Evolutionary Genomics

Retrodiction in Evolutionary Genomics - A Philosophical Perspective.- Searching for Phylogenetic Networks.- Phylogenetic Placement using SCAMPP and Batch-SCAMPP.- Impact of Data Error on Phylogenetic Network Inferences from Gene Trees under the Multispecies Network Coalescent.- PhyloSystemX: Enhancing the Analysis of Interaction Networks.- Discovering, Genotyping, and Annotating Structural Variants with the Genome Analysis Toolkit (GATK).- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.- Methods to Characterize Mutant Spectra of RNA Viruses. The Case of SARS-CoV-2.- Geographic and Temporal Dynamics of Viral Proteome Sequences.- Proteome-wide Ab Initio Structure Prediction of Evolving Viruses.- Phylogenomic Tree Reconstruction from Bacterial Genomes.- Feature Frequency Profile (FFP) Method: A Language Model for Whole-Genome('Organism') Phylogeny.- Phylogeny Building for Structural Phylogenomic Research.- A Pipeline for Generating Datasets of 3-Dimensional Tertiary Interaction Characters for Model-Based Structural Phylogenetics.- MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures using Molecular Dynamics.- Studying the Evolution of Protein Structure one Superfamily at a Time.- Protein Architecture Comparisons and the Reconstruction of the Last Universal Common Ancestor (LUCA).- Tracing the Origin and Evolution of the Secondary Structure of RNA.- Tracing Molecular Chronologies onto Growing Biological Networks.