Kristian G. Andersen

The paper analyzes the spread of H5N1 B3.13 in U.S. dairy cattle using genomic data and movement networks, finding that cattle movement, not birds, drives the outbreak.

This study tracks the emergence and molecular evolution of H5N1 influenza viruses in U.S. dairy cattle, identifying increased mutation rates and positive selection after spillover from birds.

The paper uses phylogenetic analysis to examine natural selection in zoonotic viruses, finding no evidence of pre-zoonotic adaptation for human transmission but detecting selection changes in the 1977 H1N1 reemergence.

Delphy provides a fast, scalable Bayesian phylogenetic analysis tool for outbreak tracking, achieving 1,000x speedups while maintaining state-of-the-art accuracy.

Reanalysis of public environmental metatranscriptomes from the Huanan market links SARS-CoV-2 positivity to one wildlife stall containing raccoon dog, civet and bamboo rat genetic material.

The paper introduces outbreak.info Research Library, a platform that aggregates and standardizes over 350,000 COVID-19 resources from sixteen repositories for easy search and exploration.

EMPress provides an interactive tool for visualizing phylogenetic trees alongside multi-omic data, enabling exploratory analyses of microbiome and metabolome datasets.

This paper describes a method to sequence Zika and other virus genomes directly from clinical samples using multiplex PCR and portable sequencing technologies, achieving complete genomes in 1-2 days.

This study sequenced 110 Zika virus genomes from 10 countries, revealing rapid expansion in Brazil, multiple introductions into other regions, and undetected circulation before confirmed cases.

The paper uses ZIKV genomes to estimate the origin and spread of Zika virus in Brazil and the Americas, providing a timeframe for baseline microcephaly rates.