An experimental phylogeny to benchmark ancestral sequence reconstruction

Selection on protein structure, interaction, and sequence

(2016) Peter B. Chi et al.   PROTEIN SCIENCE

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

(2015) Wandrille Duchemin et al.   BMC GENOMICS

The molecular origin and evolution of dim-light vision in mammals

(2015) Constanze Bickelmann et al.   EVOLUTION

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

(2015) Tomotaka Matsumoto et al.   GENETICS

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

(2015) Joanne K. Hobbs et al.   JOURNAL OF MOLECULAR EVOLUTION

Assessing the prediction fidelity of ancestral reconstruction by a library approach

(2015) Hagit Bar-Rogovsky et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Using ancient protein kinases to unravel a modern cancer drug's mechanism

(2015) C. Wilson et al.   SCIENCE

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

(2015) Tomotaka Matsumoto et al.   GENETICS

Toward More Accurate Ancestral Protein Genotype–Phenotype Reconstructions with the Use of Species Tree-Aware Gene Trees

(2014) Mathieu Groussin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Engineering and characterizing monomeric fluorescent proteins for live-cell imaging applications

(2014) Hui-wang Ai et al.   Nature Protocols

Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches

(2014) Ning Yang et al.   PLoS One

Evolutionary history and metabolic insights of ancient mammalian uricases

(2014) J. T. Kratzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relative and absolute determination of fluorescence quantum yields of transparent samples

(2013) Christian Würth et al.   Nature Protocols

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Utilizing natural diversity to evolve protein function: applications towards thermostability

(2011) Megan F Cole et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Exploiting Models of Molecular Evolution to Efficiently Direct Protein Engineering

(2010) Megan F. Cole et al.   JOURNAL OF MOLECULAR EVOLUTION

Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty

(2010) Victor Hanson-Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Diversity and Evolution of Coral Fluorescent Proteins

(2008) Naila O. Alieva et al.   PLoS One