Publications

Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty Genome Biology and Evolution http://doi.org/10.1093/gbe/evv127.

ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models Systematic Biology http://doi.org/10.1093/sysbio/syu062

Class of multiple sequence alignment algorithm affects genomic analysis Molecular Biology and Evolution http://doi.org/10.1093/molbev/mss256

Measuring the distance between multiple sequence alignments Bioinformatics http://doi.org/10.1093/bioinformatics/btr701.

Phylogenetic substitution models for detecting heterotachy during plastid evolution
Molecular Biology and Evolution http://doi.org/10.1093/molbev/msq215.

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs
Nature Genetics http://doi.org/10.1038/ng.564.

Changing Selective Pressure during Antigenic Changes in Human Influenza H3
PLoS Pathogens http://doi.org/10.1371/journal.ppat.1000058.

Assessing the Accuracy of Ancestral Protein Reconstruction Methods
PLoS Computational Biology http://doi.org/10.1371/journal.pcbi.0020069.

Population Dynamics Simulations of Functional Model Proteins
Journal of Chemical Physics http://doi.org/10.1063/1.2056545.

Three Dimensional Functional Model Proteins: Structure, Function and Evolution
Journal of Chemical Physics http://doi.org/10.1063/1.1590310.

Multimeme Algorithms for Protein Structure Prediction
Lecture Notes in Computer Science http://doi.org/10.1007/3-540-45712-7_74.

Evolution of Functional Model Proteins
Journal of Chemical Physics http://doi.org/10.1063/1.1383051.

Book Chapter