Modeling site-and-branch heterogeneity in phylogenetic datasets Due to widely varying mutation and selection effects, realistic phylogenetic models for protein sequences from diverse taxa require…

Handling uncertainty in ancestral gene orders reconstruction Over the last thirty years, the algorithms used for reconstructing ancestral gene orders from extant gene orders have evolved from…

Understanding animal evolution through multi-scale synteny Animal genomes record evolutionary history across multiple scales, from local gene neighborhoods to chromosome-wide architectures, but most…

Reconstructing the evolution of homologous genomic regions through gain and loss events Several biological systems rely on sets of colocalized genes sharing a common evolutionary history, and…

Quantitative measurement of cancer evolutionary history from single-sample bulk DNA methylation data Cancers evolve. Current methods to measure evolutionary dynamics rely on genome sequencing of…

Tumor Evolution over Space and Time Cancer is the result of an evolutionary process where genomic mutations and epigenetic alterations accumulate in cells that form a tumor. Modern single-cell and…

Modeling tumor progression from single-cell sequencing data Cancer progression is a somatic evolutionary process characterized by the accumulation of genetic alterations and responsible for tumor…

Applying phylogenetics in public health: Past, present, and potential for the futureWith the rapid growth of pathogen genomics in public health comes the inc...

Practicing the theory: Applying genomic epidemiology to guide public health action

Genomic Surveillance of Human Respiratory Syncytial Virus in Minnesota – Statewide Efforts, Global ImpactsOver the past two respiratory seasons, we’ve succes...

Deep Models of Protein EvolutionModels of protein evolution seek to quantify how proteins evolve over time while experiencing intricate constraints and adapt...

Reconstruction of ancestral protein sequences using autoregressive generative modelsAncestral sequence reconstruction (ASR) is an important tool to understan...

Modeling sequence evolution by learning epistatic terms from protein familiesThe use of coevolutionary information, i.e. the knowledge of amino acid or nucle...

Segment trees can not identify viral genomic reassortmentReassortment is an evolutionary process common in viruses with segmented genomes. These viruses can ...

Phylodynamics via Markov genealogy processes (2/2)Phylodynamic inference allows us to extract information on determinants of epidemic dynamics from sampled p...

Phylodynamics via Markov genealogy processes (2/2)Phylodynamic inference allows us to extract information on determinants of epidemic dynamics from sampled p...

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