and evolution.

[47]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[48]  T. Jukes.  CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[49]  H. Munro,et al.  Mammalian protein metabolism , 1964 .