Denise Kühnert

Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

Fast and alignment-free flavivirus classification from low-coverage genomes

The paper introduces DiCNN-UniK, a model for flavivirus classification using k-mer embeddings, achieving 99% accuracy on low-coverage genomes.

SIMPLICITY: an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution.

SIMPLICITY models SARS-CoV-2 intra- and between-host evolution, showing that immune waning and infection history drive realistic evolutionary dynamics.

Machine Learning Reveals Key Glycoprotein Mutations and Rapidly Assigns Lassa Virus Lineages

The paper identifies key glycoprotein mutations in Lassa virus lineages and develops a tool for rapid lineage classification.

Ancient bacterial genomes reveal a formerly unknown diversity of Treponema pallidum strains in early modern Europe

This study identifies previously unknown Treponema pallidum strains in early modern Europe, suggesting a complex history of treponemal diseases.

A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

The paper analyzes a 17th-century Mycobacterium tuberculosis genome to estimate the origin of the MTBC, finding a Neolithic emergence around 3683 years before present.

Origin of modern syphilis and emergence of a contemporary pandemic cluster

This study analyzes the genetic patterns of modern syphilis strains and identifies a globally dominant pandemic cluster with azithromycin resistance.