Cristina Lanzas

Scalable phylodynamic inference of mutational and epistatic fitness effects with multi-feature birth-death models

This paper develops a Bayesian framework for inferring mutational and epistatic fitness effects in microbial evolution using multi-feature birth-death models and applies it to Escherichia coli phylogenies.

Risk factors for fluoroquinolone- and macrolide-resistance among swine Campylobacter coli using multi-layered chain graphs

The paper uses chain graphs to identify risk factors for fluoroquinolone- and macrolide-resistance in Campylobacter coli from swine farms, finding genotype and host exposures explain significant variance in MICs.

Influence of Sequencing Technology on Pangenome-level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens

This study compares short-read and long-read sequencing technologies for detecting antimicrobial resistance genes in ESKAPE pathogens, highlighting the strengths and limitations of each approach and advocating for hybrid assembly for comprehensive analysis.

Quantifying the genomic determinants of fitness in E. coli ST131 using phylodynamics

This study quantifies the genomic determinants of fitness in E. coli ST131 using phylodynamic models, finding that fluoroquinolone resistance mutations provide a major fitness advantage.

Distilling Mechanistic Models From Multi-Omics Data

The paper presents a four-step approach to distill mechanistic models from multi-omics data, applied to murine Clostridioides difficile infection data to identify the Stickland reactor's role in toxin production.