Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space

Reconstructing a Missing Link in the Evolution of a Recently Diverged Phosphotriesterase by Active-Site Loop Remodeling

(2012) Livnat Afriat-Jurnou et al.   BIOCHEMISTRY

Insertions and deletions trigger adaptive walks in Drosophila proteins

(2012) E. V. Leushkin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Exploring the Structure–Function Loop Adaptability of a (β/α)8-Barrel Enzyme through Loop Swapping and Hinge Variability

(2011) Adrián Ochoa-Leyva et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolutionary Walk between (β/α)8 Barrels: Catalytic Migration from Triosephosphate Isomerase to Thiamin Phosphate Synthase

(2011) Gloria Saab-Rincón et al.   JOURNAL OF MOLECULAR BIOLOGY

Slow protein evolutionary rates are dictated by surface-core association

(2011) A. Toth-Petroczy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

(2011) Michael J. McDonald et al.   PLOS BIOLOGY

Correlated Evolution of Nearby Residues in Drosophilid Proteins

(2011) Benjamin Callahan et al.   PLoS Genetics

Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae

(2011) Anthony R. Borneman et al.   PLoS Genetics

Evolutionary Origin of a Secondary Structure: π-Helices as Cryptic but Widespread Insertional Variations of α-Helices That Enhance Protein Functionality

(2010) Richard B. Cooley et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

(2010) K. Hashimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable element insertions have strongly affected human evolution

(2010) R. J. Britten   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A time-invariant principle of genome evolution

(2010) S. De et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increased Mutagenesis and Unique Mutation Signature Associated with Mitotic Gene Conversion

(2010) W. M. Hicks et al.   SCIENCE

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Converting an Esterase into an Epoxide Hydrolase

(2009) Helge Jochens et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein Design through Systematic Catalytic Loop Exchange in the (β/α)8 Fold

(2009) Adrián Ochoa-Leyva et al.   JOURNAL OF MOLECULAR BIOLOGY

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

(2009) J.-Q. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

Alteration of enzyme specificity by computational loop remodeling and design

(2009) P. M. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins

(2009) Michelle Simon et al.   GENOME BIOLOGY

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

(2008) Amarendran R Subramanian et al.   Algorithms for Molecular Biology

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

(2008) Dacheng Tian et al.   NATURE

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH

Evolution of tRNA nucleotidyltransferases: A small deletion generated CC-adding enzymes

(2008) A. Neuenfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Built-in loops allow versatility in domain-domain interactions: Lessons from self-interacting domains

(2008) E. Akiva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology

Hypermutability of Damaged Single-Strand DNA Formed at Double-Strand Breaks and Uncapped Telomeres in Yeast Saccharomyces cerevisiae

(2008) Yong Yang et al.   PLoS Genetics